.. _release_notes: EasyBuild release notes ======================= The latest version of EasyBuild provides support for building and installing **2,798** different software packages, including 37 different (compiler) toolchains. It contains 248 software-specific easyblocks and 37 generic easyblocks, alongside 15,535 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. .. _release_notes_eb470: EasyBuild v4.7.0 (January 9th 2023) ----------------------------------- feature release **framework** * print deprecation warning with running EasyBuild with Python 2 (`#4136 `_) * various enhancements, including: * add support for checksums specified in external ``checksums.json`` file (`#3749 `_) * vendor ``distutils.version.LooseVersion`` as ``easybuild.tools.LooseVersion`` (since distutils is deprecated in Python 3.10) (`#3794 `_, `#4156 `_) * take into account custom configuration options specified in easystack file (`#4057 `_) * add support for using ``--output-format=md`` (MarkDown) (`#4117 `_, `#4155 `_) * add support for `--filter-rpath-sanity-libs` to skip RPATH sanity check for designated libraries (`#4119 `_) * add sanity_check_load_module method to EasyBlock to provide control over when module is loaded during sanity check step (`#4125 `_) * add ``eb_bash_completion_local.bash`` script to ``setup.py`` (`#4127 `_) * check whether ``nvidia-smi/rocm-smi`` command is available before trying to run it in ``get_gpu_info`` (`#4131 `_) * add ``gfbf`` as subtoolchain of foss (`#4143 `_) * add support for ``postinstallmsgs`` (`#4145 `_) * make ``iimkl`` toolchain aware of ``intel-compilers`` (`#4146 `_) * add definition for ``nvofbf`` toolchain (`#4157 `_, `#4163 `_) * various bug fixes, including: * also use EasyConfig instances cache in process_easyconfig when ``build_specs`` is empty dict (`#4107 `_) * fix build options that should have empty list as default value (`#4108 `_) * catch easyconfig parsing failure so we can generate and post a test report (`#4109 `_) * add explicit return when no checksums match those specified in a tuple (`#4112 `_) * tweak ``findPythonDeps.py`` script to use canonical package names (`#4118 `_) * add ``-fdefault-double-8`` to ``r8`` toolchain compiler option for GCC (to be consistent with Intel) (`#4121 `_) * always start with empty list for banned/requires libraries to avoid that corresponding build option is updated in-place (`#4137 `_) * fix container tests by using EPEL archive URL for downloading Singularity RPM (`#4138 `_) * use ``-march=x86-64 -mtune=generic`` instead of ``-xSSE2`` when using Intel oneAPI compilers (`#4147 `_) * partially ``skip test_det_copy_ec_specs`` if no GitHub token is available (`#4149 `_) * other changes: * drop support for easystack files using ``'software'`` top-level key (`#4057 `_) * also run unit tests with Python 3.11 + add Python 3.11 to classifiers in ``setup.py`` (`#4092 `_, `#4141 `_) * use new EasyBuild logo in README (`#4123 `_) * automatically cancel Github Action workflow runs for outdated commits (`#4132 `_) * auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0 (`#4135 `_) * trim CI test configurations to avoid hitting GitHub rate limits (`#4148 `_) * various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format (`#4129 `_, `#4130 `_, `#4154 `_, `#4160 `_, `#4162 `_, `#4168 `_) * update copyright lines for 2023 (`#4161 `_) **easyblocks** * add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage (`#2816 `_) and JuliaBundle (`#2830 `_) * minor enhancements and updates, including: * enhance TensorFlow easyblock to take into account provided OpenSSL dependency (`#2575 `_) * add fix_shebang to ``install_step`` of PythonPackage easyblock so that we can fix shebangs when installing extensions (`#2680 `_) * update PETSc easyblock for newer versions (>= 3.17) (`#2796 `_) * update Clang easyblock to add support for new directory structure in Clang versions >= 14 + support Flang (`#2800 `_) * update Xmipp easyblock since versions >= 3.20.07 use ``noAsk`` option to configure (`#2809 `_) * add ``include/opencv4`` to ``$CPATH`` for OpenCV versions >= 4.0 (`#2818 `_) * add extra option for disabling LAPACK in ESMF (`#2821 `_) * enable building of static libraries for libxml2 >= 2.10 (`#2825 `_) * update Xmipp easyblock to handle effects of CUDA at SYSTEM level and newer CUDA version requirements for stdc++ (`#2831 `_) * update LLVM easyblock to put ``'cmake'`` symlink in place so separate CMake modules required for LLVM 15+ can be found (`#2832 `_) * set ``$TEMPDIRPATH`` for testsuite in the BerkeleyGW easyblock, to avoid polluting ``/tmp`` (`#2836 `_) * add ``configure_no_prefix`` option to skip addition of prefix to configure command in ConfigureMake easyblock (`#2842 `_) * update ``qscintilla.py`` to be compatible with EB install of PyQt5 >= 5.15 (`#2845 `_) * add UCC to known_dependencies in OpenMPI EasyBlock (`#2847 `_) * update Clang-AOMP easyblock to handle version 5.2 and newer (`#2851 `_) * various bug fixes, including: * fix installing of Clang with RPATH linking (`#2799 `_) * fix ``--module-only`` for Clang + fix sanity check for Clang 11.x (`#2800 `_) * create ``$XDG_CACHE_HOME`` for PyTorch tests (`#2806 `_) * make PythonPackage easyblock compatible with ``--sanity-check-only`` by loading module early during sanity check step (`#2828 `_) * fix docstring of PythonBundle generic easyblock (`#2833 `_) * fix counting of failures in PyTorch tests (`#2834 `_, `#2840 `_) * make sure that ANSYS INSTALL script has execute permissions (`#2852 `_, `#2853 `_) * other changes: * remove useless ``-openmp`` build option for MRtrix v3.x (`#2822 `_) * update HDF5 easyblock to use ``--enable-threadsafe`` configure option to make C API thread safe (`#2824 `_) * use new EasyBuild logo in README (`#2827 `_) * automatically cancel Github Action workflow runs for outdated commits (`#2835 `_) * use fixed names for ``bazel/wrapper`` subdirectories used when building TensorFlow, to make debugging easier (`#2841 `_) * also run unit tests with Python 3.11 (`#2844 `_) * tweak docstring in some generic easyblocks so it renders nicely in auto-generated documentation (`#2849 `_) * update copyright lines for 2023 (`#2850 `_) **easyconfigs** * added easyconfigs for ``foss/2022b``, ``intel/2022b`` common toolchains (`#16961 `_ and `#16962 `_) * see also https://docs.easybuild.io/en/latest/Common-toolchains.html * added easyconfigs for NVHPC-based toolchains ``nvompi/2022.07`` and ``nvofbf/2022.07`` (`#16724 `_) * added example easyconfig files for 107 new software packages: * Alfred (`#16780 `_), attrdict3 (`#16856 `_), bamFilters (`#16735 `_), bcl-convert (`#16351 `_), Beagle (`#346 `_), Boost.MPI (`#15757 `_), captum (`#16477 `_), CAT-BAT (`#16577 `_, `#16634 `_), cdo-bindings (`#16669 `_), Chemaxon-Marvin (`#13954 `_), CliMetLab (`#16842 `_), CloudCompare (`#16944 `_), cmocean (`#16659 `_), COBRApy (`#16616 `_), CodAn (`#16902 `_), CoSymLib (`#17049 `_), CPPE (`#16749 `_), cryoCARE (`#16534 `_), CTPL (`#16498 `_), CUDA-Samples (`#16914 `_), cwltool (`#16503 `_), Cytoscape (`#16682 `_), DeepLabCut (`#16391 `_), DeepMod2 (`#17008 `_), Dice (`#16752 `_), dlb (`#16845 `_), DRAGMAP (`#16532 `_), ecBuild (`#16842 `_), EGTtools (`#16704 `_), ESM-2 (`#16528 `_), flair-NLP (`#15588 `_), FMS (`#16965 `_), Godon (`#16574 `_), gsw (`#16643 `_), HighFive (`#16737 `_), humann (`#16853 `_), HyperQueue (`#16753 `_), IJulia (`#16494 `_, `#16665 `_), infercnvpy (`#16712 `_), InParanoid (`#16572 `_), jupyter-server (`#14844 `_), KaHIP (`#16861 `_), KITE (`#16550 `_), lagrangian-filtering (`#16654 `_), LHAPDF (`#17028 `_), librttopo (`#16856 `_), libwpe (`#16088 `_), Magics (`#16842 `_), matlab-proxy (`#14270 `_), mcu (`#16566 `_), MEMOTE (`#16772 `_), memtester (`#16763 `_), meson-python (`#16911 `_), minizip (`#16856 `_), MITgcmutils (`#16623 `_), MONAI (`#16519 `_), MOOSE (`#13824 `_), mstore (`#16892 `_, `#17029 `_), MultilevelEstimators (`#15630 `_, `#16665 `_), n2v (`#16535 `_), NanoLyse (`#16575 `_), napari (`#16468 `_), NECI (`#16751 `_), nf-core-mag (`#16613 `_), oceanspy (`#16640 `_), olego (`#16909 `_), OmegaFold (`#16698 `_), OVITO (`#16811 `_), Panedr (`#16564 `_), Parcels (`#16838 `_), polars (`#16989 `_), PsiCLASS (`#16906 `_), pyccel (`#16823 `_), PyCheMPS2 (`#16710 `_), PyDamage (`#16576 `_), PyImageJ (`#16757 `_), pysteps (`#16783 `_), python-libsbml (`#16610 `_), python-telegram-bot (`#16442 `_), pyWannier90 (`#16447 `_), resolos (`#16649 `_), RLCard (`#16695 `_), SAP (`#5200 `_), scikit-misc (`#16457 `_), scvi-tools (`#16457 `_), SELFIES (`#17032 `_), SeuratDisk (`#16951 `_), sfftk (`#16466 `_), simint (`#16886 `_), SISSO++ (`#15759 `_), slamdunk (`#15197 `_), spaCy (`#17027 `_), Sphinx-RTD-Theme (`#16736 `_), SPOOLES (`#16756 `_), Squidpy (`#16880 `_), svist4get (`#16505 `_), task-spooler (`#17048 `_), TBA (`#16497 `_), TensorFlow-Datasets (`#16421 `_), TFEA (`#16476 `_), TinyXML (`#16992 `_), tokenizers (`#15587 `_), torchsampler (`#16464 `_), trimesh (`#16858 `_), UCX-ROCm (`#17033 `_), wpebackend-fdo (`#16093 `_), xmitgcm (`#16637 `_) * added additional easyconfigs for various supported software packages, including: * Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8, CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2, cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1, FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35, HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2, ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0, libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0, libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1, LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3, libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4, MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2, Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7, OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0, OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4, phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3, pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3, Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5, QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3, scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0, SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007, SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0, typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2, wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0, XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6 * minor enhancements, including: * enable building of dev tools in recent PyQt5 easyconfigs (`#16469 `_) * add extensions to R v4.2.1: LMERConvenienceFunctions (`#16512 `_), HGNChelper 4.2.1 (`#16744 `_) * add extensions to R-bundle-Bioconductor 3.15: SPOTlight (`#16569 `_), HiCcompare (`#16581 `_), ROntoTools (`#16636 `_), scDblFinder (`#16686 `_), numbat (`#16777 `_), HiCBricks (`#16913 `_), zellkonverter (`#16952 `_) * add libmad dependency to SoX v14.4.2 (`#16758 `_) * also install subtree support in recent git easyconfigs (`#16784 `_, `#16785 `_) * add extensions to ESM-2 to enhance it for esmfold (`#16841 `_) * add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (`#16844 `_) * add KaHIP dependency to OpenFOAM v2206 (`#16974 `_) * enable dataset support for recent versions of Arrow (`#16956 `_) * various bug fixes, including: * define ``$JUPYTER_PATH`` via modextrapaths rather than modextravars for IRkernel 1.x (`#15776 `_) * add patches to fix PyTorch 1.10.0 build on POWER (`#15904 `_) * fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (`#16485 `_) * add patch for M4 1.4.18 to fix glibc v2.34 ``SIGSTKSZ`` compatibility (`#16486 `_) * add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (`#16487 `_) * work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (`#16490 `_) * fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (`#16502 `_) * add OpenBLAS patches to disable FMA in ``[cz]cal`` and fix crash in ``zdot`` (`#16510 `_) * add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (`#16516 `_) * build nodejs with OpenSSL and ICU provided as proper dependencies (`#16529 `_) * also define ``$JUPYTER_CONFIG_PATH`` in IPython and JupyterLab easyconfigs (`#16556 `_) * define ``$GTKDOCIZE`` as ``'echo'`` before generating configure script for recent HarfBuzz versions (`#16570 `_) * disable use of ``-Werror`` in recent NSS easyconfigs (`#16571 `_) * use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (`#16611 `_) * avoid that zlib + htslib are downloaded and built during installation of MetaBAT (`#16624 `_) * add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (`#16633 `_) * add missing pyWannier90 dependency for mcu + enhance sanity check (`#16667 `_) * fix ``source_urls`` for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (`#16693 `_) * add patches to fix or skip PyTorch 1.12.1 tests (`#16793 `_) * fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (`#16819 `_) * upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (`#16839 `_) * fix checksum for dlllogger extension in OpenFold v1.0.0 (`#16694 `_) * make sure that Python dependency is actually used for VTK 9.0.1 (`#16741 `_) * fix homepage for pocl v1.8 (`#16857 `_) * fix source_urls in MUMPS easyconfigs (`#16931 `_, `#16932 `_) * fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (`#16946 `_) * add missing OpenSSL dependency to DCMTK 3.6.7 (`#16979 `_) * fix source URL for PCRE2 (`#16987 `_) * add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (`#16990 `_) * add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (`#17001 `_) * add missing zlib and zstd to GnuTLS (`#17013 `_) * add missing pkgconf build dependency to Transformers v4.24.0 (`#17020 `_) * fix checksums for ``xxx-rocm-4.5.0.tar.gz`` source tarballs for Clang-AOMP 4.5.0 (`#17042 `_) * replace useless test step for simint 0.7 with (lightweight) sanity check command (`#17044 `_) * other changes: * only give read permissions in GitHub Actions workflows (`#16263 `_) * remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (`#16492 `_) * include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (`#16578 `_) * use new EasyBuild logo in README (`#16641 `_) * rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (`#16697 `_) * automatically cancel Github Action workflow runs for outdated commits (`#16754 `_) * use geo moduleclass for SimPEG 0.14.1 (`#16847 `_) .. _release_notes_eb462: EasyBuild v4.6.2 (October 21st 2022) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add support for easystack file that contains easyconfig filenames + implement parsing of configuration options (`#4021 `_) * skip over unset ``$EB_PYTHON``/``$EB_INSTALLPYTHON`` in eb wrapper script (`#4080 `_) * add ``GITHUB_RELEASE`` and ``GITHUB_LOWER_RELEASE`` templates (`#4084 `_) * add ``%(cuda_cc_cmake)s`` template (`#4087 `_) * various bug fixes, including: * make ``check_sha256_checksums`` verify all checksums if they're specified as a dict value (`#4076 `_) * replace use of symlink with copied files in ``alt_location`` tests to fix failing EasyBuild installation on BeeGFS (`#4083 `_) * fix trying to generate RPATH wrappers for Clang (`#4088 `_) * make sure that GitPython version is a proper version before checking minimal required version (`#4090 `_, `#4091 `_) * first look for patch in ``alt_location`` when it is specified (`#4093 `_) * other changes: * make scripts executable (`#4081 `_) * make ``--inject-checksums`` inject dictionary value for checksums which maps filename to SHA256 checksum (`#4085 `_) * update to v3 of actions/checkout and actions/setup-python in CI workflows (`#4089 `_) * use ``SYSTEM`` template constant in dependencies instead of ``True`` in framework tests (`#4094 `_) **easyblocks** * 2 new software-specific easyblock: * CUDA compatibility libraries (`#2764 `_) and mamba (`#2808 `_) * minor enhancements and updates, including: * update OpenFOAM easyblock to support OpenFOAM 10 + clean up variant/version checks (`#2766 `_) * added support for ESMPy in ESMF (`#2789 `_) * enhance OpenBLAS easyblock to support running LAPACK test suite + checking how many tests fail (`#2801 `_) * make numexpr easyblock aware of toolchain with GCC + imkl (`#2810 `_) * add sanity check commands for netCDF (`#2811 `_) * various bug fixes, including: * handle problems copying symlink that points to CUDA folder that is not created for non CUDA builds of SuiteSparse (`#2790 `_) * don't install docs (to avoid trouble with Java) + add Rocky support for ABAQUS (`#2792 `_) * correctly count the number of failing tests (not failing test suites) in PyTorch builds (`#2794 `_, `#2803 `_) * fix docstring for PyTorch easyblock (`#2795 `_) * handle iterative builds with MakeCp easyblock (`#2798 `_) * accept both ``None`` and empty value for optarch to let OpenCV detect host CPU (`#2804 `_) * enhance EasyBuildMeta easyblock: auto-enable installing with pip + fix setup.py of easyconfigs package so installation with setuptools >= 61.0 works (`#2805 `_) * use ``python -m pip`` instead of ``pip`` in PythonPackage easyblock (`#2807 `_) * other changes: * make the test output from PythonPackage less verbose by disabling default search for error patterns done by ``run_cmd`` (`#2797 `_) **easyconfigs** * add easyconfig for intel/2022.09 toolchain (`#16435 `_) * added example easyconfig files for 25 new software packages: * AGAT (`#16261 `_), AMAPVox (`#16438 `_), Avogadro2 (`#16257 `_), buildingspy (`#16308 `_), CDBtools (`#16436 `_), Compress-Raw-Zlib (`#16307 `_), CUDAcompat (`#15892 `_), CWIPI (`#16342 `_), enchant-2 (`#16082 `_, `#16319 `_), f90wrap (`#16346 `_), Imath (`#16276 `_), Mamba (`#16432 `_), Miller (`#16221 `_), nghttp2 (`#16096 `_), ngtcp2 (`#16098 `_), NVSHMEM (`#16254 `_), pairsnp (`#16331 `_), paladin (`#16320 `_), PyMOL (`#16394 `_), python-irodsclient (`#16328 `_), ruffus (`#16428 `_), TELEMAC-MASCARET (`#16274 `_), torchdata (`#16344 `_), Waylandpp (`#16092 `_), x13as (`#16163 `_) * added additional easyconfigs for various supported software packages, including: * Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3, dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2, GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6, Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30, libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0, NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4, PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1, scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0, sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0, TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107, VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5 * minor enhancements, including: * configure recent pocl versions with ``-DLLC_HOST_CPU=native`` to avoid CPU auto-detection (`#16246 `_) * add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (`#16316 `_) * enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of ``-ftree-vectorize`` (`#16406 `_) * add ``GITHUB_(LOWER_)RELEASE`` to known constants in ``setup.cfg`` (`#16422 `_) * add AMAPVox extension to R v4.2.1 (`#16439 `_) * add OpenEXR dependency to POV-Ray 3.7.0.10 (`#16408 `_) * various bug fixes, including: * add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (`#16199 `_) * skip flaky test in PyTorch 1.9.0 (`#16258 `_) * add ``--with-versioned-syms`` to ncurses 6.2 and 6.3 (`#16270 `_) * add missing pkg-config build dependency to Guile (`#16317 `_) * add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (`#16332 `_) * add patches to fix PyTorch 1.11 on POWER (`#16339 `_) * add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (`#16343 `_) * use Intel MPI from EasyBuild toolchain in AMS (`#16363 `_) * fix execution permissions for ``bin/ngm*`` for NextGenMap v0.5.5 (`#16383 `_) * fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating ``mplsetup.cfg`` rather than ``setup.cfg`` (`#16396 `_) * fix GitHub download link in for libpsl 0.21.1 (`#16397 `_) * stick to http in source URL for ``stride.tar.gz`` in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (`#16403 `_) * add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (`#16407 `_) * add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (`#16410 `_) * add patch to GCC 11.x + 12.x to fix vectorizer bug (`#16411 `_) * fix checksum for GULP 6.1 (`#16423 `_) * add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (`#16450 `_) * other changes: * drop Java dep from ABAQUS 2022 (`#16314 `_) * deprecate use of ``True`` in favour of ``SYSTEM`` for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (`#16384 `_) * update easyconfigs to use ``SYSTEM`` template constant instead of ``True`` in dependencies (`#16386 `_, `#16418 `_) * update libxml2 + libxslt easyconfigs to use ``gnome.org`` source URL (`#16429 `_) .. _release_notes_eb461: EasyBuild v4.6.1 (September 12th 2022) -------------------------------------- bugfix/update release **framework** * various enhancements, including: * add script to find dependencies of Python packages (`#3839 `_) * add ``ai`` default module class (`#4053 `_) * various bug fixes, including: * fix code style issues reported by recent flake8 linter (`#4049 `_) * stick to autopep8 < 1.7.0 with Python 2.7 (`#4055 `_) * ensure we call ``EasyBlock.patch_step`` for ``postinstallpatches`` (`#4063 `_) * fix leaked handles in ``set_columns``, ``complete_cmd``, ``run_cmd_qa``, ``det_terminal_size functions`` + tests (`#4066 `_) * fix ``quote_str`` when string with both ``'`` and ``"`` ends with a double quote (`#4068 `_) * fix type-checking of patches to allow dict values + correctly handle patches specified as dict values in ``--new-pr`` (`#4070 `_) * relax toolchain test by accepting both ``-march=native`` (x86_64) and ``-mcpu=native`` (aarch64) (`#4071 `_) * other changes: * run python in the same process as ``eb`` wrapper script by using ``exec`` (`#4048 `_) * add ``get_linked_libs_raw`` function, and use it from both ``check_linked_shared_libs`` and ``sanity_check_rpath`` (`#4051 `_) * update CI workflows (except container tests) to use Ubuntu 20.04, since Ubuntu 18.04 is deprecated (`#4064 `_) * use ``SYSTEM`` constant for dependency that uses system toolchain in dumped easyconfig (`#4069 `_) **easyblocks** * minor enhancements and updates, including: * update LAMMPS easyblock for LAMMPS/23Jun22 (`#2213 `_) * reduce the number of command line options for ``cmake`` command in CMakeMake generic easyblock (`#2514 `_) * update libQGLViewer easyblock to take into account changes in the shared library names depending on Qt versions they are compiled with (`#2730 `_) * improve PLUMED detection in GROMACS easyblock (`#2749 `_) * make ``$LD_LIBRARY_PATH`` detection more robust for LAMMPS (`#2765 `_) * enhance NVHPC easyblock to avoid superfluous warning (`#2767 `_) * enhance PyTorch easyblock to also capture tests failing with signal (`#2768 `_) * enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when ``return_output_ec=True`` (`#2770 `_) * set ``$NVHPC_CUDA_HOME`` for NVHPC 22.7+ (`#2776 `_) * various bug fixes, including: * make Amber easyblock aware of FlexiBLAS (`#2720 `_) * update PyTorch easyblock to configure without breakpad support on POWER (`#2763 `_) * use ``lib*`` in ``post_install`` step of FFTW.MPI easyblock to fix paths not being found on Linux distros favouring lib64 (like Suse/SLES) (`#2771 `_) * use ``det_cmake_version`` function to determine CMake version in CMakeMake generic easyblock (`#2772 `_) * don't enable building of ``ld.gold`` when installing binutils on a RISC-V system + don't configure GCC to use gold as default linker on a RISC-V system (`#2780 `_) * tweak Amber(Tools) easyblock to run tests from top-level directory (`#2781 `_) * fix version check for NVPTX library in sanity check of Clang easyblock (`#2783 `_) * other changes: * update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (`#2779 `_) **easyconfigs** * added example easyconfig files for 37 new software packages: * AptaSUITE (`#8583 `_), BigDFT (`#15860 `_), colossalai (`#15971 `_), CrystFEL (`#8407 `_), Dakota (`#15883 `_, `#16210 `_), FastFold (`#15972 `_), fastparquet (`#15020 `_), FOX-Toolkit (`#15986 `_), GLM-AED (`#15879 `_), hiredis (`#16071 `_), how_are_we_stranded_here (`#16220 `_, `#16227 `_), indicators (`#16209 `_), JavaFX (`#8583 `_), json-fortran (`#15979 `_), jupyter-resource-usage (`#15834 `_), libev (`#16086 `_), libmad (`#16067 `_), libplinkio (`#13040 `_), LuaJIT2-OpenResty (`#16047 `_), MetaMorpheus (`#15825 `_), mgltools (`#16226 `_), miniasm (`#15858 `_), muMerge (`#16115 `_), nano (`#16198 `_), nghttp3 (`#16097 `_), olaFlow (`#16021 `_), OpenFAST (`#15983 `_, `#15983 `_), OpenFold (`#15971 `_), Phantompeakqualtools (`#15871 `_), pyGenomeTracks (`#16143 `_), QuickPIC (`#15978 `_), RheoTool (`#16077 `_), Satsuma2 (`#16068 `_), SMC++ (`#16017 `_), stripy (`#15866 `_), UCC-CUDA (`#15956 `_), VESTA (`#16217 `_) * added additional easyconfigs for various supported software packages, including: * alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39, BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1, Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2, GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8, glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2, HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1, libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1, maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2, MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1, ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0, pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2, PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0, scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62, Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0, Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0 * minor enhancements, including: * add alternate download URL for Voro++ (`#15898 `_) * add extra symlinks and sanity checks for libtinfo in ncurses (`#15903 `_) * include some easyconfig constants in flake8 configuration file (`#16040 `_) * add pigz dependency for cutadapt v3.4 + v3.5 (`#16056 `_) * add sanity check commands for recent gettext versions (>= 0.20.x) (`#16091 `_) * various bug fixes, including: * use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (`#13375 `_) * fix set-alias statements for MaxQuant v2.0.3.0 (`#15743 `_) * add Autotools build dependency to R 4.2.0 w/ foss 2021b (`#15822 `_) * add patch for BLIS to fix auto-detection of POWER (`#15826 `_) * downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (`#15840 `_) * explicitly enable HDF5 from kallisto v0.46.2 onwards (`#15843 `_) * add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (`#15856 `_) * use build environment set by EasyBuild and add missing dependency on zlib to minimap2 (`#15859 `_) * add missing dependencies and execute tests on Trycycler v0.5.2 (`#15864 `_) * add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (`#15874 `_) * exclude (flaky) ``fault_tolerance_test`` and fix non-x86 build for TensorFlow 2.7.1 (`#15882 `_) * work around miscompilation of OpenBLAS on POWER by compiling with ``-fstack-protector-strong`` (`#15885 `_) * fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (`#15889 `_) * add and fix patches for PyTorch 1.9.0 on POWER (`#15919 `_) * exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (`#15932 `_) * consistently add libffi + elfutils dependencies to recent Clang easyconfigs (`#15935 `_, `#16225 `_) * add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (`#15968 `_) * refactor checksum test for extensions to use ``collect_exts_file_info`` (`#15973 `_) * fix dependency on FOX Toolkit in SUMO (`#15986 `_) * add missing SciPy-bundle dependency for rMATS-turbo (`#15988 `_) * explicitly download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (`#15993 `_) * restore ploteig in EIGENSOFT 7.2.1 (`#15996 `_) * add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (`#16011 `_) * add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (`#16027 `_) and 2021 (`#16026 `_) * exclude failing test in TensorFlow 2.4.1 (`#16042 `_) * skip NASA performance and remote server tests in netCDF v4.9.0 (`#16050 `_, `#16158 `_) * use versioned symbols in ncurses built with system toolchain (by adding ``--with-versioned-syms`` configure option) (`#16064 `_) * add patch to fix pkgconfig file for Blitz++ v1.0.2 (`#16102 `_) * add missing BCFtools dependency for recent medaka versions (`#16107 `_) * add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (`#16112 `_) * fix checksum for Stacks v2.62 (due to silent re-release without version bump) (`#16134 `_) * fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (`#16145 `_) * fix top level Makefile for AmberTools 20 and enable tests (`#16150 `_) * add missing patches + enable running tests for AmberTools 21 with intel/2021a (`#16151 `_) and intel/2021b (`#16152 `_) * replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (`#16153 `_) * remove modextrapaths to add top-level install directory to ``$PATH ``for recent InterProScan easyconfigs (now done by default by Binary easyblock) (`#16167 `_) * fix sources + source URL + homepage for Molekel v5.4.0 (`#16219 `_) * consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (`#16231 `_) * fix checksum for CUDA 11.4.1 aarch64 installer (`#16234 `_) * remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (`#16238 `_) * add direct Pango dependency in recent ImageMagick easyconfigs (`#16237 `_) * other changes: * remove superfluous ``-DCMAKE_BUILD_TYPE=Release``, use of ``build_type = Release``, or enabling ``separate_build_dir`` from easyconfigs using CMakeMake easyblock (`#13384 `_) * synchronize ncurses easyconfigs using system toolchain (`#15903 `_) * stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (`#15906 `_) * speed up OpenMPI 4.1.4 configure by not running ``autogen.pl --force``, but only running required Autotools commands (`#15957 `_) * replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (`#15958 `_) * simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (`#15981 `_) * update Java/11 to 11.0.16 and Java/17 to 17.0.4 (`#16001 `_) * remove unnecessary patch in recent JupyterLab (`#16030 `_) * update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (`#16070 `_) * make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses ``SYSTEM`` constant (`#16126 `_) .. _release_notes_eb460: EasyBuild v4.6.0 (July 8th 2022) -------------------------------- feature release **framework** * various enhancements, including: * allow searching for sources/patches in alternative location by specifying '``alt_location``' in source/patch spec (`#3994 `_) * show URLs used for download attempts in trace output (`#4026 `_) * add support for setting environment variables via '``pushenv``' with ``modextravars`` (`#4030 `_) * add support for OneAPI compilers using toolchain option '``oneapi``' (`#4031 `_, `#4032 `_, `#4039 `_) * make ``check_linked_shared_libs`` more robust by taking into account that '``ldd``' may fail (`#4033 `_) * fall back to sequential extension install if parallel install is not implemented (`#4034 `_) * add support for using template values in name/version of extensions (`#4036 `_) * various bug fixes, including: * make sure that ``ARCH`` constant has '``aarch64``' (rather than '``arm64``') as value on macOS ARM (`#4018 `_) * tweak '``eb``' wrapper script to correctly handle errors when python command being considered fails to run (`#4019 `_) * tweak ``is_patch_for`` function to make it more robust (`#4028 `_) * other changes: * update Lmod used to run tests to version 8.7.6 (`#4027 `_, `#4030 `_) * tweak ``apply_patch`` to not create ``.orig files`` (by default) when applying patch files (`#4038 `_) **easyblocks** * new software-specific easyblock for STAR-CCM+ (`#1613 `_) * minor enhancements and updates, including: * update Siesta EasyBlock to support GCC 10+ by adding ``-fallow-argument-mismatch`` Fortran compiler option (`#2690 `_) * enable building of shared library for Libint 2.7+ (`#2738 `_) * allow some PyTorch tests to fail + print warning if one or more tests fail (`#2742 `_) * also support OpenSSL 3.0 in OpenSSL wrapper easyblock (`#2746 `_) * add more logging to ``install_pc_files`` method of OpenSSL wrapper easyblock (`#2752 `_) * make WPS easyblock aware of ``(pre)buildopts`` (`#2754 `_) * add Abseil system dependency for TensorFlow 2.9+ (`#2757 `_) * disable altivec when building FFTW versions < 3.4 with single-precision with GCC on POWER (`#2758 `_) * various bug fixes, including: * make VEP easyblock compatible with ``--sanity-check-only`` (`#2743 `_) * update Rosetta easyblock to take into account that ``$LD_LIBRARY_PATH``, ``$CPATH``, ``$PATH`` may not be defined (`#2744 `_) * only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension (`#2747 `_) * make sure that ``CMakeMakeCp`` uses correct build dir (`#2748 `_) * enhance Bazel easyblock to avoid writing to ``$HOME`` in sanity check (`#2756 `_) **easyconfigs** * added easyconfigs for ``foss/2022a``, ``intel/2022a`` common toolchains (`#15755 `_) * see also https://docs.easybuild.io/en/latest/Common-toolchains.html * add easyconfig for ``gfbf/2022a`` toolchain (`#15653 `_, `#15755 `_) * added example easyconfig files for 24 new software packages: * BLT (`#15624 `_), category_encoders (`#15638 `_), fio (`#10321 `_), FSON (`#15721 `_), G-PhoCS (`#7619 `_), GCTA (`#15649 `_), Gibbs2 (`#15702 `_), InterProScan_data (`#15717 `_), Jorg (`#15346 `_), libopus (`#15682 `_), Minipolish (`#15713 `_), mm-common (`#15764 `_), MONA (`#15696 `_), NetPyNE (`#15606 `_), pfind (`#15685 `_), regionmask (`#15786 `_), samplot (`#15686 `_), SISSO (`#15766 `_), sklearn-pandas (`#15637 `_), STAR-CCM+ (`#7398 `_), SWIPE (`#6795 `_), topaz (`#15739 `_), uncertainty-calibration (`#15612 `_), Virtuoso-opensource (`#14102 `_) * added additional easyconfigs for various supported software packages, including: * AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6, cppy 1.2.1, deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0, gdbm 1.21, geopandas 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 4.0.3, GULP 6.1, h5py 3.7.0, HDF5 1.13.1, hifiasm 0.16.1, IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, IRkernel 1.3, jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17, libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1, LittleCMS 2.13.1, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 2.12.12, netCDF 4.9.0, nettle 3.8, networkx 2.8.4, NEURON 7.8.2, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2, Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0, protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2, Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, Ray-project 1.13.0, RE2 2022-06-01, redis-py 4.3.3, ReFrame 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, Shapely 1.8.2, Siesta 4.1.5, SimpleITK 2.1.1.2, SpectrA 1.0.1, TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1, UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 3.9.1, Xvfb 21.1.3 * minor enhancements, including: * add extensions to R v4.2.0: hypergeo (`#15701 `_), rtdists (`#15734 `_), geeM (`#15810 `_) * add patch for GCCcore 11.3.0 to support using ``-fuse-ld=mold`` (`#15715 `_) * add patch for porefoam to fix hardcoded ``mpirun`` command and take into account ``$POREFOAM_MPIRUN_CMD`` (`#15730 `_) * various bug fixes, including: * switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1 (`#15636 `_) * avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (`#15657 `_) * add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (`#15691 `_) * correct configopts in deal.II v9.1.1 easyconfig (`#15692 `_) * add missing Python dependency for HPDBSCAN to fix unresolved ``%(pyshortver)s`` template (`#15694 `_) * other changes: * disable flaky GPU test for TensorFlow 2.6.0 (`#15824 `_) .. _release_notes_eb455: EasyBuild v4.5.5 (June 8th 2022) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), ``gfbf`` (GCC, FlexiBLAS, FFTW) (`#4006 `_) * add support for ``FFTW.MPI`` toolchain component (``$FFT*DIR`` variables) (`#4012 `_) * add support for customizing EasyBuild command used in jobs via ``--job-eb-cmd`` (`#4016 `_) * various bug fixes, including: * fix copying of easyconfig file with ``--copy-ec`` without ``--rebuild`` if module is already installed (`#3993 `_) * ignore deprecation warnings regarding cryptography in Python 3.6 + Blowfish with Python 3.10 in test suite output (`#3999 `_) * fix typo in debug log message in ``easyblock.py`` (`#4000 `_) * fix printing of list of attempted download URLs when url-encoded characters are used in URL (`#4005 `_) * set ``$FFT(W)_LIB_DIR`` to imkl-FFTW's lib path in build environment if usempi toolchain option is enabled (`#4011 `_) * correctly identify Apple Silicon M1 as Arm 64-bit by also considering arm64 next to aarch64 (`#4014 `_) * fix '``eb --show-system-info``' on Apple M1 system (`#4015 `_) * other changes: * change '``eb``' command to ``import easybuild.framework`` to check if EasyBuild framework is available (`#3995 `_, `#3998 `_) **easyblocks** * new software-specific easyblock for FFTW.MPI (`#2724 `_) * minor enhancements and updates, including: * update NEURON easyblock to use CMakeMake for recent versions (`#2304 `_) * enhance Clang easyblock to add support for building with AMDGPU offload (`#2684 `_, `#2729 `_) * update sanity check in OpenMPI easyblock to support OpenMPI v5.0.0 (`#2709 `_) * don't use ``gold`` linker by default for GCC >= 11.3 (`#2711 `_) * update sanity check in R easyblock for versions >= 4.2.0, since S.h is not included anymore (`#2713 `_) * update ABAQUS easyblock for ABAQUS 2022 (`#2716 `_) * update LLVM easyblock for LLVM v14.0.x (`#2718 `_) * update Mesa easyblock to remove swr driver configopts for versions 22+ (`#2719 `_) * enhance Clang easyblock to support also installing Python bindings (`#2721 `_, `#2725 `_) * enhance SuperLU easyblock to support building on top of FlexiBLAS and be compatible with SuperLU v5.3 (`#2722 `_) * update TensorFlow easyblock for version 2.8.0 (`#2723 `_) * modify FFTW's sanity check step to allow checking only for MPI parts of FFTW installation (`#2724 `_) * add support to ConfigureMake for tweaking (first part of) test command via '``test_cmd``' (`#2726 `_, `#2737 `_) * enhance MrBayes easyblock with custom sanity check command (`#2727 `_) * update cudnnarch string templates used to compose source tarball names from cuDNN 8.3.3 onwards (`#2728 `_) * add sanity check command to OpenSSL wrapper easyblock to verify that system certificates are available to OpenSSL (`#2735 `_) * ignore exit code of ``pkg-config`` command in OpenSSL wrapper easyblock, since with ``pkgconf`` they exit with a non-zero exit code if the OS package is not installed (`#2736 `_) * various bug fixes, including: * remove system-compiled binutils dirs from ``$LDFLAGS`` in binutils easyblock (`#2712 `_) * fix for FreeSurfer easyblock: define ``$FREESURFER`` needed by recon_all (`#2717 `_) * also symlink ``cert.pem`` in from-source OpenSSL installation (if it exists) (`#2735 `_) **easyconfigs** * add candidates for 2022a common toolchains: ``foss/2022.05`` (`#15561 `_), intel/2022.05 (`#15485 `_) * added example easyconfig files for 35 new software packages: * Albumentations (`#15302 `_), AMPtk (`#15435 `_), arosics (`#15249 `_), CellTypist (`#15530 `_), detectron2 (`#15442 `_), EigenExa (`#15234 `_), Fastaq (`#15332 `_), FFTW.MPI (`#15561 `_), FreeBarcodes (`#15350 `_), gcloud (`#15443 `_), GST-plugins-bad (`#15446 `_), gsutil (`#15507 `_), GTK4 (`#15447 `_), hector (`#15397 `_), i7z (`#15236 `_), libde265 (`#15395 `_), libheif (`#15395 `_), ModelTest-NG (`#15448 `_), num2words (`#15473 `_), OGDF (`#15407 `_), panito (`#15314 `_), parameterized (`#15481 `_), purge_dups (`#15385 `_), redis-py (`#15475 `_), ruamel.yaml (`#15531 `_), SCGid (`#15065 `_), scPred (`#15575 `_), slow5tools (`#15457 `_), smooth-topk (`#15506 `_), SPOTPY (`#15326 `_), tmap (`#14601 `_), UCC (`#14291 `_), Wayland (`#11107 `_), XGrafix (`#15268 `_), XPLOR-NIH (`#15479 `_) * added additional easyconfigs for various supported software packages, including: * ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0, breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187, EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6, freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8, geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0, Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12, HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3, IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1, libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1, libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7, libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0, Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2, Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0, OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1, Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0, PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0, RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0, SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0, vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 * minor enhancements, including: * use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (`#15227 `_) * also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (`#15347 `_) * add extensions to R v4.1.2 + v4.2.0 easyconfigs: * Hmsc (`#15393 `_), MonteCarlo + RhpcBLASctl (`#15438 `_), chkptstanr (`#15540 `_), chkptstanr + MLmetrics + renv (`#15573 `_) * add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (`#15405 `_) * use redist source_urls for cuDNN > 7.5 (`#15411 `_) * add download_instructions to Java 1.8 > 200 (`#15412 `_) * update Arrow to use EB versions of some dependencies and enable all compression codecs (`#15512 `_) * add csh -> tcsh symlink in recent tcsh easyconfigs (`#15571 `_) * allow external tools to be located elsewhere for ETE (`#15578 `_) * add additional sanity check commands for IQ-TREE v2.2.1 (`#15596 `_) * various bug fixes, including: * fix source URL for freetype 2.6.5 with ``foss/2016b`` (`#14204 `_) * fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (`#15206 `_) * use x.py to bootstrap Rust so that build options are properly passed through (`#15211 `_) * fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (`#15280 `_, `#15615 `_) * add hwloc dependency to tbb v2021.4.0 (`#15294 `_) * tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (`#15313 `_) * remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (`#15316 `_) * update source URL for isl in GCCcore easyconfigs (`#15320 `_) * update source URLs for YAXT 0.9.x to fix download (`#15323 `_) * define ``$HHLIB`` as path to HH-suite installation directory, required by Perl scripts (`#15324 `_) * add missing parallel and tbl2asn dependencies for prokka 1.14.5 (`#15360 `_, `#15381 `_) * add missing dependencies for libheif (libpng, libjpeg-turbo) (`#15408 `_) * switch to configuring build of libheif with CMake so libde265 dependency is picked up (`#15408 `_) * disable use of ``-ftree-vectorize`` for OpenFOAM v2112 with ``foss/2021b`` (`#15495 `_) * add patch for OpenMPI 4.1.1 to support building using ``--with-cuda=internal`` (`#15528 `_, `#15589 `_) * add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (`#15566 `_) * also build shared library + fix ``$PYTHONPATH`` for gmsh 4.9.0 (`#15579 `_) * add patch for GLib 2.68.2 to fix use of close_range (`#15594 `_) * fix download of thrift 0.12.0 for Arrow 0.16.0 (`#15597 `_) * add Bison and flex build dependencies to SCOTCH 6.1.x (`#15618 `_) * add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (`#15619 `_) * add missing dependencies + switch to non-static build for Arriba v2.1.0 (`#15623 `_) * other changes: * add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to ``foss/2021b`` toochain (`#15216 `_) * update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (`#15592 `_) * install sklearn meta-package with scikit-learn v1.0.1 (`#15613 `_) * switch from ``pkg-config`` to ``pkgconf`` as build dependency for OpenSSL wrapper easyconfigs (`#15616 `_, `#15617 `_) .. _release_notes_eb454: EasyBuild v4.5.4 (March 31st 2022) ---------------------------------- bugfix/update release **framework** * various enhancements, including: * warn about potentially missing patches in ``--new-pr`` (`#3759 `_, `#3966 `_) * add support for '``clone_into``' field in git_config source spec to specify different name for top-level directory (`#3949 `_) * add bash completion for easyconfigs from local dir but not robot search path (`#3953 `_) * add a 'sync pr' message when the PR has a mergeable state but is showing a failed status for the test suite on the last commit (`#3967 `_) * add ``gmpit`` toolchain definition (GCC + MPItrampoline) (`#3971 `_) * use '``zypper search -i``' to check whether specified OS dependency is installed on openSUSE + make sure that rpm is considered for checking OS dependencies on RHEL8 (`#3973 `_) * add support for post-install patches (`#3974 `_) * add support for '``download_instructions``' easyconfig parameter key to specify some download or installation steps for user in case of complicated way of obtaining needed files (`#3976 `_, `#3981 `_) * also try collecting AMD GPU info (via ``rocm-smi``) for ``--show-system-info`` (`#3978 `_, `#3982 `_) * various bug fixes, including: * ensure ``--review-pr`` can find dependencies included in PR (`#3979 `_) * run '``apt-get update``' in GitHub Actions workflow for container tests to update container package list before installing anything (`#3985 `_) * other changes: * enable code linting check for all supported Python versions (`#3725 `_) * update copyright lines for 2022 (`#3986 `_) **easyblocks** * minor enhancements and updates, including: * update Clang-AOMP easyblock to add support for ROCm v5.0 (`#2681 `_) * enable system SSL certificates in OpenSSL installations (`#2683 `_) * enhance MRtrix easyblock: build in parallel + enable OpenMP support for MRtrix >= 3.0 (`#2685 `_) * avoid dependency on '``which``' command in sanity check for Python, use '``command -v``' instead (`#2687 `_) * enhance Tarball easyblock to support using it for installing extensions (`#2688 `_) * update wxPython easyblock to support wxPython v4.1 (`#2689 `_) * enhance Gurobi easyblock to also update ``$MATLABPATH`` (`#2691 `_) * build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via ``$FLEXIBLAS_LIBRARY_PATH`` (`#2694 `_) * various bug fixes, including: * added regex to replace /lib/cpp with cpp in OpenFOAM's wmake rules file (`#2331 `_) * set ``$NINJAFLAGS`` to make sure Ninja doesn't use all visible cores when building Qt5 (`#2338 `_) * update Siesta EasyBlock to use serial FFTW (`#2662 `_) * fix support for imkl for numexpr 2.8.0+ in numexpr easyblock (`#2678 `_) * make sure TensorFlow doesn't see the ``nvptx-none`` dir when searching for ``gcc`` include dir (`#2682 `_) * force use of bash for Anaconda install script (`#2692 `_) * add guess for path to add to ``$MANPATH`` for intel-compilers (`#2696 `_) * change permissions of the Java build directory to avoid permission denied error (`#2698 `_) * also consider ``$MKLROOT/lib/pkgconfig`` for ``$PKG_CONFIG_PATH`` for imkl (`#2701 `_) * close log after installing Bundle component (`#2702 `_) * fixes problem of log leaking across installations (`framework issue #3533 `_) * replace hardcoded /tmp to make sure that Bazel build respects ``$TMPDIR`` (`#2703 `_) * other changes: * minor code cleanup in numexpr easyblock (`#2679 `_) * update copyright lines for 2022 (`#2705 `_) **easyconfigs** * added example easyconfig files for 29 new software packages: * Abseil (`#15102 `_), AMS (`#13155 `_), ArchR (`#15119 `_), CMAverse (`#14963 `_), CmdStanR (`#15198 `_), CONN (`#15052 `_), Devito (`#14984 `_, `#15009 `_), GraphMap (`#10299 `_), gRPC (`#14728 `_), Hydra (`#15025 `_), jupyter-server-proxy (`#14844 `_), M1QN3 (`#15002 `_), MAGeCK (`#15082 `_), matplotlib-inline (`#15084 `_), MEGAN (`#15064 `_), MNE-Python (`#15174 `_), ONNX (`#15158 `_), ONNX-Runtime (`#15158 `_), ont-remora (`#15162 `_), Optuna (`#15021 `_), patch (`#15035 `_), porefoam (`#15067 `_), presto (`#15119 `_), PyFrag (`#15184 `_), skorch (`#15175 `_), SlamDunk (`#15197 `_), SPM (`#15050 `_), STRique (`#14980 `_), XML-Compile (`#15177 `_) * added additional easyconfigs for various supported software packages, including: * ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1, CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0, ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0, IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0, KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a, MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2, NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3, parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1, RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3, VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0 * minor enhancements, including: * add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (`#15027 `_) * add check to verify that patch files touched in PRs have a description in place (`#15061 `_) * add extensions to R v4.1.2 easyconfig: hash (`#15098 `_), nabor + harmony (`#15117 `_), apluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps (`#15141 `_) * also install rMATS_P commands in rMATS-turbo easyconfig (`#15113 `_) * add extensions to Bioconductor v3.14 easyconfig: chromVAR (`#15118 `_), EnsDb.Hsapiens.v79 (`#15154 `_), WGCNA (`#15178 `_) * add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (`#15176 `_), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (`#15190 `_) * enable running of tests for MEME with ``gompi/2021b`` (`#15191 `_, `#15199 `_) * various bug fixes, including: * add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (`#14847 `_) * downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using ``GCCcore/10.3.0`` toolchain (`#14942 `_) * add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (`#14987 `_), optmatch (`#14993 `_) * avoid pollution in the tmp directory when running the AlphaFold tests (`#14989 `_) * consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (`#15039 `_) * fix GBprocesS easyconfig by switching to source tarball created using ``git_config`` (`#15048 `_) * add patches for mauveAligner to fix build on RHEL8 (`#15049 `_) * fix installation of RDKit by using ``-DBoost_NO_BOOST_CMAKE=ON`` (`#15051 `_) * add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (`#15054 `_) * avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (`#15055 `_) * fix ``python`` shebang in cutadapt script for cutadapt 1.18 w/ ``GCCcore/8.3.0`` (`#15059 `_) * don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (`#15060 `_) * add M4 as build dependency for CCL-1.12 (`#15075 `_) * configure libffi 3.4.2 with ``--disable-exec-static-tramp`` to prevent segfaults (`#15086 `_) * set ``XLA_PYTHON_CLIENT_ALLOCATOR=platform`` for running tests in jax CUDA easyconfigs (`#15097 `_) * remove disable flag for RTTI in snappy v1.1.9 (`#15099 `_) * fix grconvert build for Grace 5.1.25 with ``foss/2021a`` by adding libtirpc dependency + related patch (`#15121 `_) * clean up PSolver and futile easyconfigs and add dynamic libs (`#15148 `_) * enhance vcflib easyconfigs to also install scripts (`#15181 `_) * add patch to fix shared linking in vcflib (`#15203 `_) * fix failing sanity check for PRINSEQ (`#15205 `_) * other changes: * use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (`#15003 `_) * disable building of documentation for DBus 1.13.18 (`#15010 `_) * consistently use system toolchain in EasyBuild easyconfigs (`#15126 `_) * use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (`#15149 `_) .. _release_notes_eb453: EasyBuild v4.5.3 (February 11th 2022) ------------------------------------- bugfix/update release **framework** * various enhancements, including: * also check for git in ``--check-eb-deps`` (`#3954 `_) * add end2end test for ``eb --containerize`` (`#3958 `_) * various bug fixes, including: * take into account that patch files can also be zipped when checking filename extension for patches (`#3936 `_) * initialize ``BACKUP_PKG_URL`` with empty string in ``install_eb_dep.sh`` script (`#3939 `_) * fix ``get_os_name`` and ``get_os_version`` to avoid reporting ``UNKNOWN`` in output of ``eb --show-system-info`` (`#3942 `_) * consistently use ``actions/setup-python@v2`` in CI workflows (`#3944 `_) * switch to using ``pip3`` for installing EasyBuild in container recipes generated by EasyBuild (`#3945 `_) * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#3947 `_) * avoid crash in ``get_os_version`` on modern SLES-based OSs (`#3955 `_) * other changes: * indicate compatibility with Python 3.10 in ``setup.py`` (`#3940 `_) **easyblocks** * new software-specific easyblock for reticulate R package (`#2668 `_) * minor enhancements and updates, including: * set CUDA target architecture(s) for GROMACS based on ``cuda_cc_semicolon_sep`` template value (`#2655 `_) * add support to NAMD easyblock to opt out of building with CUDA support even if CUDA is included as dependency (`#2666 `_) * update sanity check in CUDA easyblock: CUDA 11.6 no longer includes samples (`#2669 `_) * various bug fixes, including: * also run easyblocks test suite with Python 3.8-3.10 + consistently use ``actions/setup-python@v2`` in CI workflows (`#2664 `_) * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#2667 `_) * other changes: * remove vulnerable binaries from sanity check of HDF5, no longer installed by default with HDF5 1.10.8 (`#2670 `_) **easyconfigs** * added example easyconfig files for 25 new software packages: * Arcade-Learning-Environment (`#14753 `_), Bambi (`#14811 `_), CASTEP (`#14420 `_), Crumble (`#14785 `_), deepmedic (`#14953 `_), FoBiS (`#14771 `_), histolab (`#14945 `_), Iris (`#14788 `_), Jasmine (`#14789 `_), libexif (`#14823 `_), libgdiplus (`#14823 `_), MuJoCo (`#14965 `_), mujoco-py (`#14776 `_, `#14965 `_), namedlist (`#14814 `_), OpenCensus-python (`#14837 `_), PyEVTK (`#14911 `_), pyradiomics (`#14851 `_), PyTorch-Lightning (`#14933 `_), Redis (`#14783 `_), rising (`#14952 `_), SoXt (`#14803 `_), SURVIVOR (`#14786 `_), tensorboard (`#14926 `_), xtensor (`#14944 `_), xxd (`#14846 `_) * added additional easyconfigs for various supported software packages, including: * aiohttp 3.8.1, AOCC 3.2.0, ArviZ 0.11.4, BeautifulSoup 4.10.0, bokeh 2.4.2, Boost.Python 1.77.0, Bowtie 1.3.1, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.5.1, ConnectomeWorkbench 1.5.0, Crumble 0.8.3, CUDA 11.5.1 + 11.6.0, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepTools 3.5.0, dm-tree 0.1.6, DROP 1.1.1, ecCodes 2.24.2, Emacs 27.2, FDS 6.7.7, file 5.41, Flask 2.0.2, FORD 6.1.6, GATE 9.1, Geant4 11.0.0, GEMMA 0.98.5, GnuTLS 3.7.3, Go 1.17.6, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, Guile 3.0.7, HDF5 1.10.8, imageio 2.13.5, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libpsml 1.1.10, libRmath 4.1.2, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, likwid 5.2.1, MaxQuant 2.0.3.0, MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, Mono 6.12.0.122, MUSCLE 5.1, nanomax-analysis-utils 0.4.3, ncbi-vdb 2.11.2, NCIPLOT-4.0 20200624, Nextflow 21.10.6, NGS 2.11.2, nvtop 1.2.2, OpenCV 4.5.5, openslide-python 1.1.2, pftoolsV3 3.2.11, picard 2.26.10, pydicom 2.2.2, pyFAI 0.20.0, Pysam 0.18.0, pytest-xdist 2.5.0, Racon 1.5.0, RAxML 8.2.12, ReFrame 3.10.1, ROOT 6.24.06, scikit-image 0.19.1, SDL2 2.0.20, SeqKit 2.1.0, Siesta 4.1.5, SimpleITK 2.1.1, SqueezeMeta 1.5.0, tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing-extensions 3.10.0.2 * minor enhancements, including: * also install Python bindings for SHTns 3.5.1 (`#14893 `_) * add catlearn extension to easyconfig for R v4.1.2 (`#14940 `_) * various bug fixes, including: * update TALYS sources to (hopefully) ensure constant checksums (`#14797 `_) * add missing graphite2 + HarfBuzz dependencies to Qt5 v5.15.2 (`#14802 `_) * add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 (`#14859 `_) * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#14870 `_) * add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 (`#14873 `_) and R 4.1.2 (`#14880 `_) easyconfigs * add patch to fix Kraken2 ncbi ``ftp``/``https`` check in ``rsync_from_ncbi.pl`` for versions 2.0.9-2.1.1 (`#14889 `_) * disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build (`#14923 `_) * disable use of ``-Werror`` for recent NSS versions (`#14924 `_) * fix download URL in UDUNITS v2.2.28 easyconfigs (`#14954 `_) * remove unnecessary CUDAcore dependency from nvtop v1.2.1 easyconfig (`#14957 `_) * consistently apply patch for mapDamage 2.2.1 to use external seqtk (`#14961 `_) * fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: ``$(name)s`` should be ``%(name)s`` (`#14962 `_) * other changes: * update Java/17 wrapper to Java 17.0.2 (`#14868 `_) * use ``actions/setup-python@v2`` in CI workflows + trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (`#14857 `_, `#14881 `_) .. _release_notes_eb452: EasyBuild v4.5.2 (January 24th 2022) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * automatically prepend value for ``env-for-shebang`` configuration setting with sysroot (`#3919 `_) * enhance ``update_build_option`` to return original value + add support for ``update_build_options`` (`#3923 `_) * fix compatibility with Python 3.10 (`#3926 `_, `#3933 `_) * also take ``/etc/os-release`` into account in ``get_os_name`` and ``get_os_version`` (`#3930 `_) * enhance ``get_cpu_architecture`` and ``get_cpu_family`` to be aware of RISC-V (`#3931 `_) * various bug fixes, including: * relax pattern checks in ``test_toy_exts_parallel`` (`#3921 `_) * use ``sources.easybuild.io`` as backup URL for downloading Environment Modules sources to run test suite (`#3928 `_) * make intelfftw toolchain component aware of GCCcore (`#3929 `_) * other changes: * deprecate use of (actual) patch files that don't have a filename ending with ``.patch`` (`#3920 `_) * remove version restriction for keyring in ``requirements.txt`` to test with latest version (`#3925 `_) * simplify ``requirements.txt`` by removing Python 2.6 support (`#3927 `_) * only run GitHub tests when testing with Lua module syntax, to avoid hitting GitHub rate limit when running tests (`#3938 `_) **easyblocks** * minor enhancements and updates, including: * remove necessity for license for oneAPI versions (>= 2021.x) in itac easyblock (`#2492 `_) * add CUDA support in SuiteSparse easyblock (`#2627 `_) * use all available cores for running Perl test suite (`#2637 `_) * add option to not copy the license file for Gurobi (`#2639 `_, `#2641 `_) * update AOCC easyblock to support version 3.2.0 (`#2643 `_) * don't grep for specific version in ``--version`` output of Intel compiler commands for versions 2022.x (`#2644 `_) * add support for enabling sanity checks for specific components in the Bundle easyblock (`#2649 `_) * update Libint easyblock for LibInt v2.7.0 which requires configuring via CMake (`#2650 `_) * update Mathematica easyblock for version 13 (`#2652 `_) * add sanity check command for Bazel (`#2653 `_) * update NAMD easyblock to allow non-system csh (`#2654 `_) * enhance CUDA easyblock to create version independent pkgconfig files (`#2656 `_) * add ``util`` subdirectory to ``$PATH`` for WPS (`#2658 `_) * various bug fixes, including: * convert version numbers to strictly numerical in Siesta easyblock (`#2553 `_) * fix shebang of scripts in Perl installation if installation prefix is too long (`#2640 `_) * enhance IntelBase easyblock to avoid crash when ``$USER`` is not set (`#2642 `_) * fix quotes in definition of default platform macro and enhance sanity check in GATE easyblock (`#2645 `_) * avoid excessively long shebang line in compile script for WRF (`#2648 `_) * fix checking of Intel Fortran compiler version in CP2K easyblock for recent toolchains (`#2651 `_) **easyconfigs** * added easyconfig for intel/2022.00 toolchain (`#14620 `_) * added example easyconfig files for 48 new software packages: * alevin-fry (`#14617 `_), AMD-uProf (`#14626 `_), ANGEL (`#11857 `_), atropos (`#7580 `_), Austin (`#14596 `_), AutoDock-GPU (`#14671 `_), AutoDock-Vina (`#14675 `_), boost_histogram (`#14516 `_), CAFE5 (`#14603 `_), Calcam (`#7488 `_), Carma (`#14527 `_), Cogent (`#14278 `_), dlib (`#14556 `_), DualSPHysics (`#14632 `_), dune-core (`#14693 `_), dune-fem (`#14693 `_), DyMat (`#14615 `_), elbencho (`#14548 `_), Embree (`#7471 `_), ExaML (`#14530 `_), FMPy (`#14481 `_), genozip (`#14583 `_), hivtrace (`#14691 `_), intervaltree-python (`#8995 `_), IsoNet (`#14075 `_), MACSE (`#14709 `_), MetaPhlAn (`#12917 `_), MicrobeAnnotator (`#14549 `_), mold (`#14595 `_), numdiff (`#14609 `_), OpenFace (`#14556 `_), PhyloPhlAn (`#14564 `_), PREQUAL (`#14722 `_), PuLP (`#14581 `_), PyCalib (`#14616 `_), PyTorch3D (`#13240 `_), QCG-PilotJob (`#14337 `_), RaGOO (`#8995 `_), RAPSearch2 (`#13199 `_), SCopeLoomR (`#14518 `_), ShengBTE (`#14557 `_), SHTns (`#14682 `_), STRUMPACK (`#14560 `_), TALYS (`#14716 `_), TN93 (`#14691 `_), xxHash (`#14251 `_), yaml-cpp (`#14547 `_), Zgoubi (`#14516 `_) * added additional easyconfigs for various supported software packages, including: * annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0, cDNA_Cupcake 26.0.0, CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, dotNET-Core-Runtime 6.0.1, dotNET-SDK 6.0.101, Extrae 3.8.3, fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, GTK3 3.24.31, h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2, libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428, numba 0.54.1, NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 3.4.1, OpenFOAM v2112, ORCA 5.0.2, phonopy 2.12.0, Pillow 8.3.2, Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 0.12.3, python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 1.0.0, statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0 * minor enhancements, including: * add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (`#14547 `_) * include output of failing code style check in message produced by failing easyconfigs style test (`#14578 `_) * bundle LAPACKE with FlexiBLAS 3.0.4 (`#14591 `_), `#14769 `_) * add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX (`#14634 `_), FactorCopula (`#14648 `_), rpact, ldbounds (`#14750 `_) * add extensions to R-bundle-Bioconductor 3.14: ExomeDepth (`#14684 `_), DSS (`#14748 `_), pathview (`#14806 `_) * various bug fixes, including: * fix ``homepage`` and ``source_urls`` for GLIMMER 3.02b (`#7945 `_) * fix source URL for Trilinos 12.12.1 with foss/2019b (`#14547 `_) * use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (`#14565 `_) * fix checksum and versions of annovar v20191024 (`#14579 `_) * add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (`#14584 `_) * retain version in filename for cromwell sources (`#14586 `_) * specify compiler to use in WildMagic easyconfig (`#14594 `_) * avoid need for git build dependency for recent x265 easyconfigs (`#14605 `_) * fix broken patch file for recent GPAW versions (`#14619 `_) * add alternative checksum for Siesta-4.1-MaX-1.0 (`#14643 `_) * add missing PCRE dependency for pullseq + add sanity check commands (`#14650 `_) * use ``%(arch)s`` template to avoid hardcoding ``x86_64`` in recent XML-LibXML easyconfigs (`#14655 `_) * fix name for (binary) AutoDock-Vina v1.1.2 (`#14675 `_) * add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (`#14726 `_) * set ``$GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS`` for installing grcpio extension included with: * TensorFlow 2.2.3-2.4.1 with 2020* toolchain (`#14729 `_) and 2.5.0+ (`#14728 `_) * Ray-project (`#14730 `_) * enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (`#14741 `_) * add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (`#14743 `_) * also install ``libaio.so.1`` symlink in easyconfigs for libaio v0.3.112 (`#14745 `_) * do not use external libgcrypt or python for libxslt with recent toolchains (`#14756 `_) * add patches to fix CVE-2021-23437 for Pillow (`#14765 `_) and Pillow-SIMD (`#14792 `_) * add libXfont2 patch to fix build when libbsd is present (`#14821 `_) * other changes: * update Java 1.8 wrapper to 1.8.0_311 for x86_64 (`#14644 `_) * bring gffread back down to GCCcore level for toolchain version 10.3.0 (`#14660 `_) * update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (`#14731 `_), `#14755 `_) * bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (`#14738 `_) .. _release_notes_eb451: EasyBuild v4.5.1 (December 13th 2021) ------------------------------------- bugfix/update release **framework** * various enhancements, including: * also dump environment to reprod directory (`#3374 `_) * determine which extensions can be skipped in parallel (if ``--parallel-extensions-install`` is enabled) (`#3890 `_) * fall back to sequential installation for extensions with unknown dependencies when using ``--parallel-extensions-install`` (`#3906 `_) * allow oversubscription in sanity check for OpenMPI-based toolchains (`#3909 `_) * various bug fixes, including: * don't try to ensure absolute path for path part of ``repositorypath`` (`#3893 `_, `#3899 `_) * fix typo in EULA agreement error message (`#3894 `_) * only remove lock if it was created in the same EasyBuild session (not if it existed already) (`#3889 `_) * introduce ``EasyBlock.post_init`` method to correctly define ``builddir`` variable when ``build-in-installdir`` mode is enabled in easyconfig or easyblock (`#3900 `_) * also show download progress bar when using ``--inject-checksums`` (`#3905 `_) * pick up custom ``extract_cmd`` specified for extension (`#3907 `_) * make ``test_run_cmd_async`` more robust against fluke failures (`#3908 `_) **easyblocks** * new software-specific easyblock for Clang-AOMP (`#2617 `_) * minor enhancements and updates, including: * enhance Rpm generic easyblock to support installing tarball of RPMs (by unpacking it first) + take into account ``(pre)installopts`` (`#2580 `_) * add option to control use of MKL-DNN in jaxlib easyblock (`#2619 `_) * update SAMtools easyblock to support installation of SAMtools 1.14 (`#2620 `_) * add option to ignore PLUMED version check for GROMACS (`#2621 `_) * update Inspector easyblock for recent versions (>= 2021, oneAPI versions) (`#2624 `_) * enhance tbb easyblock by adding option to build Python bindings (`#2626 `_) * fix patching of ``CMakeLists.txt`` for Eigen v3.4 (`#2633 `_) * various bug fixes, including: * update CP2K easyblock to use ``-D__MKL`` for CP2K versions newer than 2.3 (`#2586 `_) * set OpenMPI configuration for ORCA sanity check (`#2596 `_) * allow oversubscription in OpenMPI sanity check (`#2611 `_) * set ``wm_*`` class variables in OpenFOAM easyblock constructor (to fix ``--sanity-check-only``) (`#2616 `_) * remove newline from easybuild-easyblocks package description (required to avoid installation error with setuptools>=59.0.0) (`#2623 `_) * avoid patching binary files + other enhancements for MUMmer easyblock (`#2630 `_) * enable ``build-in-installdir`` mode in constructor of PETSc and SLEPc easyblocks (`#2631 `_) * skip netcdf4-python tests that require network connectivity (`#2634 `_) **easyconfigs** * added example easyconfig files for 71 new software packages: * ANIcalculator (`#14478 `_, `#14494 `_, `#14510 `_), arrow-R (`#14267 `_), ASAP (`#14367 `_), BabelStream (`#14503 `_), bamtofastq (`#14391 `_), bcbio-gff (`#14322 `_), biom-format (`#13205 `_), Blosc2 (`#14247 `_), boto3 (`#14452 `_), Brotli-python (`#14528 `_), Brunsli (`#14247 `_), Clang-AOMP (`#14327 `_), CLEASE (`#14413 `_), CMSeq (`#14326 `_), cpu_features (`#14385 `_), cromwell (`#12125 `_), cxxopts (`#14487 `_, `#14504 `_), dRep (`#14479 `_), DUBStepR (`#14495 `_), eht-imaging (`#14239 `_), einops (`#14373 `_), ELFIO (`#14488 `_, `#14504 `_), elprep (`#14422 `_), epiScanpy (`#14447 `_), FMM3D (`#14257 `_), FORD (`#13653 `_), GPy (`#14380 `_), HIP (`#14339 `_), idemux (`#14499 `_), imagecodecs (`#14247 `_), InChI (`#13902 `_), jupyter-matlab-proxy (`#14270 `_), jxrlib (`#14247 `_), LBFGS++ (`#14230 `_), LERC (`#14247 `_), libaec (`#14247 `_), libavif (`#14246 `_), LibLZF (`#14246 `_), libnsl (`#14494 `_), libtree (`#14501 `_), LPeg (`#14157 `_), Megalodon (`#14256 `_), nnU-Net (`#14249 `_), PAL2NAL (`#14430 `_), photontorch (`#14410 `_), pkgconf (`#14426 `_), pmx (`#14319 `_), PPanGGOLiN (`#14449 `_), ProFit (`#14340 `_), pugixml (`#14367 `_, `#14492 `_), PySide2 (`#13460 `_), Relate (`#14443 `_), ROCm (`#14355 `_), rocm-cmake (`#14327 `_), ROCm-CompilerSupport (`#14327 `_), rocminfo (`#14327 `_), rocm-smi (`#14354 `_), ROCR-Runtime (`#14327 `_), ROCT-Thunk-Interface (`#14327 `_), SCENIC (`#14260 `_), Shasta (`#14385 `_), SimNIBS (`#14257 `_), SMV (`#14157 `_), SRST2 (`#14253 `_), STACEY (`#14293 `_), termcolor (`#14489 `_, `#14504 `_), ThemisPy (`#14231 `_), TOBIAS (`#14452 `_, `#14458 `_), zfp (`#14246 `_), zlib-ng (`#14246 `_), Zopfli (`#14246 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 9.6.2, ABRicate 1.0.0, AlphaFold 2.1.1, antiSMASH 6.0.1, Arrow 6.0.0, astropy 4.3.1, BCFtools 1.14, BeautifulSoup 4.9.3, Boost 1.77.0, bpp 4.4.0, Bracken 2.6.2, CapnProto 0.9.1, CellRanger 6.1.2, Eigen 3.4.0, enaBrowserTool 1.6, ESMF 8.2.0, Flye 2.9, FMRIprep 1.4.1, FSL 6.0.4, GATK 4.2.3.0, gc 8.2.0, GDB 11.1, git 2.33.1, Go 1.17.3, Gurobi 9.5.0, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, Infernal 1.1.4, Inspector 2021.4.0 ITK 5.2.1, jax 0.2.24, Julia 1.7.0, Kent_tools 422, king 2.2.7, libdwarf 20210528, MAFFT 7.490, makeinfo 6.8, Mash 2.3, matplotlib 3.4.3, MCR R2021b, minimap2 2.22, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, nlohmann_json 3.10.4, NVHPC 21.9, OpenMPI 4.0.7 + 4.1.2, panaroo 1.2.9, pangolin 3.1.16, pkgconfig 1.5.5, plotly.py 5.4.0, pyfaidx 0.6.3.1, Pysam 0.17.0, PyTorch 1.10.0, R 4.1.2, R-bundle-Bioconductor 3.14, ReFrame 3.9.1, rpy2 3.4.5, scikit-image 0.18.3, scikit-learn 1.0.1 SimpleITK 2.1.0, snakemake 6.10.0, SPAdes 3.15.3, tbb 2021.4.0, torchtext 0.10.0, torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, WPS 4.3.1, xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4 * minor enhancements, including: * add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 (`#14259 `_) * add extensions for R v4.1.x: * geex + momentfit (`#14299 `_); StatMatch, leaflet, tmap + collapse (`#14328 `_), genoPlotR + penfa (`#14433 `_), adcovsim (`#14484 `_) * add M3Drop extension to R-bundle-Bioconductor 3.14 (`#14436 `_) * various bug fixes, including: * specify to use Python provided as dependency, remove ``separate_build_dir``, and fix URL in comment for Arrow 0.17.1 (`#14263 `_) * fix ``gettid`` nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 0.29.1, and 1.1.0 (`#14269 `_) * restore and fix sanity check commands in RStudio-Server 1.4 (`#14275 `_) * add pkg-config build dependency to Python easyconfigs, to ensure OpenSSL wrapper is detected (`#14316 `_) * add patch for UCX v1.11.2 to fix missing include statement for ``string.h`` (`#14317 `_) * set ``$DALTON_TMPDIR`` to build directory to run Dalton tests (`#14341 `_) * add patch for libfabric v1.12.1 to fix ``unknown link width 0x10`` warning (`#14387 `_) * add missing Automake dependency to PhyML 3.3.20200621 (`#14397 `_) * add git as build dependency to Python 3.8.x and 3.9.x easyconfigs (required for pbr extension) (`#14421 `_) * add missing XZ dependency to recent PROJ easyconfigs (`#14429 `_) * fix homepage/source URL for king v2.2.4 (`#14444 `_) * add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers (`#14453 `_) * add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers (`#14454 `_) * add patch to fix CVE-2021-43527 in NSS (`#14497 `_) * pass tests on A* GPUs by setting ``NVIDIA_TF32_OVERRIDE=0`` in jax 0.2.19 (`#14502 `_) * add patch to fix broken (hanging) Mash binaries (`#14511 `_) * add missing Perl build dependency for Longshot (`#14535 `_) * add googletest build dependency for Highway (`#14536 `_) * seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs (`#14537 `_) * other changes: * rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme (`#14262 `_) * comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (`#14335 `_) * don't add ``bin`` subdir to ``$PATH`` via ``modextrapaths`` in ReFrame easyconfigs (`#14415 `_) * consistently use 'Grace' software name + sync ``homepage``/``source_urls`` (`#14493 `_) * move cxxopts, termcolor and ELFIO header only libraries to ``SYSTEM`` toolchain (`#14504 `_) .. _release_notes_eb450: EasyBuild v4.5.0 (October 29th 2021) ------------------------------------ feature release **framework** * various enhancements, including: * add ``--review-pr-max`` and ``--review-pr-filter`` options to limit easyconfigs used by ``--review-pr`` + retain order of easyconfigs being compared with (`#3754 `_) * use Rich (if available) to show progress bars when installing easyconfigs (`#3823 `_, `#3826 `_, `#3833 `_, `#3835 `_, `#3844 `_, `#3864 `_, `#3867 `_, `#3882 `_) * see also https://docs.easybuild.io/en/latest/Progress_bars.html * add support for checking required/optional EasyBuild dependencies via ``eb --check-eb-deps`` (`#3829 `_) * add support for collecting GPU info (via ``nvidia-smi``), and include it in ``--show-system-info`` and test report (`#3851 `_) * added support for ``--insecure-download`` configuration option (`#3859 `_) * make intelfftw toolchain component aware of imkl-FFTW module (`#3861 `_) * make sure the contrib/hooks tree is included in the source tarball for easybuild-framework (`#3862 `_) * add ``check_async_cmd`` function to facilitate checking on asynchronously running commands (`#3865 `_, `#3881 `_) * add initial/experimental support for installing extensions in parallel (`#3667 `_, `#3878 `_) * see also https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html * filter out duplicate paths added to module files, and print warning when they occur (`#3770 `_, `#3874 `_) * various bug fixes, including: * ensure that path configuration options have absolute path values (`#3832 `_) * fix broken test by taking into account changed error raised by Python 3.9.7 when copying directory via ``shutil.copyfile`` (`#3840 `_) * ensure newer location of CUDA stubs is taken into account by RPATH filter (`#3850 `_) * replace ``which`` by ``command -v`` in ``eb`` wrapper script to avoid dependency on ``which`` command (`#3852 `_) * refactor EasyBlock to decouple collecting of information on extension source/patch files from downloading them (`#3860 `_) * in this context, the ``EasyBlock.fetch_extension_sources`` method was deprecated, and replaced by ``EasyBlock.collect_exts_file_info`` * fix library paths to add to ``$LDFLAGS`` for intel-compilers toolchain component (`#3866 `_) * remove ``--depth 1`` from git clone when ``commit`` specified (`#3871 `_, `#3872 `_) * make sure correct include directory is used for FlexiBLAS toolchain component (`#3875 `_) * explicitly disable rebase when pulling develop branch to create a merge commit, since not specifying how to reconcile divergent branches is an error with Git 2.33.1 and newer (`#3879 `_) * tweak ``test_http_header_fields_urlpat`` to download from ``sources.easybuild.io`` rather than ``https://ftp.gnu.org`` (`#3883 `_) * other changes: * change ``copy_file`` function to raise an error when trying to copy non-existing file (`#3836 `_, `#3855 `_, `#3877 `_) * only print the hook messages if EasyBuild is running in debug mode (`#3843 `_) * deprecate old toolchain versions (pre-2019a common toolchains) (`#3876 `_, `#3884 `_) * see also https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains **easyblocks** * new software-specific easyblock for imkl-FFTW (`#2599 `_) * minor enhancements and updates, including: * add support for installing R extensions in parallel (`#2408 `_) * update MotionCor2 easyblock to consider to locations for built binary (`#2541 `_, `#2598 `_) * let GROMACS runtime logs show EasyBuild was used by setting ``-DGMX_VERSION_STRING_OF_FORK`` configuration option (`#2571 `_) * adjust qa list in WIEN2k easyblock to handle new questions + fix sanity check for v21.1 (`#2572 `_) * enhance GCC easyblock to add support for AMD GPU offloading (`#2578 `_) * add support for specifying subdirectory for target installation directory in CMakeMake (`#2579 `_) * enhance COMSOL easyblock to change permission on build directory during extract step (to allow using patches) (`#2584 `_) * enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend (`#2588 `_) * update MATLAB easyblock for 2021b (jre is no longer included) (`#2589 `_) * update OpenCV easyblock to detect GTK3 and GTK2 dependencies (next to GTK+) (`#2591 `_) * avoid that path to CUDA install directory is added to ``$PATH`` (`#2593 `_) * enhance imkl easyblock to add support for installing with NVHPC (`#2595 `_) * enhance PETSc easyblock to run tests in parallel (`#2601 `_) * update ELSI easyblock to support two new external dependencies (`#2602 `_) * add custom custom easyconfig parameter ``backends`` in FlexiBLAS easyblock to specify backends (`#2605 `_) * detect problem with compiling CPU detection code in configure output in GROMACS easyblock (`#2609 `_) * use correct include directory for FlexiBLAS (`#2610 `_) * various bug fixes, including: * unset ``$EASYBUILD_*`` environment variables when running sanity check in EasyBuildMeta easyblock + also unset ``$MODULES_LMCONFLICT`` to avoid conflict when loading EasyBuild module (`#2568 `_) * ensure that all ABAQUS components get installed for ABAQUS 2021.x (+ add support for enabling/disabling fe-safe) (`#2569 `_) * fix subdir path in VTune easyblock for 2021.x versions + add sanity check command (`#2576 `_) * make sure custom easyblock for installing EasyBuild respects requested version of Python (like ``$EB_PYTHON``) (`#2581 `_) * restore RPATH wrappers for OpenMPI sanity check (`#2582 `_) * fix installation of libcp2k for recent CP2K versions (`#2585 `_) * make version regex in OpenSSL wrapper easyblock less strict (version string does not always end with a letter) (`#2597 `_) * redefine ``collect_exts_file_info`` instead of now deprecated fetch_extension_sources in OCaml easyblock (`#2603 `_) * other changes: * don't use ``--config=mkl`` for TensorFlow 2.4+ (`#2583 `_) * this fixes some performance related issues for TensorFlow, see https://github.com/easybuilders/easybuild-easyblocks/issues/2577 and https://github.com/easybuilders/easybuild-easyconfigs/issues/14120 * fix support for recent imkl version in numexpr easyblock (`#2606 `_) * derive custom easyblock from MotionCor2 from PackedBinary instead of EasyBlock (`#2607 `_) **easyconfigs** * added easyconfigs for foss/2021b (`#14217 `_) and intel/2021b (`#14218 `_) common toolchains * see also https://docs.easybuild.io/en/latest/Common-toolchains.html * add easyconfig for gobff/2021a toolchain (`#14019 `_, `#14038 `_) * added example easyconfig files for 39 new software packages: * abTEM (`#13974 `_), ARTS (`#9651 `_), AutoGeneS (`#13903 `_), bashplotlib (`#13942 `_), CIRI-long (`#13985 `_), DFT-D4 (`#12803 `_), ELSI-RCI (`#14147 `_), ESL-Bundle (`#14179 `_), expecttest (`#14106 `_), fdict (`#14161 `_), flook (`#14161 `_), FreeTDS (`#13952 `_), HDBSCAN (`#14062 `_), imkl-FFTW (`#14195 `_), isoCirc (`#13982 `_), libfdf (`#14173 `_), libmbd (`#14129 `_), libpspio (`#14173 `_), libSBML (`#14050 `_), longread_umi (`#13987 `_), Mesa-demos (`#14123 `_), MixMHC2pred (`#14041 `_), NTPoly (`#14183 `_), OpenSceneGraph (`#14197 `_), panaroo (`#14203 `_), PEPT (`#14077 `_), pycoQC (`#14012 `_), python-docx (`#13930 `_), QD (`#14122 `_), radeontop (`#14124 `_), Rgurobi (`#14188 `_), RInChI (`#14049 `_), scGeneFit (`#13963 `_), swifter (`#14114 `_), TOML-Fortran (`#13929 `_), TRUST4 (`#14035 `_), ucx-py (`#14051 `_), vawk (`#14040 `_), VMTK (`#14023 `_) * added additional easyconfigs for various supported software packages, including: * AlphaFold 2.0.1, artic-ncov2019 2021.06.24, BerkeleyGW 3.0.1, bokeh 2.4.1, Boost.Python 1.76.0, canu 2.2, Cartopy 0.20.0, CP2K 8.2, CUDA 11.4.2, Dalton 2020.0, dask 2021.9.1, edlib 1.3.9, ELSI 2.7.1, FFTW 3.3.10, GD 2.73, GDAL 3.3.2, GTDB-Tk 1.7.0, ImageJ 1.52q, jax 0.2.20, Kraken2 2.1.2, leidenalg 0.8.7, libfabric 1.13.2, libspatialindex 1.9.3, libxc 5.1.6, libxsmm 1.16.2, lifelines 0.26.3, Longshot 0.4.3, LSD2 2.2, MAFFT 7.487, MEME 5.4.1, MotionCor2 1.4.4, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.3, Nextflow 21.08.0, OpenBLAS 0.3.18, OpenCV 4.5.3, OrthoFinder 2.5.4, OSU-Micro-Benchmarks 5.8, PhyML 3.3.20200621, PostgreSQL 13.4, pygraphviz 1.7, pyproj 3.1.0, python-Levenshtein 0.12.1, PyTorch-Geometric 2.0.1, QIIME2 2021.8.eb, Qiskit 0.31.0, QuantumESPRESSO 6.8, Racon 1.4.21, rampart 1.2.0, rclone 1.56.0, RDKit 2021.03.4, SAMtools 1.13, scanpy 1.8.1, scikit-allel 1.3.3, SciPy-bundle 2021.10, Seaborn 0.11.2, SHAPEIT4 4.2.2, spglib 1.16.2, UCX 1.11.2, UCX-CUDA 1.11.2, VSEARCH 2.18.0, Z3 4.8.12, zarr 2.10.1 * minor enhancements, including: * add JASPAR2020 to R-bundle-Bioconductor 3.13 (`#13962 `_) * add Autotools as build dependency for CubeGUI-4.6 (`#14109 `_) * add compiler/parallel/tcltk R libraries included in base installation to extensions in recent R easyconfigs (`#14189 `_, `#14190 `_, `#14194 `_) * required for parallel installation of extensions for these R easyconfigs * also add location to MPI startup tests to ``$PATH`` in OSU-Micro-Benchmarks easyconfigs (`#14126 `_) * various bug fixes, including: * add missing Brotli dependency to freetype (`#13915 `_, `#14002 `_) * add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (`#13923 `_) * fix source URL + add alternate checksum for ADMIXTURE 1.3.0 (`#13933 `_) * just use ``cp`` to copy ``stereo_chemical_props.txt`` to AlphaFold installation directory (`#13938 `_) * add UnZip build dependency to TensorFlow 2.4.1 (`#13958 `_), 2.5.0 (`#13959 `_) and 2.6.0 easyconfigs (`#13960 `_) * add missing Python dependency for WIEN2k 21.1 + patch to fix build failure for ``lapw0_mpi`` with libxc (`#13961 `_) * add additional valid checksum for lhs 1.1.1 extension in recent R 4.0.x and 4.1.0 easyconfigs (`#13969 `_) * fix Fortran system call stdout/err redirection for WIEN2k v21.1 (`#13972 `_) * add OpenSSL dependency to Kent_tools 418 easyconfig to fix a link error (`#13989 `_) * make binutils a build-only dependency for Brotli + add sanity check command (`#14004 `_) * fix installation of Racon v1.4.7 with gcccuda/2019b after move of ClaraGenomicsAnalysis repository (`#14010 `_) * fix source URL for KEGG.db extension in R-bundle-Bioconductor 3.13 easyconfig (since it's a deprecated library now) (`#14013 `_) * add patch for BLIS 0.8.1 to fix dgemm FPE signalling on Broadwell (`#14018 `_) * add patch to fix installation of TensorFlow 2.2.3 on POWER (`#14025 `_) * fix AmberTools v20 easyconfig using intel/2020a toolchain (`#14028 `_) * fix download + permissions of binary for USEARCH v11.0.667 (`#14036 `_) * remove h5py 3.x dependency for Keras with 2020b toolchain, since TensorFlow provides (and requires) h5py 2.x (`#14052 `_) * correctly specify install prefix for CUDA in OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a (`#14063 `_) * add patch to fix failing file system cache test for jax on recent Linux kernels (`#14067 `_), `#14070 `_) * fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (`#14073 `_) * add missing dependencies for recent LibTIFF versions: XZ, jbigkit, zstd (`#14079 `_) * add missing header file to existing versions of jbigkit (`#14081 `_) * fix source URL for SUNDIALS 5.x (`#14092 `_, `#14096 `_) * add Perl and Python runtime dependencies to Bowtie2 2.4.4 (`#14097 `_) * fix source URL for SCOTCH 6.1.0 (`#14099 `_) * drop tcmalloc from SymEngine as it causes crashes with scipy (`#14119 `_) * fix homepage + description in SimpleITK easyconfigs (`#14125 `_) * add missing scripts from ``utils`` and ``analysis_scripts`` to ``bin`` for cryoDRGN (`#14137 `_) * patch ``rsync_from_ncbi.pl`` in Kraken2 v2.1.2 to allow syncing with NCBI servers over HTTPS (`#14148 `_) * skip ``mkl_fused_batch_norm_op_test`` test (broken on AMD EPYC systems) for TensorFlow 2.5.0 and 2.6.0 (`#14151 `_, `#14153 `_) * fix incorrect module load message and update morphology plugin of ImageJ 1.51k (`#14152 `_) * fix XCrySDen v1.6.2 linking to libdl and Togl (`#14160 `_) * add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0 (`#14177 `_) * add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests (`#14178 `_) * fix spatstat.* downloads for Seurat v4.0.1 (`#14199 `_) * add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection (`#14212 `_) * other changes: * remove help2man build dependency for flex using system toolchain (because it requires Perl) (`#13922 `_) * use proper dependency for python-Levenshtein in CIRI-long easyconfig (`#13985 `_) * in-place updates for foss/2021b and intel/2021b common toolchains * update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (`#14090 `_) * update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (`#14164 `_) * update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 with GCCcore/11.2.0 toolchain (`#14167 `_) * update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (`#14176 `_) * remove format mapping from homepage of Subread easyconfigs (`#14145 `_) * add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 0.3.4 with GCC/11.2.0 toolchain (`#14225 `_) .. _release_notes_eb442: EasyBuild v4.4.2 (September 7th 2021) ------------------------------------- bugfix/update release **framework** * various enhancements, including: * add per-extension timing in output produced by ``eb`` command (`#3734 `_) * add definition for new toolchain ``nvpsmpic`` (NVHPC + ParaStationMPI + CUDA) (`#3736 `_) * include list of missing libraries in warning about missing FFTW libraries in ``imkl`` toolchain component (`#3776 `_) * check for recursive symlinks by default before copying a folder (`#3784 `_) * add ``--filter-ecs`` configuration option to filter out easyconfigs from set of easyconfigs to install (`#3796 `_) * check type of ``source_tmpl`` value for extensions, ensure it's a string value (not a list) (`#3799 `_) * also define ``$BLAS_SHARED_LIBS`` & co in build environment (analogous to ``$BLAS_STATIC_LIBS``) (`#3800 `_) * report use of ``--ignore-test-failure`` in success message in output (`#3806 `_) * add ``get_cuda_cc_template_value`` method to ``EasyConfig`` class (`#3807 `_) * add support for ``fix_bash_shebang_for`` (`#3808 `_) * pick up ``$MODULES_CMD`` to facilitate using Environment Modules 4.x as modules tool (`#3816 `_) * use more sensible branch name for creating easyblocks PR with ``--new-pr`` (`#3817 `_) * various bug fixes, including: * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#3767 `_) * don't add directory that doesn't include any files to ``$PATH`` or ``$LD_LIBRARY_PATH`` (`#3769 `_) * make logdir writable also when ``--stop``/``--fetch`` is used and ``--read-only-installdir`` is enabled (`#3771 `_) * fix forgotten renaming of ``l`` to ``char`` in ``__init__.py`` that is created for included Python modules (`#3773 `_) * fix ``verify_imports`` by deleting all imported modules before re-importing them one by one (`#3780 `_) * fix ``ignore_test_failure`` not set for Extension instances (`#3782 `_) * update ``iompi`` toolchain to ``intel-compiler`` subtoolchain for oneAPI versions (>= ``iompi`` 2020.12) (`#3785 `_) * don't parse patch files as easyconfigs when searching for where patch file is used (`#3786 `_) * make sure git clone with a tag argument actually downloads a tag (`#3795 `_) * fix CI by excluding GC3Pie 2.6.7 (which is broken with Python 2) and improve error reporting for option parsing (`#3798 `_) * correctly resolve templates for patches in extensions when uploading to GitHub (`#3805 `_) * add ``--easystack`` to ignored options when submitting job (`#3813 `_) * other changes: * speed up tests by caching checked paths in ``set_tmpdir`` + less test cases for ``test_compiler_dependent_optarch`` (`#3802 `_) * speed up ``set_parallel`` method in ``EasyBlock`` class (`#3812 `_) **easyblocks** * 4 new software-specific easyblocks: * CRISPR-DAV (`#2487 `_), jaxlib (`#2545 `_), ORCA (`#2504 `_), RepeatModeler (`#2470 `_) * minor enhancements, including: * update ABAQUS easyblock to support installation of v2020 (`#2034 `_) * enable make check and sanity check exec for OpenMPI (`#2444 `_) * fixed sanity check for later versions of Molpro (`#2499 `_) * add Ampere to known GPU architectures for Kokkos in LAMMPS easyblock (`#2510 `_) * update sanity check in ESMF easyblock to take into account new binary names from version 8.1.0 onwards (`#2512 `_) * use ``report_test_failure`` in TensorFlow easyblock (`#2519 `_) * add support for imkl 2021.x in easyblocks for * Amber (`#2527 `_), BerkeleyGW (`#2528 `_), CP2K (`#2529 `_), FreeFEM (`#2530 `_), GROMACS (`#2531 `_), numexpr (`#2532 `_) * add ``install_src`` option and enhance ``buildcmd`` option in PythonPackage easyblock (`#2534 `_) * make sure AOCC commands like clang/flang pick up ``GCCcore`` as GCC toolchain (`#2538 `_) * create ``CMakeConfig`` files for tbb >= 2020 (`#2539 `_) * find source dir for libunwind when building ldd for Clang versions >= 12.0.1 (`#2540 `_) * fix motorBike test in sanity check for OpenFOAM 9 (`#2544 `_) * generate and install pkg-config files for OpenSSL wrapper (`#2549 `_) * don't run ``setup.py config`` for numpy >= 1.21, since it's no longer supported (`#2554 `_) * update WIEN2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (`#2558 `_) * remove PCRE from list of system libraries for TensorFlow 2.6.0 (`#2559 `_) * add support for also installing Tosca component in ABAQUS (`#2560 `_) * update ABAQUS easyblock to support installing of version 2021 with hot fixes (`#2562 `_) * update sanity check in VTune easyblock for 2021.x versions (`#2563 `_) * various bug fixes, including: * handle failure of running ``nvidia-smi`` in TensorFlow tests (`#2506 `_) * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#2507 `_) * clean up installation of Tkinter (`#2509 `_) * remove redundant ``$CPATH`` entry of tbb modules + fix ``--module-only`` (`#2511 `_) * honor ``--ignore-test-failure`` in PythonPackage (`#2516 `_) * use correct GTK+ version for OpenCV based on dependencies (`#2520 `_) * ensure Python prep is done in sanity check + support debug builds in TensorFlow easyblock (`#2522 `_) * correct cleanup of single-letter local variable in ``__init__`` of ``easybuild.easyblocks`` (`#2524 `_) * reset runtest to ``None`` in CMakePythonPackage (`#2536 `_) * set ``$I_MPI_ROOT`` correctly for 2021.x in impi easyblock (`#2537 `_) * let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly (`#2543 `_, `#2547 `_) * explicitly use only OpenBLAS for PyTorch if MKL is not used (`#2448 `_) * keep symlinks in cuDNN installations (`#2550 `_) * use ``${BLAS,LAPACK}_SHARED_LIBS`` in GROMACS easyblock for FlexiBLAS-based toolchains (`#2552 `_) * copy the list to avoid changing the original lists in ``DEFAULT_TARGETS_MAP`` for Clang and LLVM (`#2556 `_) * fix ``pathsep`` ``join`` bug that breaks installation of CUDA versions < 10.1 if ``$PERL5LIB`` is defined (`#2561 `_) * other changes: * simplify Boost easyblock (`#2513 `_) * remove deprecated options from PythonPackage (`#2535 `_) **easyconfigs** * added easyconfig for foss/2021.07 (candidate for foss/2021b) (`#13788 `_) and iomkl/2021a (`#13521 `_) toolchains * added example easyconfig files for 79 new software packages: * AlphaFold (`#13867 `_), andi (`#13768 `_), aria2 (`#13709 `_), AUTO-07p (`#13831 `_), babl (`#13216 `_), BAli-Phy (`#13484 `_), biogeme (`#13735 `_), Bio-SearchIO-hmmer (`#13419 `_), BuDDy (`#13907 `_), c-ares (`#13709 `_), CellRank (`#13408 `_), Coin (`#13818 `_), Co-phylog (`#13769 `_), cppy (`#13823 `_), CREST (`#13648 `_), CRISPR-DAV (`#13139 `_), CSBLAST (`#13794 `_), DGL (`#13793 `_), DistributedStream (`#13659 `_), Excel-Writer-XLSX (`#13139 `_), FBPIC (`#13500 `_), freebayes (`#12859 `_), freud-analysis (`#13354 `_), fumi_tools (`#13517 `_), GEGL (`#13216 `_), GIMP (`#13216 `_), glib-networking (`#13216 `_), GOATOOLS (`#13364 `_, `#13629 `_), gofasta (`#13651 `_), GTK2 (`#13900 `_), GTK3 (`#13900 `_), Highway (`#13453 `_), hipSYCL (`#13837 `_), ISA-L (`#13663 `_), jax (`#13760 `_), JSON-GLib (`#13216 `_), Kalign (`#13463 `_), LADR (`#13351 `_), lDDT (`#13794 `_), libdivsufsort (`#13768 `_), libjxl (`#13453 `_, `#13829 `_), libmypaint (`#13216 `_), libtecla (`#13908 `_), lie_learn (`#13793 `_), longestrunsubsequence (`#13800 `_), Maude (`#13909 `_), mimalloc (`#13726 `_), MINPACK (`#13802 `_), Mish-Cuda (`#13759 `_, `#13784 `_), muparserx (`#13779 `_), nlohmann_json (`#13777 `_), OpenStackClient (`#13644 `_), OSPRay (`#12852 `_), pandapower (`#13687 `_), pangolin (`#13733 `_, `#13848 `_), PSIPRED (`#13794 `_), PYPOWER (`#13689 `_), PyPSA (`#13673 `_), PyRosetta (`#13793 `_), pysamstats (`#13139 `_), pytest-benchmark (`#13622 `_), python-isal (`#13663 `_), QCxMS (`#13650 `_), RepeatModeler (`#13126 `_), Schrodinger (`#11698 `_), sklearn-som (`#13699 `_), SoQt (`#13818 `_), spdlog (`#13778 `_), SpectrA (`#13743 `_), SymEngine-python (`#13652 `_), SyRI (`#13800 `_), torchinfo (`#13662 `_), TRAVIS-Analyzer (`#13503 `_), UShER (`#13708 `_), Vampire (`#13352 `_), VBZ-Compression (`#13536 `_), VisPy (`#13468 `_), wgsim (`#13475 `_), Yices (`#13906 `_) * added additional easyconfigs for various supported software packages, including: * ABAQUS 2020.eb, ANTs 2.3.5, AOCC 3.1.0, Arb 2.19.0, archspec 0.1.2, Armadillo 10.5.3, ASE 3.22.0, Autotools 20210726, BamTools 2.5.2, bgen 4.1.3, Biopython 1.79, bitarray 1.5.3, Boost 1.76.0, Bowtie2 2.4.4, bpytop 1.0.67, Cartopy 0.19.0.post1, Centrifuge 1.0.4, Clang 12.0.1, CMake 3.21.1, CRISPResso2 2.2.1, CUDA 11.4.1, cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, DIAMOND 2.0.11, DROP 1.1.0, Dsuite 20210718, dtcmp 1.1.2, ecCodes 2.22.1, Elk 7.2.42, ESMF 8.1.1, expat 2.4.1, fastq-tools 0.8.3, Fiona 1.8.20, FLINT 2.7.1, g2clib 1.6.3, g2lib 3.2.0, GCC(core) 11.2.0, GDCM 3.0.8, GDRCopy 2.3, GenomeTools 1.6.2, GffCompare 0.12.2, gffread 0.12.7, GLib 2.69.1, GMT 6.2.0, Go 1.16.6, GPAW 21.6.0, Gradle 6.9.1.eb, GROMACS 2021.3, HarfBuzz 2.8.2, HDF5 1.12.1, Horovod 0.22.1, hwloc 2.5.0, hypothesis 6.14.6, igraph 0.9.4, ImageMagick 7.1.0, IMOD 4.11.5, IPython 7.26.0, Java 16, Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kent_tools 418, lavaan 0.6-9, libfabric 1.13.0, libffcall 2.4, libffi 3.4.2, libgeotiff 1.7.0, libRmath 4.1.0, LIBSVM 3.25, LibTIFF 4.3.0, likwid 5.2.0, LLVM 12.0.1, LMDB 0.9.29, magma 2.6.1, MariaDB 10.6.4, MATIO 1.5.21, matplotlib 3.4.2, MEGA 10.0.5, Mesa 21.1.7, Meson 0.59.1, Metal 2020-05-05, Mini-XML 3.2, molmod 1.4.8, MPICH 3.4.2, nanopolish 0.13.3, NCCL 2.10.3, ncdu 1.16, NCO 5.0.1, neptune-client 0.10.5, netcdf4-python 1.5.7, networkx 2.5.1, nodejs 14.17.6, NSPR 4.32, NSS 3.69, NVHPC 21.7, OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2106, OpenMM 7.5.1, OpenMolcas 21.06, openpyxl 3.0.7, Pango 1.48.8, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.13, PCRE2 10.37, PCRE 8.45, Perl 5.34.0, PETSc 3.15.1, petsc4py 3.15.0, Pillow 8.3.1, Pillow-SIMD 8.3.1, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, pybind11 2.7.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, PyQt5 5.15.4, pyshp 2.1.3, Python 3.9.6, python-igraph 0.9.6, QTLtools 1.3.1, RAxML-NG 1.0.3, R-bundle-Bioconductor 3.13, re2c 2.2, ReFrame 3.8.0., RStudio-Server 1.4.1717, Rust 1.54.0, Scalasca 2.6, scVelo 0.2.3, Shapely 1.8a1, shrinkwrap 1.1.0, SLEPc 3.15.1, slepc4py 3.15.1, snakemake 6.6.1, snappy 1.1.9, snippy 4.6.0, snpEff 5.0e, SOCI 4.0.2, SpaceRanger 1.3.0, Spack 0.16.2, spatialreg 1.1-8, spglib-python 1.16.1, SQLite 3.36, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, SymEngine 0.7.0, TensorFlow 2.6.0, TetGen 1.6.0, Tkinter 3.9.6, torchtext 0.9.1, tqdm 4.61.2, UCX 1.11.0, UCX-CUDA 1.11.0, unrar 6.0.2, util-linux 2.37, VTune 2021.6.0, WIEN2k 21.1, WPS 4.2, WRF 4.3, X11 20210802, x264 20210613, xarray 0.19.0, XlsxWriter 1.4.4, XML-Parser 2.46, zstd 1.5.0 * minor enhancements, including: * add extensions to recent R v4.x easyconfigs: PCAmatchR (`#13448 `_), hal9001 (`#13451 `_), cobalt (`#13544 `_), CBPS (`#13549 `_), SBdecomp (`#13565 `_), lwgeom (`#13674 `_), naturalsort (`#13762 `_), finalfit + gtsummary (`#13766 `_) * add VBZ compress capability to nanopolish 0.13.3 (for fast5 files) (`#13536 `_) * add CMake build dependency to easyconfig for tbb 2020.03 (`#13704 `_) * also build shared libs for MUMPS 5.3.5 (`#13702 `_) and 5.4.0 (`#13705 `_) * add dependency on pkg-config to OpenSSL wrappers (`#13765 `_) * various bug fixes, including: * fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded ``-xHost`` (`#11577 `_) * fix sanity check error for OpenCV v4.5.1 by adding (and using) freetype and HarfBuzz dependencies (`#12517 `_) * add patches for TensorFlow 1.13.1 to fix installation (`#13326 `_) * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#13349 `_) * switch back to Bundle easyblock for PyQt5 5.15.1 + add back source URLs for components (`#13371 `_) * add pkg-config build dependency for GDAL 3.2.1 (`#13383 `_, `#13808 `_), Rust (`#13538 `_), GenomeTools (`#13805 `_), x264 (`#13834 `_) * add missing Python 3 build dependency for Rust v1.52.1 (`#13399 `_) * fix order of cffi extension in old Python easyconfigs (`#13400 `_) * patch out ``__asm__`` use in ctffind to avoid build failure on ppc64le (`#13409 `_) * disable building man pages in Gdk-Pixbuf (`#13410 `_) * add missing Bio-Search-hmmer dependency for prokka (`#13419 `_) * avoid downloading old numpy version during install for h5py (`#13428 `_) * add patch for Qt5 5.8.0 to fix compilation failure in webkit (`#13434 `_) * avoid downloading and building freetype and qhull for matplotlib 3.4.2 (`#13437 `_) * fix order of components in recent GTK+ easyconfigs to avoid dependency on system GTK+ in GTK+ themes (`#13449 `_) * fix Python 2.7.13 easyconfigs by adding missing extensions (`#13456 `_) * add TensorFlow patch to fix crash on shutdown (`#13462 `_) * allow for non-x86_64 in ``postinstallcmds`` for CuPy (`#13501 `_) * disable default EULA acceptance in easyconfig for NVHPC v21.5 (`#13516 `_) * fix error with p7zip's 7z command not finding ``7z.dll`` (`#13542 `_) * patch MaxBin2 Perl script to use provided Perl dependency (`#13551 `_) * add missing zlib dependency to libarchive (`#13579 `_) * fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig with GCCcore/11.2.0 toolchain) (`#13581 `_) * fix build of DIRAC 19.0 easyconfig with high compiler optimizations (`#13613 `_) * fix source URLs and add alternative checksum for Hypre 2.15.1 (since it moved to a different GitHub repo) (`#13616 `_) * add new source URL for Mesa easyconfigs using 2017b toolchain (`#13617 `_) * avoid ``MPICXX`` dependency in SimpleElastics ITK (`#13623 `_) * add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (`#13628 `_) * add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault) (`#13665 `_) * enable EGL in recent libepoxy ECs (`#13684 `_) * remove unused ``buildcmd`` from libgpuarray easyconfigs (`#13720 `_) * add patch to fix building Qt5.10.1 against newer glibc (`#13730 `_) * add Python 3 as a builddependency to recent fontconfig easyconfigs (`#13731 `_) * update source_URL in BLAST 2.2.26 easyconfig (`#13732 `_) * restore error message on failing easyconfigs test suite, required by bot to determine end of output of test suite (`#13745 `_, `#13770 `_) * add Perl build dependency to recent Clang easyconfigs (`#13746 `_) * disable using system Valgrind in the json-c tests (`#13750 `_) * use Archive source URL for spatstat.geom extension in Seurat (`#13761 `_) * add ld.gold relocts patch to binutils 2.30 (`#13785 `_) * add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 (`#13786 `_) * add alternative checksum for AFNI 18.3.00 (`#13790 `_) * update tensorflow-probability easyconfigs to include ``--release`` flag in ``installopts`` (`#13810 `_) * fix source URL for DB 18.1.32 (`#13813 `_) * add missing cppy build dependency for matplotlib 3.4.2 (`#13823 `_) * disable bash completion in recent x264 easyconfigs (`#13834 `_) * add Perl as build dependency for ELPA 2021.05.001 + patch to fix hardcoded ``/usr/bin/perl`` (`#13835 `_) * add archive source URL to Spark 3.x easyconfigs to fix broken download (`#13842 `_) * fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 (`#13861 `_) * add Perl build dependency for HMMER 3.3.2 + patch to ensure it is used (`#13870 `_) * stick to intel-compilers toolchain for DFT-D3 v3.2.0 (`#13878 `_) * add missing flex build dependency for leidenalg (`#13884 `_) * update CMake build dependency for Eigen 3.3.4 + 3.3.5 (`#13889 `_) * fix source URL for Yasm 1.3.0 (+ add missing checksum) (`#13901 `_) * update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check (`#13910 `_) * fix shebang for RepeatMasker 4.1.2-p1 Perl script (`#13911 `_) * other changes: * use custom ORCA easyblock in easyconfigs for ORCA v4.x (`#13348 `_) * move archived easyconfig files to correct ``__archive__`` folder (`#13422 `_) * rename NINJA to TWL-NINJA to avoid nameclash (`#13529 `_) * remove superfluous ``configopts`` and add sanity checks/checksums in CLHEP easyconfigs (`#13614 `_) * remove superfluous ``-DCMAKE_BUILD_TYPE`` configuration option in Arrow easyconfigs (`#13615 `_) * switch ITK easyconfigs to CMakePythonPackage easyblock, also enable ``-DITK_USE_SYSTEM_HDF5`` configuration option, fix download URLs (`#13619 `_) * use ``build_type`` instead of ``-DCMAKE_BUILD_TYPE=RELEASE`` in ``configopts`` in MMseqs2 easyconfigs (`#13620 `_) * avoid using system GTK+3 and remove ``-DCMAKE_BUILD_TYPE=RELEASE`` configure option in OpenCV easyconfigs (`#13621 `_) * remove ``-DCMAKE_BUILD_TYPE=RELEASE`` configure option and add checksums in LLVM easyconfigs (`#13624 `_) * create libtinfo symlinks in easyconfigs for ncurses with system toolchain (`#13658 `_), 6.1 (`#13661 `_) and 6.2 (`#13660 `_) * increase test timeouts for PyTorch 1.8.1 and 1.9.0 (`#13700 `_) * rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda, to ensure that ``get_software_root('CUDA')`` used in easyblocks works (`#13874 `_) * use CUDA instead of CUDAcore in recent NVHPC comments (`#13875 `_) .. _release_notes_eb441: EasyBuild v4.4.1 (July 6th 2021) -------------------------------- bugfix/update release **framework** * various enhancements, including: * enhance detection of patch files supplied to ``eb`` command with better error messages (`#3709 `_) * add per-step timing information (`#3716 `_) * add ``module-write hook`` (`#3728 `_) * add ``ignore-test-failure`` configuration option to ignore failing test step (`#3732 `_) * add toolchain definition for nvompic (NVHPC + OpenMPI) (`#3735 `_) * warn about generic milestone in ``--review-pr`` and ``--merge-pr`` (`#3751 `_) * various bug fixes, including: * don't override ``COMPILER_MODULE_NAME``, inherited from ``Ffmpi``, in Fujitsu toolchain definition (`#3721 `_) * avoid overwriting ``pr_nr`` in ``post_pr_test_report`` for reports with ``--include-easyblocks-from-pr`` (`#3724 `_, `#3726 `_) * fix crash in ``get_config_dict`` when copying modules that were imported in easyconfig file (like ``import os``) (`#3729 `_) * parse C standard flags in ``CFLAGS`` for Fujitsu compiler (`#3731 `_) * fix error message for ``--use-ccache`` (`#3733 `_) * error out when passing a list to ``run_cmd*`` to avoid running wrong command unintended, unless ``shell=True`` is used (`#3737 `_) * minor fixes to output of test reports when using multiple PRs (`#3741 `_) * fix location for modules installed with intel-compilers toolchain in HierarchicalMNS by always checking toolchain compiler name against template map (`#3745 `_) * avoid checking ``msg`` attribute of ``GitCommandError`` (`#3756 `_) * consider sources provided as dict in ``EasyBlock.check_checksums_for`` (`#3758 `_) * don't make changes to software installation directory when using ``--sanity-check-only`` (`#3761 `_) * honor specified easyblock for extensions (`#3762 `_) * other changes: * make sure that tests requiring a github token have ``github`` in the test name so that they can be easily filtered (`#3730 `_) * deprecate EasyBuild bootstrap script (`#3742 `_) * use temporary download folder in ``test_http_header_fields_urlpat`` (`#3755 `_) **easyblocks** * 5 new software-specific easyblocks: * AOMP (`#2435 `_, `#2462 `_, `#2464 `_), FreeFEM (`#1969 `_), NCCL (built from source) (`#2337 `_, `#2460 `_), torchvision (`#2467 `_), UCX plugins (`#2491 `_) * minor enhancements, including: * enhance Amber easyblock to support installing Amber via CMake (`#2445 `_) * enhance ConfigureMake generic easyblock to add support for building multiple build targets (`#2449 `_, `#2479 `_, `#2480 `_) * enhance sanity check for Clang to verify if CUDA offload library was produced (`#2454 `_) * update custom easyblock for Boost to always build single and multi threaded versions (`#2456 `_) * enhance ``sitecustomize.py`` in Python easyblock to support overriding core Python packages, and allowing overriding in virtualenv (`#2458 `_, `#2483 `_) * update CMakeMake to handle old and new Boost/Boost.Python builds using custom easyblock for Boost (`#2461 `_) * add file prefix option to XALT easyblock (`#2463 `_) * enhance Java easyblock to define ``%(jdkarch)s`` template (`#2472 `_) * adjust Perl easyblock to only check for a ``man`` subdirectory if groff is a dependency (`#2474 `_) * support arbitrary version strings in OpenSSL wrapper and add ``minimum_openssl_version`` option (`#2475 `_) * enhance Python easyblock to explicitly disable installing core-pip when ``install_pip`` is not ``True`` (`#2476 `_) * enhance intel-compiler easyblock to include multipath include dir in ``$CPATH`` (`#2477 `_) * enhance Hypre easyblock to enable CUDA support (`#2482 `_) * update Xmipp easyblock for new version (v3.20.07) (`#2486 `_) * enhance FFTW easyblock to skip tests if ``--mpi-tests`` EasyBuild configuration option is disabled (`#2490 `_) * use ``PYPI_SOURCE`` as the default for ``source_urls`` of extensions of Python easyconfigs (`#2493 `_) * various bug fixes, including: * only use siterc fix for NVHPC < 21.3 (`#2453 `_) * fix CPU-only runtime for dpcpp-generated executables in custom easyblock for intel-compilers (`#2457 `_) * always add ``distinct_host_configuration=false`` to build command for TensorFlow (`#2459 `_) * disable installation of bundled BioPerl and HTSLib if they are dependencies of VEP (`#2468 `_) * don't use list value for command to detect installed Python packages in TensorFlow easyblock (`#2469 `_) * change Bundle easyblock to also collect ``altroot`` and ``altversion`` in the module step so they are set when running ``--module-only`` (`#2485 `_) * always strip output from ``gcc -print-multiarch`` in intel-compilers easyblock (`#2489 `_) * don't overwrite all of ``exts_default_options`` in TensorFlow easyblock (`#2494 `_) * enhance GCC easyblock to make sure that system GCC provides LTO support, and disable LTO when building MPFR if not (`#2498 `_) * rework the dependency handling of OpenMPI to use explicit configure options to disable features if required dependency is not provided (`#2500 `_, `#2501 `_) **easyconfigs** * added example easyconfig files for 39 new software packages: * AMPHORA2 (`#13003 `_), AOMP (`#12909 `_), CAMPARI (`#13152 `_), CSB (`#12877 `_), dijitso (`#10719 `_), DosageConvertor (`#13278 `_), dSFMT (`#12971 `_), exiv2 (`#13204 `_), FEniCS (`#10719 `_), FreeFEM (`#9902 `_), futhark (`#12921 `_), futile (`#12864 `_), gappa (`#13186 `_), GenomeWorks (`#13083 `_, `#13092 `_), gexiv2 (`#13204 `_), HAL (`#13267 `_), hipify-clang (`#12961 `_), inline (`#12029 `_), libcint (`#13214 `_), LTR_retriever (`#13125 `_), mapDamage (`#13172 `_), MbedTLS (`#13061 `_), microctools (`#13010 `_), Nektar++ (`#12664 `_), NINJA (`#13125 `_), OBITools3 (`#12969 `_), ont-fast5-api (`#13033 `_), OpenMM-PLUMED (`#13268 `_), phototonic (`#13241 `_), PyFoam (`#12675 `_), RagTag (`#13247 `_), RcppGSL (`#13172 `_), RECON (`#13123 `_), RepeatScout (`#13124 `_), retworkx (`#13228 `_), UCX-CUDA (`#13260 `_), unimap (`#13247 `_), Vala (`#13204 `_), WhatsHap (`#12989 `_) * added additional easyconfigs for various supported software packages, including: * Amber 20.11, BBMap 38.90, Beast 2.6.4, BLIS 3.0 (AMDo fork), Bonito 0.4.0, CellRanger-ARC 2.0.0, CellRanger-ATAC 2.0.0, Check 0.15.2, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, cuDNN 8.2.1.32, CVXOPT 1.2.6, DOLFIN 2019.1.0.post0, eggnog-mapper 2.1.4, ELPA 2021.05.001, FDS 6.7.6, FFC 2019.1.0.post0, FFmpeg 4.3.2, FIAT 2019.1.0, flatbuffers 2.0.0, flatbuffers-python 2.0, FLTK 1.3.6, gc 8.0.4, GCC 8.4.0 + 9.4.0, GDAL 3.3.0, Gdk-Pixbuf 2.42.6, geopy 2.1.0, Ghostscript 9.54.0, git 2.32.0, GitPython 3.1.18, GLFW 3.3.4, gmsh 4.8.4, gnuplot 5.4.2, GnuTLS 3.7.2, Go 1.16.5, GObject-Introspection 1.68.0, gperftools 2.9.1, GraphicsMagick 1.3.36, Graphviz 2.47.2, GSL 2.7, GTK+ 2.24.33, Guile 2.2.7, h5py 3.2.1, HarfBuzz 2.8.1, Horovod 0.22.0, Hypre 2.21.0, ICU 69.1, ImageMagick 7.0.11-14, IOR 3.3.0, IPython 7.25.0, IRkernel 1.2, ispc 1.16.0, JupyterLab 3.0.16, LDC 1.26.0, libcerf 1.17, libepoxy 1.5.8, libgd 2.3.1, libStatGen 1.0.15, libxc 5.1.5, LittleCMS 2.12, LMfit 1.0.2, Lua 5.4.3, M4 1.4.19, MCR R2021a.3, medaka 1.4.3, Mercurial 5.8, minimap2 2.20, MMseqs2 13, MrBayes 3.2.7, MUMPS 5.4.0, NCCL 2.9.9, netCDF 4.8.0, Nim 1.4.8, nodejs 14.17.0, Nsight-Compute 2021.2.0, numba 0.53.1, NVHPC 21.5.eb, nvtop 1.2.1, Octave 6.2.0, OPARI2 2.0.6, openkim-models 20210128, OpenMPI 4.0.6, OTF2 2.3, p11-kit 0.24.0, Pango 1.48.5, parallel 20210622, petsc4py 3.12.0, picard 2.25.5, Pillow 8.2.0, PROJ 8.0.1, protobuf 3.17.3, protobuf-python 3.17.3, PSolver 1.8.3, PySCF 1.7.6, pyspoa 0.0.8, pytest-xdist 2.3.0, PyTorch 1.9.0, PyYAML 5.4.1, Qhull 2020.2, Quandl 3.6.1, R 4.0.5 + R 4.1.0, Ragout 2.3, RE2 2021-06-01, ReFrame 3.6.2, RepeatMasker 4.1.2, rgdal 1.5-23, RMBlast 2.11.0, Ruby 3.0.1, scikit-learn 0.24.2, Score-P 7.0, Seurat 4.0.3, slepc4py 3.12.0, spoa 4.0.7, Subread 2.0.2, Subversion 1.14.1, SuiteSparse 5.10.1, sympy 1.8, tensorboardX 2.2, TensorFlow 2.5.0, Tk 8.6.11, tmux 3.2a, torchtext 0.8.1, torchvision 0.9.1, UDUNITS 2.2.28, UFL 2019.1.0, utf8proc 2.6.1, VEP 103.1, VMD 1.9.4a51, vsc-mympirun 5.2.6, XCFun 2.1.1, Xvfb 1.20.11, Z3 4.8.11, ZeroMQ 4.3.4 * minor enhancements, including: * update cuDNN 8.0.x easyconfigs with a download location (`#12368 `_) * add extensions to recent R easyconfigs: GxEScanR (`#13039 `_), cSEM (`#13208 `_), cubelyr + broom.mixed (`#13252 `_), grf (`#13261 `_), twang + xgboost (`#13284 `_), neuralnet (`#13330 `_) * add check to easyconfigs test suite to ensure OpenSSL wrapper is used in easyconfigs using a recent toolchain (`#13079 `_) * add gipaw to QuantumESPRESSO/6.7 (`#13087 `_) * add checksum for aarch64 installation file for CUDAcore easyconfigs (`#13014 `_, `#13097 `_) * add Perl dependency to makeinfo easyconfigs (`#13166 `_) * set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper (`#13188 `_) * add JIT support for CUDA 11 to PyTorch 1.7.1 (`#13207 `_) * add ``ninja --version`` as sanity check command in Ninja easyconfigs (`#13222 `_) * code cleanup + improvements for easyconfigs test suite (`#13257 `_) * various bug fixes, including: * download sources via git for XGBoost 20171120 easyconfig due to use of submodules (`#6880 `_) * add elfutils as build dependency for Clang 8.0.x and 9.0.1 (`#13015 `_) and Clang 11.0.1 (`#13008 `_) easyconfigs that have a CUDA dependency * add missing CMake option to Geant4 v10.7.1 in order to actually use external CLHEP (`#13019 `_) * add new checksum for mvabund extension to R v4.0.4 eaysconfigs (`#13020 `_, `#13021 `_) * add patch to fix numpy ``test_ccompiler_opt`` in SciPy-bundle v2021.05 (`#13042 `_) * add patch to fix installation of HDF 4.2.15 on aarch64 (`#13059 `_) * make sure that MbedTLS' Makefile uses ``python`` rather than ``python2`` (`#13061 `_) * fix checksum for snpEff 5.0 (`#13062 `_) * fix source URL for LIBSVM 3.24 by downloading from GitHub (`#13076 `_) * add ``preinstallopts`` for minimap2 to fix installation on aarch64 (`#13080 `_) * add patch for GCC 10.2.0 to fix internal compiler error on aarch64 (`#13086 `_) * switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b (`#13103 `_) * add astor to dependencies of TensorFlow with 2019b (`#13111 `_) and 2020b (`#13103 `_, `#13112 `_) toolchains * break cyclic dependency between groff, makeinfo and Perl by adding Perl-minimal and makeinfo-minimal easyconfigs (`#13163 `_ - `#13165 `_) * add missing rgdal dep to R-INLA (`#13179 `_) * add patch to fix ``uniq`` operation in TensorFlow 2.4.1 (`#13181 `_) * add Perl build dependency for PnetCDF 1.12.1 (`#13183 `_) * disable own avx detection of libfabric v1.12.1 (`#13215 `_) * add GCCcore-[1-9][0-9].x to ``test_dep_versions_per_toolchain_generation`` (`#13243 `_, `#13249 `_, `#13251 `_) * add patch to fix installation of TensorFlow 2.0.x (`#13248 `_) * add patch for recent GCCcore versions to fix compatibility with CUDA 11 (`#13290 `_) * fix install step for glew (`#13297 `_) * update Boost 1.74.0 easyconfigs to use ``tagged_layout`` rather than ``boost_multi_thread`` (`#13300 `_) * avoid using PMIx from system instead of PMIx dependency specified via ``--with-pmix`` for OpenMPI 4.x (`#13307 `_) * add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc (`#13310 `_) * add patch for OpenMPI 4.0.x to fix building against (system) UCX version > 1.7 (`#13329 `_) * fix build of manta 1.6.0 on top of Boost 1.74.0 (`#13338 `_) * fix recent taxator-tk easyconfigs by adding (back) ``-DBoost_NO_BOOST_CMAKE=ON`` configure option (`#13342 `_) * other changes: * disable ``debuginfod`` for elfutils to minimize required dependencies (`#13034 `_) * add bare Python 3.9.5 easyconfig and use that as builddep for LLVM 11.1.0 (`#13035 `_) * remove misleading comment from Python >= 3.7 easyconfigs, libffi is now also required for Python itself (no longer bundled) (`#13041 `_) * use new custom easyblock in torchvision easyconfigs (`#13102 `_) * remove superfluous TensorFlow patch (`#13223 `_) * cleanup of easyconfigs for (bundles) of Python packages: remove default ``PYPI_SOURCE`` source URLs + use ``PythonBundle`` rather than ``Bundle`` easyblock (`#13253 `_, `#13295 `_, `#13336 `_) * update ``README`` with instructions for MATLAB easyconfigs (`#12597 `_) .. _release_notes_eb440: EasyBuild v4.4.0 (June 2nd 2021) -------------------------------- feature release **framework** * various enhancements, including: * enhance ``apply_regex_substitutions`` to allow specifying action to take in case there are no matches (`#3440 `_) * performance improvements for easyconfig parsing and eb startup (`#3555 `_) * add support for downloading easyconfigs from multiple PRs with ``--from-pr`` (`#3605 `_, `#3707 `_, `#3708 `_) * add support for prepending custom library paths in RPATH section via ``--rpath-override-dirs`` (`#3650 `_) * allow amending easyconfig parameters which are not the default (`#3651 `_) * update HierarchicalMNS for Intel OneAPI compilers (`#3653 `_) * add support for ``--sanity-check-only`` (`#3655 `_) * add support for running commands asynchronously via ``run_cmd`` + ``complete_cmd`` functions (`#3656 `_) * add support for using oneAPI versions of 'intel' toolchain components (`#3665 `_) * add toolchain definition for gofbf (foss with FlexiBLAS rather than OpenBLAS) (`#3666 `_) * add support for using ``ARCH`` constant in easyconfig files (`#3670 `_) * honor keyboard interrupt in ``eb`` command (`#3674 `_) * add toolchain definition for Fujitsu toolchain (`#3677 `_, `#3704 `_, `#3712 `_, `#3713 `_, `#3714 `_, `#3717 `_) * extend sanity check step to check whether specific libraries are not linked into installed binaries/libraries (`#3678 `_) * via ``banned-linked-shared-libs`` and ``required-linked-shared-libs`` EasyBuild configuration options * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` methods in toolchain support * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` methods in easyblock * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` easyconfig parameters * add ``locate_solib`` function to locate Linux shared libraries (`#3682 `_) * add system agnostic function to locate shared libraries (`#3683 `_) * add ``update_build_option`` function to update specific build options after initializing the EasyBuild configuration (`#3684 `_) * allow opting out of recursively unloaded of modules via recursive_module_unload easyconfig parameter (`#3689 `_) * check for correct version values when parsing easystack file (`#3693 `_) * run post-install commands specified for a specific extension (`#3696 `_) * add support for ``--skip-extensions`` (`#3702 `_) * include PR title in output produced by ``--merge-pr`` (`#3706 `_) * various bug fixes, including: * avoid metadata greedy behaviour when probing for external module metadata (mostly relevant for integration with Cray Programming Environment) (`#3559 `_) * catch problems early on if ``--github-user`` is not specified for ``--new-pr`` & co (`#3644 `_) * re-enable write permissions when installing with ``read-only-installdir`` (`#3649 `_) * also run sanity check for extensions when using ``--module-only`` (`#3655 `_) * improve logging when failing to load class from ``exts_classmap`` (`#3657 `_) * fix use of ``--module-only`` on existing installations without write permissions (`#3659 `_) * correct help text for ``subdir-user-modules`` (`#3660 `_) * avoid picking up easyblocks outside of sandbox in framework tests (`#3680 `_) * use unload/load in ``ModuleGeneratorLua.swap_module``, since ``swap`` is not supported by Lmod (`#3685 `_) * update HierarchicalMNS to also return 'Toolchain//' as ``$MODULEPATH`` extension for cpe* Cray toolchains (`#3686 `_) * make ``EasyConfigParser.get_config_dict`` return a copy rather than a reference (`#3692 `_) * make sure that ``$TAPE`` is unset when using piped tar (`#3698 `_) * fix extending message for changed files in ``new_pr_from_branch`` (`#3699 `_) * enhance ``sched_getaffinity`` function to avoid early crash when counting available cores on systems with more than 1024 cores (`#3701 `_) * correctly strip extension from filename in ``extract_cmd`` and ``back_up_file`` functions (`#3705 `_) * other changes: * deprecate adding a non-existing path to ``$MODULEPATH`` (`#3637 `_) * bump cryptography requirement from 3.2.1 to 3.3.2 (`#3643 `_, `#3648 `_) * test bootstrap script in separate workflow, and limit test configurations a bit (`#3646 `_) * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#3647 `_) * replace ``log_error`` parameter of ``which()`` by ``on_error`` (`#3661 `_, `#3664 `_) * don't skip sanity check for ``--module-only --rebuild`` (`#3645 `_) * move ``disable_templating`` function into the EasyConfig class (`#3668 `_) * pin GitPython version for Python<3.6, don't test bootstrap script against Python 3.8/3.9 (`#3675 `_) * tweak foss toolchain definition to switch from OpenBLAS to FlexiBLAS in foss/2021a (`#3679 `_) * suggest missing SSH key when not able to read from remote repository in ``--check-github`` (`#3681 `_) * drop support for Python 2.6 (`#3715 `_) **easyblocks** * 3 new software-specific easyblocks: * FlexiBLAS (`#2369 `_, `#2422 `_, `#2424 `_, `#2426 `_) * dm-reverb (`#2413 `_) * custom easyblock to install OpenSSL wrapper for OpenSSL installed in OS, with fallback to build and install OpenSSL from source if not available in OS (`#2429 `_) * minor enhancements, including: * also add ``-pthread`` to ``prebuildopts`` of cryptography (`#2270 `_) * don't unpack Python wheel (*.whl) files by default in generic PythonPackage easyblock (`#2366 `_, `#2442 `_) * enable installation of samples for CUDA > 10.1 (`#2374 `_) * add option to disable pip connecting to PyPi (enable use of ``--no-index``) (`#2390 `_) * update MotionCor2 easyblock to handle new version and be aware of CUDAcore (`#2394 `_) * make it possible to force disabling kernel features in Qt easyblock (`#2403 `_) * update imkl easyblock to support oneAPI versions (>= 2021.x) (`#2407 `_) * add``"gurobi_cl --help`` as default sanity check command for Gurobi (`#2411 `_) * enhance BWA easyblock to copy includes and libraries (`#2417 `_) * allow ``default`` versions to be defined by ModuleRC easyblock (`#2418 `_) * enhance MesonNinja and CMakeMake easyblocks to create unused build dir when ``separate_build_dir`` is set (`#2419 `_) * enable ``sanity_pip_check`` by default for Python easyconfigs if pip >= 9.0 will be installed (`#2423 `_) * enhance FFTW easyblock to support SVE CPU feature and building with Fujitsu compiler (`#2425 `_) * make ScaLAPACK easyblock aware of FlexiBLAS (`#2427 `_) * update imkl easyblock to unpack example tarballs and set ``$MKL_EXAMPLES`` (+ some code cleanup) (`#2430 `_) * update list of system libs for TensorFlow 2.5 (`#2432 `_) * allow disabling MPI tests when installing Intel MPI (impi) via ``--disable-mpi-tests`` (`#2440 `_) * exclude bottleneck tests in PyTorch (`#2450 `_) * various bug fixes, including: * ensure lib subdirectory is found in stage 2 of GCC installation + fall back to lib64 (`#2339 `_) * fix permission on MATLAB installer config file so it can be written to (`#2385 `_) * fix problem with installing older CUDA versions that uses the Perl based installer (`#2387 `_) * enhance Python easyblock: add option to install pip with core Python, tweak defaults, create unversioned pip symlink (`#2388 `_) * fix ``installopts`` before installing the extension in GROMACS easyblock (`#2391 `_) * updated numpy easyblock to use ``read_file`` for patch (`#2395 `_) * use explicit build toolset and compiler path in Boost easyblock (`#2402 `_) * replace hardcoded ``2021.1.1`` with ``self.version`` in impi easyblock (`#2405 `_) * set ``$SANDCASTLE`` when running PyTorch tests to disable some tests as-if we are on Facebook's CI (`#2412 `_) * make GROMACS easyblock work with ``--module-only`` (`#2414 `_) * make sure OpenFOAM sanity checks don't require builddir write permissions (`#2415 `_) * make Tkinter easyblock work with ``--module-only`` (`#2416 `_) * also disable altivec with FFTW 3.3.9 on POWER (`#2437 `_) * make sure that ``self.python_cmd`` is set before using it in ``PythonPackage.sanity_check_step`` (`#2447 `_) * other changes, including: * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#2384 `_) * use ``on_error`` rather than deprecated ``log_error`` named argument for ``which`` function (`#2406 `_) * remove ``cuda_compute_capabilities`` from custom easyconfig parameters for Clang, LAMMPS and TensorFlow (now supported as general easyconfig parameter) (`#2433 `_) **easyconfigs** * added easyconfigs for new Fujitsu toolchain: FCC/4.5.0 (`#12999 `_, `#12995 `_, `#13007 `_), ffmpi/4.5.0 (`#13000 `_) and Fujitsu/21.05 (`#13001 `_, `#13007 `_) * add easyconfigs for updates of common toolchains: foss/2021a (`#12867 `_, `#12975 `_), intel/2021a (`#12885 `_, `#12975 `_) * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added easyconfig for gomkl/2021a toolchain (`#12987 `_) * added example easyconfig files for 58 new software packages: * Archive-Zip (`#12651 `_), BirdNET (`#12737 `_, `#12712 `_, `#12737 `_), cell2location (`#12448 `_), cryoDRGN (`#12704 `_), dm-reverb (`#12824 `_), DROP (`#12559 `_, `#12801 `_, `#12950 `_), fastahack (`#12841 `_), fermi-lite (`#12856 `_), filevercmp (`#12841 `_), FlexiBLAS (`#12476 `_), freetype-py (`#12918 `_), fsom (`#12841 `_), garnett (`#12529 `_), gawk (`#12716 `_), gemmi (`#12855 `_), georges (`#12570 `_), hifiasm (`#12897 `_), intervaltree (`#12838 `_), LDC (`#12671 `_), libidn2 (`#12670 `_), librosa (`#10477 `_), librsb (`#12780 `_), line_profiler (`#12556 `_), loompy (`#12804 `_), mmtf-cpp (`#12580 `_), mongolite (`#12632 `_), msgpack-c (`#12580 `_), multichoose (`#12839 `_), networkTools (`#12810 `_), NewHybrids (`#12528 `_), Octopus-vcf (`#12598 `_), onedrive (`#12671 `_), p4-phylogenetics (`#12549 `_), pagmo (`#12678 `_), pyfaidx (`#12872 `_), pyfasta (`#12952 `_), pygmo (`#12678 `_), pysheds (`#12791 `_), R-INLA (`#12955 `_, `#12927 `_, `#12955 `_), RegTools (`#12874 `_), request (`#12448 `_), rMATS-turbo (`#12982 `_), scanpy (`#12731 `_), SeqLib (`#12856 `_), SeuratData (`#12993 `_), SeuratWrappers (`#12994 `_), smithwaterman (`#12841 `_), snp-sites (`#12900 `_), SSW (`#12856 `_), tabixpp (`#12837 `_), TagDust (`#11599 `_), TALON (`#12963 `_), tMAE (`#12559 `_), TranscriptClean (`#12952 `_), umap-learn (`#12448 `_), vcflib (`#12841 `_), xESMF (`#12799 `_), XlsxWriter (`#12820 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 9.4.1, apex 20210420, astropy 4.2.1, binutils 2.36.1, BLIS 0.8.1, Bonito 0.3.8, BUSCO 5.1.2, canu 2.1.1, carputils 20210513, CastXML 0.4.3, ccache 4.2.1, CDO 1.9.10, CIRCexplorer2 2.3.8, CLHEP 2.4.4.0, CMake 3.20.1, CNVkit 0.9.8, CUDA(core) 11.3.0, CuPy 8.5.0, cURL 7.76.0, DFA 2.1.2, Doxygen 1.9.1, Eigen 3.3.9, FastANI 1.33, FFTW 3.3.9, GATK 4.2.0.0, GCC 10.3.0 + 11.1.0, GDB 10.2, gdc-client 1.6.0, GDRCopy 2.2, Geant4 10.7.1, Geant4-data 20210510, GeneMark-ET 4.65, glew 2.2.0, GLib 2.68.2, GLPK 5.0, GMP 6.2.1, Go 1.16.3, Graphviz 2.47.0, GROMACS 2021.2, GStreamer 1.18.4, GTDB-Tk 1.5.0, Gurobi 9.1.2, HMMER 3.3.2, Horovod 0.21.3, hwloc 2.4.1, hypothesis 6.13.1, IGV 2.9.4, impi 2021.2.0, imkl 2021.2.0, intel-compilers 2021.2.0, JasPer 2.0.28, Julia 1.6.1, Kraken2 2.1.1, KronaTools 2.8, libarchive 3.5.1, libdeflate 1.7, libdrm 2.4.106, libfabric 1.12.1, libreadline 8.1, libRmath 4.0.0, libsndfile 1.0.31, LIBSVM 3.24, LibTIFF 4.2.0, libunwind 1.5.0, libwebp 1.2.0, LLVM 11.1.0, LMDB 0.9.28, LUMPY 0.3.1, lz4 1.9.3, Mako 1.1.4, MATLAB 2021a, Mesa 21.1.1, meshalyzer 2.2, Meson 0.58.0, MetaBAT 2.15, metaWRAP 1.3, minimap2 2.18, Molden 6.8, MotionCor2 1.4.2, ncview 2.1.8, NetPIPE 5.1.4, nettle 3.7.2, NiBabel 3.2.1, Nilearn 0.7.1, Nim 1.4.6, Ninja 1.10.2, NLopt 2.7.0, NSS 3.65, numactl 2.0.14, NWChem 7.0.2, OpenBLAS 0.3.15, openCARP 6.0, OpenEXR 3.0.1, OpenMM 7.5.0, OpenMPI 4.1.1, OpenSSL 1.1 (wrapper), OSU-Micro-Benchmarks 5.7.1, Pandoc 2.13, parallel 20210322, parasail 2.4.3, PAUP 4.0a168, PCRE2 10.36, Perl 5.32.1, pigz 2.6, PMIx 3.2.3, Primer3 2.5.0, PRSice 2.3.3, py-aiger 6.1.14, pybind11 2.6.2, PyCharm 2021.1.1, pydot 1.4.2, pyproj 3.0.1, PySAT 0.1.7.dev1, PyTorch 1.8.1, python-parasail 1.2.4, Pylint 2.7.4, Python 3.9.5, Qt5 5.15.2, R-keras 2.4.0, rasterio 1.2.3, RAxML-NG 1.0.2, rclone 1.54.1, re2c 2.1.1, ReFrame 3.5.2, Rmath 4.0.4, Rust 1.52.1, Sambamba 0.8.0, samblaster 0.1.26, samclip 0.4.0, scikit-allel 1.3.2, SciPy-bundle 2021.05, SCons 4.1.0.post1, snakemake 6.1.0, SQLite 3.35.4, SRPRISM 3.1.2, Tcl 8.6.11, TCLAP 1.2.4, tmux 3.2, tqdm 4.60.0, UCX 1.10.0, Valgrind 3.17.0, WannierTools 2.5.1, wget 1.21.1, wxWidgets 3.1.4, X11 20210518, x264 20210414, x265 3.5, xorg-macros 1.19.3, YAXT 0.9.0, zarr 2.8.1, zstd 1.4.9 * minor enhancements, including: * add additional extensions to R v4.0.3 and v4.0.4: miceadds, visdat, UpSetR, naniar, stringdist, image.binarization (`#12735 `_), lassosum (`#12821 `_), lslx, regsem, semPLS (`#13005 `_) * add GenABEL to R-bundle-Bioconductor (`#12822 `_) * various bug fixes, including: * disable automatic acceptance of NVHPC EULA (`#12014 `_) * enhance RStudio-Server, add patch to inherit environment variables, add sanity check commands to verify installation (`#12544 `_) * add fix to scipy to handle ``NaN`` arguments to ``vi`` function (`#12551 `_) * copy all binaries + examples & co for PAML v4.9j (`#12567 `_) * add patch to fix hardcoded ``num_cores`` in DMCfun extension included with R 4.0.x (`#12583 `_) * backport Charm++ patch for NAMD/2.14 on intel/2020a to handle newer glibc (`#12594 `_) * add setuptools_scm and pytest-runner extensions to Pylint easyconfigs (`#12599 `_) * fix typo in Delly easyconfig to actually do parallel build (`#12633 `_) * fix potential memory leak in OpenBLAS 0.3.12 (`#12649 `_) * consistently use pip to install Python packages in recent Python easyconfigs (`#12650 `_) * replace bintray source url for Groovy (`#12652 `_) * add missing Python & Perl dependencies to AUGUSTUS v3.4.0 with foss/2020b (`#12662 `_) * fix wget dependency: use libidn2 rather than libidn (`#12670 `_) * fix source URLs for recent ELPA versions (`#12700 `_) * override host compiler check in CUDAcore (`#12701 `_) * add Python build dependency to libpsl 0.21.0 easyconfigs (`#12715 `_) * fix error in libgpg-error 1.36 with gawk builtin (`#12716 `_) * add libtool build dependency to leidenalg (`#12741 `_) * fix source URLs for Boost 1.71.0 - 1.74.0 easyconfigs (`#12743 `_) and Boost.Python (`#12744 `_) * add patches for PyTorch 1.7.1 avoiding failures on POWER and A100 (`#12753 `_) * add patch for OpenPGM 5.2.122 eaysconfigs to fix non-existent directory in *.pc (pkgconfig) file (`#12774 `_) * add missing Perl build dependency to recent wget easyconfigs (`#12787 `_) * make sure Python dependency is used in preCICE 2.x easyconfigs (`#12793 `_) * don't skip source step in FastTree easyconfigs + fix SHA256 checksum for FastTree 2.1.11 (`#12794 `_) * add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64 (`#12836 `_) * add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 (`#12865 `_) * fix checksum for MaxBin 2.2.7 (`#12869 `_) * run ``make clean`` before building FragGeneScan, to clean up object files included in source tarball (`#12870 `_) * clean up install of KronaTools (`#12871 `_) * add UCX dependency to OneAPI versions of impi (`#12873 `_) * correct description in libdeflate easyconfig (`#12886 `_) * override Makefile with hardcoded ``CC=cc`` in UnZip easyconfigs (`#12887 `_) * fix compatibility of FLAIR v1.5.1-20200630 with rpy2 v3.x (`#12899 `_) * fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking (`#12912 `_) * fix source URLs in BLAST 2.10.x easyconfigs (`#12914 `_) * add missing xproto build dependency to imake easyconfig (`#12930 `_) * add patch to fix GCC 10.2.0 rejecting valid code on PPC (`#12948 `_) * in easyconfig tests, check version of dependencies named Python, not if dependencies with certain versions are named Python (`#12962 `_) * update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes (`#12967 `_, `#12988 `_) * fix download URL for DB 18.1.40 (`#12974 `_) * fix test failure in TensorFlow 2.4.1 on recent CUDA drivers (`#12979 `_) * fix error in ``configopts`` for netCDF and HDF5 and add missing dependencies of ABINIT 9.x (`#12981 `_) * add patch to fix buffer overflow in OpenMPI 4.1.x (`#12983 `_) * other changes: * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#12565 `_) * add ``-Java`` versionsuffix for Hadoop easyconfig using GCCcore/10.2.0 toolchain, since it depends on Java 1.8 (`#12709 `_) * remove unnecessary workaround for missing version of OpenDataCube and Spyder for 2020+ toolchains (`#12757 `_) * remove ``unpack_sources = False`` from recent easyconfigs that use a *.whl file as source (`#12783 `_) * whitelist Seaborn 0.10.1 for NanoComp 1.13.1 and NanoPlot 1.33.0 (`#12790 `_) * add check to make sure that source step is not being skipped (`#12807 `_) * use ``EasyConfig.disable_templating`` method in test suite (`#12848 `_) * disable usNIC by default in libfabric to avoid problems due to linking to both libnl and libnl-3 (`#12854 `_) * use OpenSSL wrapper as dependency in easyconfigs using GCCcore/10.3.0 toolchain (`#12922 `_, `#12944 `_) * dump easyconfig before initializing easyblock in order to compare it with original easyconfig (`#12925 `_) * remove postinstallcmds from imkl 2020.x easyconfigs, easyblock now installs examples (`#12937 `_) .. _release_notes_eb434: EasyBuild v4.3.4 (Apr 9th 2021) ------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for filtering dependencies by using ``False`` as version (`#3506 `_) * add ``create_unused_dir`` function to create a directory which does not yet exist (`#3551 `_) * avoid running expensive ``module use`` and ``module unuse`` commands when using Lmod as modules tool, update ``$MODULEPATH`` directly instead (`#3557 `_, `#3633 `_) * create CUDA cache (for JIT compiled PTX code) in build dir instead of ``$HOME`` (`#3569 `_) * add "Citing" section to module files (`#3596 `_) * add support for using fallback ``arch=*`` key in dependency version specified as arch->version mapping (`#3600 `_) * also check for pending change requests and mergeable_state in ``check_pr_eligible_to_merge`` (`#3604 `_) * ignore undismissed ``changes requested`` review if there is an ``approved`` review by the same user (`#3607 `_, `#3608 `_) * sort output of ``eb --search`` in natural order (respecting numbers) (`#3609 `_) * enhance ``eb`` command to ensure that ``easybuild.main`` can be imported before settling on python* command to use (`#3610 `_) * add ``--env-for-shebang`` configuration option to define the ``env`` command to use for shebangs (`#3613 `_) * add templates for architecture independent Python wheels (`#3618 `_) * mention easyblocks PR in gist when uploading test report for it + fix ``clean_gists.py`` script (`#3622 `_) * also accept regular expression value for ``--accept-eula-for`` (`#3630 `_) * update ``validate_github_token`` function to accept GitHub token in new format (`#3632 `_) * various bug fixes, including: * fix ``$BLAS_LIB_MT`` for OpenBLAS, ensure ``-lpthread`` is included (`#3584 `_) * use ``--opt=val`` for passing settings from config file to option parser to avoid error for values starting with ``-`` or ``--`` (`#3594 `_) * avoid raised exception when getting output from interactive command in ``run_cmd_qa`` (`#3599 `_) * add option to write file from file-like object and use in ``download_file`` (`#3614 `_) * make sure that path to ``eb`` is always found by tests (`#3617 `_) * other changes: * add ``pick_default_branch`` function to clean up duplicate code in ``tools/github.py`` (`#3592 `_) * refactor the CI configuration to use inclusion instead of exclusion (`#3616 `_) * use develop branch when testing push access in ``--check-github`` (`#3629 `_) * deprecate ``--accept-eula``, rename to ``--accept-eula-for`` (`#3630 `_) **easyblocks** * minor enhancements, including: * make OpenCV easyblock aware of protobuf, libwebp and OpenEXR dependencies provided via EasyBuild (`#2346 `_) * update CP2K easyblock w.r.t. running regtest for CP2K v8.1 (`#2350 `_) * update GROMACS easyblock for GROMACS/2021 with CUDA (`#2353 `_) * adjust call to ``python-config`` for Python >= 3.8 in VMD easyblock (`#2355 `_) * enhance cuDNN and CUDA easyblocks to support ``aarch64`` (`#2356 `_) * pass down compiler flags provided by EasyBuild in g2clib easyblock (`#2357 `_) * update VTune easyblock for version 2020 (`#2359 `_) * make WRF and WPS easyblocks aware of ``(pre)configopts`` (`#2361 `_) * add Clang version 12.0.0 for AOCC 3.0.0 to mapping in custom easyblock for AOCC (`#2362 `_) * use ``PYPI_SOURCE`` as the default for source_urls of PythonPackage (`#2364 `_, `#2370 `_) * enhance PythonPackage easyblock to catch faulty version (0.0.0) for installed Python packages (`#2367 `_, `#2377 `_) * enhance BWA easyblock: pass compiler flags + use ``filetools`` functions (`#2368 `_) * various bug fixes, including: * set ``$R_LIBS_SITE`` rather than ``$R_LIBS`` when installing R packages (`#2326 `_) * update PETSc easyblock to take into account that ScaLAPACK installation may not have header files + fix building in parallel (`#2348 `_) * disable CMake user package repository in CMakeMake generic easyblock (`#2351 `_) * update LAPACK easyblock to keep control of compiler options for versions >= 3.9.0 (`#2358 `_) * also set ``$TORCH_CUDA_ARCH_LIST`` for PyTorch tests (`#2363 `_) * enhance Hadoop easyblock to avoid copying same native library twice (`#2371 `_) * fix pip extension download pattern for PythonPackage easyblock (`#2372 `_) * make the CUDA stub libs take preference over system libs when linking (`#2373 `_) * improve Python package version check and add ``unversioned_packages`` easyconfig parameter (`#2377 `_) **easyconfigs** * added easyconfig for goblf/2020b toolchain (`#12381 `_, `#12535 `_) * added example easyconfig files for 41 new software packages: * amplimap (`#12205 `_), BEEF (`#12104 `_), bpp (`#12036 `_), Brotli (`#11651 `_), CDAT (`#12322 `_), cicero (`#12252 `_), CIF2Cell (`#12258 `_), CompareM (`#9377 `_), DL_POLY_4 (`#12324 `_), DMCfun (`#12412 `_), ESMPy (`#12339 `_), FLAC (`#12300 `_), gdbm (`#12322 `_), GPyOpt (`#12524 `_), json-c (`#12344 `_), libcdms (`#12322 `_), libdrs (`#12322 `_), libogg (`#12285 `_), libvorbis (`#12300 `_), LncLOOM (`#12287 `_), LPJmL (`#12344 `_), maze (`#12354 `_), MetaEuk (`#12188 `_), mrcfile (`#12497 `_), Myokit (`#12261 `_), NCCL-tests (`#12415 `_), pyABC (`#12329 `_), PyCifRW (`#12258 `_), PyOD (`#12507 `_), pyro-api (`#12447 `_), pyro-ppl (`#12447 `_), R-opencv (`#12226 `_), Ratatosk (`#12443 `_), RevBayes (`#12419 `_), sansa (`#12354 `_), scikit-cuda (`#12352 `_), Seeder (`#9057 `_), suave (`#12354 `_), voltools (`#12497 `_), vorbis-tools (`#12300 `_), YACS (`#12309 `_) * added additional easyconfigs for various supported software packages, including: * AOCC 3.0.0, Arriba 2.1.0, ArviZ 0.11.1, arpack-ng 3.8.0 BCFtools 1.12, BEDTools 2.30.0, BUSCO 5.0.0, BioPerl 1.7.8, Blosc 1.21.0, Boost.Python 1.74.0, bitarray 1.2.1, bokeh 2.2.3, CP2K 8.1, CUDAcore 11.2.2, CellRanger 6.0.0, Clang 11.0.1, DIAMOND 2.0.7, Delly 0.8.7, dask 2021.2.0, dm-tree 0.1.5, Elk 7.0.12, Extrae 3.8.0, FLUENT 2021R1, FabIO 0.11.0, Fiji 20201104, Flye 2.8.3, FreeSurfer 7.1.1, GDAL 3.2.1, GEOS 3.9.1, GLFW 3.3.3, GMAP-GSNAP 2020-12-17, GROMACS 2021, GetOrganelle 1.7.4, gmsh 4.7.1, HTSeq 0.11.3, HTSlib 1.12, Hypre 2.20.0, hyperopt 0.2.5, iVar 1.3.1, igraph 0.9.1, Jansson 2.13.1, Kent_tools 411, LAPACK 3.9.1, LAST 1179, LibSoup 2.72.0, libxc 5.1.3, MAFFT 7.475, MCR R2020a.6 + R2020b.5 + R2021a.0.eb, MDTraj 1.9.5, MUMPS 5.3.5, MaSuRCA 4.0.1, Mercurial 5.7.1, Monocle3 0.2.3, NGS 2.10.9, NVHPC 21.2, NetLogo 6.2.0, Nextflow 21.03.0, ncbi-vdb 2.10.9, OSU-Micro-Benchmarks 5.7, OpenCV 4.5.1, OpenEXR 2.5.5, OptiX 7.2.0, PETSc 3.14.4, PLUMED 2.7.0, PROJ 7.2.1, PyAMG 4.0.0, PyCUDA 2020.1, PyCairo 1.20.0, PyOpenCL 2021.1.2, PyTorch-Geometric 1.6.3, p7zip 17.03, pFUnit 4.2.0, picard 2.25.1, pocl 1.6, preCICE 2.2.0, protobuf 2.5.0, pymatgen 2022.0.4, python-igraph 0.9.0, Qtconsole 5.0.2, R 4.0.4, RASPA2 2.0.41, RDFlib 5.0.0, ReFrame 3.5.1, Ruby 2.7.2, rnaQUAST 2.2.0, SAMtools 1.12, SDL2 2.0.14, SIMPLE 3.0.0, SPAdes 3.15.2, SUNDIALS 5.7.0, Seurat 4.0.1, Spark 3.1.1, scikit-image 0.18.1, silx 0.14.0, spglib 1.16.1, sympy 1.7.1, tensorboardX 2.1, tensorflow-probability 0.12.1, tmux 3.1c, USEARCH 11.0.667, VTK 9.0.1, VTune 2020_update3 * minor enhancements, including: * verify checksum of all patch files in easyconfigs test suite (`#12221 `_) * add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a (`#12227 `_) * add sanity check commands for vorbis-tools (`#12304 `_) * add extensions to R-bundle-Bioconductor 3.12: motifmatchr (`#12390 `_), OUTRIDER + FRASER (`#12510 `_) * add DMCfun extension for R v4.0.3 + v4.0.4 (`#12409 `_) * various bug fixes, including: * add missing GNU time dependency to WRF 4.0.2 built with foss/2018b (`#12179 `_) * add archive ``source_urls`` for Hadoop and Spark (`#12220 `_) * add missing Python build dep for SeqAn 2.4.0 (`#12222 `_) * add missing pkg-config build dependency to VCFtools 0.1.16 (`#12245 `_), GObject-Introspection-1.64.0 (`#12298 `_), libsndfile (`#12303 `_) * set ``$HTSLIB_DIR`` in HTSlib for use by EnsEMBLCoreAPI & Bio-DB-HTS (`#12253 `_) * bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0 (`#12277 `_, `#12288 `_) * bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error (`#12293 `_) * skip sanity check test in IPython-7.18.1-GCCcore-10.2.0.eb (`#12294 `_) * add missing Perl and Autotools build dependencies in recent WRF easyconfigs (`#12301 `_) * add missing groff build dependency for Perl 5.30.0 and 5.32.0 (`#12307 `_) * add linkcomm + rnetcarto extensions to R v4.0.3 (`#12311 `_) * add dependency on Flask in all ASE v3.21.1 easyconfigs (`#12312 `_) * remove hard-coded ``-xHost`` from MMseqs2-11-e1a1c (`#12317 `_) * revised outdated easyconfigs for libcerf + replaced obsolete homepages and source urls (`#12323 `_) * consistently include ``new_archive`` source URL in Qt5 easyconfigs + add missing checksums (`#12325 `_, `#12426 `_) * fix source URL and add alternate checksum for Hypre 2.14.0 (`#12337 `_) * add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI (`#12340 `_) * add SourceForge fallback source URL for recent freetype easyconfigs (`#12341 `_) * revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 (`#12345 `_) * use ``-D_USE_METIS_5p1`` in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0 (`#12403 `_) * make sure that path to ``eb`` is always found by tests (`#12436 `_) * stop tests changing the EasyBuild easyconfigs (`#12454 `_) * use pip to install pkgconfig 1.5.1 (`#12455 `_) * add CI test checking if the Python default ``source_urls`` are used and fix CI check where ``use_pip=False`` was ignored (`#12456 `_, `#12471 `_) * fix source URLs in Arrow 0.x easyconfigs (`#12475 `_) * fix numpy tests for recent SciPy-bundle easyconfig on POWER (`#12481 `_) * don't download hwloc during FIRESTARTER build (`#12482 `_) * avoid 0.0.0 install version for various Python apps (`#12519 `_, `#12522 `_) * enable USER_SDPD package and disable building docs in LAMMPS 3Mar2020 (`#12527 `_) * update ``$R_LIBS_SITE`` rather than ``$R_LIBS`` in easyconfigs installing R packages (`#12534 `_) * add Python 3 build dep for HMMER 3.3.x test step (`#12536 `_) * other changes: * rename opencv_contrib and update to OpenCV v3.4.1 with contrib ``versionsuffix`` (`#12229 `_) * fix minor style issues in POV-Ray v3.7.0.8 easyconfigs (`#12342 `_) * enable ``-fPIC`` for g2clib (`#12349 `_) * consistently include Keras-Applications and Keras-Preprocessing extensions in Keras 2.3.1 easyconfigs (`#12375 `_) * remove ``PYPI_SOURCE`` source URL from easyconfigs using PythonPackage or PythonBundle (`#12541 `_, `#12452 `_, `#12453 `_) * require ``sanity_pip_check`` for all Python package/bundles (`#12464 `_) .. _release_notes_eb433: EasyBuild v4.3.3 (Feb 23rd 2021) -------------------------------- bugfix/update release **framework** * various enhancements, including: * advise PR labels in ``--review-pr`` and add support for ``--add-pr-labels`` (`#3177 `_) * add support for using customized HTTP headers in ``download_file`` (`#3472 `_, `#3583 `_) * also take toolchain dependencies into account when defining template values (`#3541 `_, `#3560 `_) * add support for ``--accept-eula`` configuration option + ``accept_eula`` easyconfig parameter (`#3535 `_, `#3536 `_, `#3546 `_) * detect ``SYSTEM`` toolchain as special case in easystack files (`#3543 `_) * enhance ``extract_cmd`` function to use ``cp -a`` for shell scripts (.sh) (`#3545 `_) * allow use of alternate envvar(s) to ``$HOME`` for user modules (`#3558 `_) * use https://sources.easybuild.io as fallback source URL (`#3572 `_, `#3576 `_) * add toolchain definition for ``iibff`` toolchain (`#3574 `_) * add ``%(cuda_cc_space_sep)s`` and ``%(cuda_cc_semicolon_sep)s`` templates (`#3578 `_) * add support for intel-compiler toolchain (>= 2021.x versions, oneAPI) (`#3581 `_, `#3582 `_) * various bug fixes, including: * add ``--init`` and ``--recursive`` options to ``git submodule update`` command that is used when creating source tarball for specific commit (`#3537 `_) * filter out duplicate paths in RPATH wrapper script (`#3538 `_) * don't clean up imported modules after verifying imports of included Python modules (`#3544 `_) * avoid no-op changes to ``$LD_*`` environment variables in ModulesTool (`#3553 `_) * fix UTF-8 encoding errors when running EasyBuild with Python 3.0.x-3.6.x (`#3565 `_) * create ``lib64`` symlink as a relative symlink (`#3566 `_) * don't reuse variable name in the loop to fix adding extra compiler flags via toolchainopts (`#3571 `_) * symlink ``lib`` to ``lib64`` if it doesn't exist (`#3580 `_) * include ``%(mpi_cmd_prefix)s`` and ``%(cuda_*)s`` templates in output of ``--avail-easyconfig-templates`` (`#3586 `_) * other changes: * rename ``EasyBlock._skip_step`` to ``EasyBlock.skip_step``, to make it part of the public API (`#3561 `_) * make symlinking of ``posix_c.so`` to ``posix.so`` in test suite configuration conditional (`#3570 `_) **easyblocks** * 2 new software-specific easyblocks: * AOCC (`#2295 `_), Intel compilers (v2021.x, oneAPI) (`#2305 `_) * minor enhancements, including: * run motorBike tutorial case as sanity check for recent (community) OpenFOAM versions (`#2201 `_) * add foamMonitor to sanity checks of OpenFOAM (`#2256 `_) * create versioned symlinks for CMake commands + create symlink for ``cmake3`` in PyTorch easyblock if ``cmake3`` command is not found (`#2259 `_) * improve Bazel easyblock: add support for running tests, enable static linking, use build dir rather than ``tmpdir``, verbose output (`#2285 `_) * add support for skipping steps in Python packages installed as extension + print progress on individual steps for installing Python packages as extensions (`#2290 `_) * update BerkeleyGW easyblock to support GCC 10 and fftlib (`#2297 `_) * update QuantumESPRESSO easyblock to support GCC 10 (`#2298 `_) * update Clang easyblock to add support for building extra tools + leveraging hwloc and Z3 as optional dependencies (`#2310 `_) * add support for running TensorFlow CPU and GPU tests (`#2263 `_, `#2292 `_, `#2312 `_) * update impi easyblock for impi 2021.x (oneAPI) (`#2313 `_) * update QuantumESPRESSO easyblock to handle v6.7 (`#2319 `_) * update OpenFOAM easyblock for changes in v2012 (`#2321 `_) * add sanity check commands to GCC (including LTO support) (`#2322 `_) * update FLUENT sanity check for v2021R1 (`#2334 `_) * various bug fixes, including: * filter out user packages in LAMMPS easyblock if corresponding dependency isn't included + only set ``-DUSER-INTEL`` on x86_64 systems (`#2254 `_) * unify handling of ``pylibdirs`` and don't add duplicated ``$PYTHONPATH`` in PythonBundle (`#2281 `_) * enhance Amber easyblock to fix running of ``update_amber`` script when ``python`` command is not available in OS (`#2282 `_) * guard ``module unload`` statements in modules for Cray* toolchains (`#2286 `_) * set ``$PYTHONNOUSERSITE`` in ``PythonBundle.extensions_step`` to avoid picking up on Python packages installed in $HOME (`#2289 `_) * create less temporary directories for TensorFlow by (only) using ``--output_user_root`` (`#2293 `_) * fix logic w.r.t. enabling Python support in PETSc (`#2299 `_) * make ``builddeps`` a list of names in SLEPc easyblock (`#2300 `_) * make ``builddeps`` a list of names in Trilinos easyblock (`#2301 `_) * make sure the installation of ``libiberty.a`` in the binutils easyblock goes into a populated directory (`#2308 `_) * fix for building GCC with ``--sysroot`` on ppc64le (`#2315 `_) * fix OpenFOAM sanity check on POWER (`#2320 `_) * use library search paths of compiler for RPATH when building binutils with system compiler + enhance sanity check by running ``--version`` for binutils commands (`#2323 `_, `#2327 `_) * pass ``$CXXFLAGS`` to PDT's configure script via ``-useropt`` (`#2324 `_) * pass down compilation flags from build environment for ESMF (`#2325 `_) * update URLs for test data for WRF to ``https`` (`#2335 `_) * read MATLAB configuration file in binary mode to avoid UTF-8 encoding errors when using Python 3.6 (`#2340 `_) * fix Boost sanity check on POWER (`#2291 `_) and aarch64 (`#2341 `_) * other changes, including: * rework module-only tests to use unique software name (rather than 'foo') (`#2287 `_) * prefer default value for extra options in easyblock tests (`#2280 `_, `#2302 `_) * add check for accepted EULA in custom easyblock for NVHPC (`#2311 `_) * update optional feature support of TensorFlow (`#2314 `_) * make symlinking of ``posix_c.so`` to ``posix.so`` in test suite configuration conditional (`#2330 `_) **easyconfigs** * add easyconfig for new iibff toolchain: iibff/2020b (`#12185 `_) * added easyconfigs for 6 new toolchains: * gobff/2020b (`#12098 `_), goblf/2018b (`#6615 `_), gomkl/2020b (`#12198 `_), iimkl/2018a (`#6092 `_), iomkl/2019b (`#11981 `_), iomkl/2020b (`#12009 `_) * added example easyconfig files for 72 new software packages: * AOCC (`#11868 `_), CHERAB (`#7141 `_), CaDiCaL (`#11966 `_), CellRanger-ARC (`#12114 `_), CuPy (`#11749 `_), DFA (`#11979 `_), FIGARO (`#11924 `_), FIRESTARTER (`#12160 `_), FIt-SNE (`#8630 `_), GPyTorch (`#12010 `_), GSEA (`#10395 `_), GetOrganelle (`#11948 `_), Glucose (`#11965 `_), GraPhlAn (`#10707 `_), ITSx (`#10558 `_), Kaleido (`#11998 `_), LAPACK (`#6615 `_), LSD2 (`#11903 `_), Lingeling (`#11964 `_), MPB (`#7026 `_), MiniCARD (`#11963 `_), MiniSat (`#11962 `_), NGSpeciesID (`#11918 `_), NanopolishComp (`#11823 `_), Nsight-Compute (`#12043 `_), Nsight-Systems (`#12042 `_), PHANOTATE (`#8667 `_), PIPITS (`#10558 `_), PyClone (`#11940 `_), PySAT (`#12000 `_), RNAmmer (`#7262 `_), Raysect (`#7141 `_), SICER2 (`#12200 `_), SOCI (`#12045 `_), SeisSol (`#7194 `_), SignalP (`#11862 `_), Stack (`#11310 `_), SuperLU_DIST (`#11693 `_), Teneto (`#12056 `_), Transformers (`#12032 `_), YANK (`#11742 `_), Z3 (`#12013 `_), bgen (`#7456 `_, `#11867 `_), bgen-reader (`#7456 `_, `#11867 `_), bpytop (`#12040 `_), byobu (`#11932 `_), chi2comb (`#11867 `_), cuTENSOR (`#11914 `_), dd (`#11978 `_), decona (`#11891 `_), dicom2nifti (`#11955 `_), eccodes-python (`#12083 `_), fftlib (`#11944 `_), flatbuffers-python (`#12148 `_), fpocket (`#11980 `_), gh (`#11851 `_), intel-compilers (oneAPI) (`#11982 `_), libGDSII (`#7026 `_), libpci (`#11871 `_), liknorm (`#7456 `_, `#11867 `_), limix (`#7456 `_, `#11867 `_), logaddexp (`#11867 `_), neptune-client (`#11985 `_), plinkQC (`#12068 `_), preCICE (`#11886 `_), py-aiger (`#11999 `_), py-aiger-bdd (`#11999 `_), pytest-xdist (`#11883 `_, `#11893 `_), samblaster (`#7378 `_), terastructure (`#12197 `_), typing-extensions (`#11636 `_), webin-cli (`#8674 `_) * added additional easyconfigs for various supported software packages, including: * ack 3.4.0, AmberTools 20, AMD-LibM 3.6.0-4, AMD-RNG 2.2, AMD-SecureRNG 2.2, annovar 20191024, ASE 3.21.1, AUGUSTUS 3.4.0, Bazel 3.7.2, bcgTree 1.1.0, BLAST+ 2.11.0, Bonito 0.3.5, Bowtie2 2.4.2, causalml 0.8.0-20200909, CGAL 5.2, ConnectomeWorkbench 1.4.2, CUDAcore 11.2.1, cuDNN 8.0.5.39, dcm2niix 1.0.20201102, DendroPy 4.5.2, DIAMOND 0.9.36 + 2.0.6, ecCodes 2.20.0, ELPA 2020.11.001, Emacs 27.1, FusionCatcher 1.30, gensim 3.8.3, GHC 8.6.5, gnuplot 5.4.1, GPAW 21.1.0, Graphviz 2.44.1, GROMACS 2020.5, Gurobi 9.1.0, HH-suite 3.3.0, HMMER 3.3.2, HTSlib 1.11, Horovod 0.21.1, imbalanced-learn 0.7.0, impi 2021.1.1, inferCNV 1.3.3, ITK 5.1.2, IQ-TREE 2.1.2, JasPer 2.0.24, JUBE 2.4.1, libgit2 1.1.0, libzip 1.7.3, likwid 5.1.0, MariaDB 10.5.8, medaka 1.2.0, Meep 1.6.0, mkl-service 2.3.0, MPICH 3.3.2, muParser 2.3.2, NanoComp 1.13.1, NanoPlot 1.33.0, networkx 2.5, NLTK 3.5, numba 0.52.0, NVHPC 20.11, nvtop 1.1.0, OpenCoarrays 2.9.2, OpenFOAM v2012, OpenJPEG 2.4.0, OpenMPI 4.1.0, parasail 2.4.2, PLUMED 2.6.2, PostgreSQL 13.2, pydicom 2.1.2, PyMC3 3.11.0, python-parasail 1.2.2, PyTorch 1.7.1, QIIME2 2020.11, QuantumESPRESSO 6.7, QuickFF 2.2.7, R 4.0.3, R-bundle-Bioconductor 3.12, ReFrame 3.4.1, RMBlast 2.10.0, RSEM 1.3.3, Salmon 1.4.0, scikit-build 0.11.1, SciPy-bundle 2020.03 w/ Python 2.7.18, Seaborn 0.11.1, SEPP 4.4.0, SHAPEIT4 4.2.0, SpaceRanger 1.2.2, Stacks 2.54, STAR 2.7.7.a, statsmodels 0.12.1, SuiteSparse 5.8.1, tbb 2020.3, TensorFlow 1.15.5 + 2.4.1, Theano 1.1.2, torchvision 0.8.2, V8 3.4.0, Wannier90 3.1.0 * minor enhancements, including: * enable building of QtWebEngine in Qt5 easyconfig using foss/2017b or intel/2017b (`#7302 `_) * enable NVPTX offload in GCCcore 9.3.0 easyconfig (`#11839 `_) * also build shared library in recent HDF easyconfigs (`#11847 `_) * add support for HDF4 to GDAL v3.0.2 and v3.0.4 (`#11855 `_) * add patch for magma 2.5.4 with fosscuda/2019b to allow any ``sm_*`` value to be passed via ``GPU_TARGET`` (`#11861 `_) * add missing M4 build dependency to recent SuiteSparse versions (`#11869 `_) * enable tests for most recent Bazel versions (3.x) (`#11894 `_) * enable gipaw in QuantumESPRESSO 6.6 easyconfig (`#11905 `_) * add RCAL + sensemakr extensions to R 4.0.0 (`#11921 `_) * add additional extensions to R v4.0.3 easyconfig (`#11922 `_, `#12057 `_) * improve sanity_check_paths for AMD-LibM (`#11933 `_) * symlink ``include``/``lib`` subdirs + enhance ``sanity_check_paths`` for AMD-RNG v2.2-4 (`#11934 `_) * improve ``sanity_check_paths`` for AMD-SecureRNG (`#11935 `_) * update Clang 10+ dependencies & build extra tools (`#12013 `_) * add Inline extension to recent Perl easyconfigs (5.30+) (`#12029 `_) * add EnsDb.Hsapiens.v86 to Bioconductor 3.11 (`#12078 `_) * add sanity check command for bam-readcount v0.8.0 to check ``--version`` output (`#12092 `_) * add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 (`#12174 `_) * add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (`#12136 `_, `#12137 `_) * various bug fixes, including: * added missing space in ``configopts`` in ParaView 5.8.0 easyconfigs using 2020a toolchain (`#10989 `_) * use bfd linker for glibc 2.30 (`#11331 `_) * add missing moduleclass in UCLUST easyconfig (`#11477 `_) * don't disable optarch for Clang 11.0.0 (`#11814 `_) * add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x (`#11837 `_) * fix compilation of TensorFlow 2.3.1 with CUDA and glibc 2.26 on POWER (`#11859 `_) * disable building of manpages for GDCM to fix installation problem with docbook (`#11866 `_) * add patch for LLVM 6.0.0 to fix missing exported symbol ``LLVMInitializeInstCombine`` (`#11873 `_) * fix name of source file for GDRCopy v2.1 (`#11887 `_) * fix Tombo to work with rpy2 v3 when creating DataFrames (`#11892 `_) * fix GCCcore 8.1.0 w.r.t. removed ``sys/ustat.h`` in glibc 2.28 (`#11896 `_) * add git as a dependency to GitPython version 3.x (`#11902 `_) * fix undefined ``__ieee128`` on ppc64le with glibc 2.26 for magma (`#11930 `_) and PyTorch (`#11936 `_) * update Hypre git location for PETSc 3.11.0 using downloaded dependencies (`#11947 `_) * fix source URL in expat easyconfigs (and consistently add custom ``sanity_check_paths``) (`#11960 `_) * use libpng provided by EasyBuild in VTK to fix build issue on ppc64le (`#11990 `_) * add missing pkg-config build dependency for GObject-Introspection v1.66.1 (`#11949 `_) * add missing plotly-orca dependency for NanoPlot (`#11967 `_, `#12015 `_) * add patch for Boost 1.74.0 to fix missing include file (`#12007 `_) * fix for ``error: 'runtime_error' is not a member of 'std'`` in qtlocation for Qt5 v5.14.2 (`#12012 `_) * fix homepage for gnuplot 5.2.8, use ``http://`` since homepage is not reachable via ``https://`` (`#12047 `_) * fix OS dependencies for libfabric (`#12058 `_) * fix vector ``mul`` and ``div`` with broadcasts in ``-masm=intel`` mode in GCCcore v9.3.0 (`#12065 `_) * add missing ESMF dependency in NCO easyconfigs (`#12071 `_, `#12072 `_) * add patch to fix version for bam-readcount 0.8.0 (`#12075 `_) * add missing Perl build dep for (recent) libcerf versions, required for ``pod2html`` command (`#12085 `_) * add missing bzip2 dependency to recent ncbi-vdb easyconfigs (`#12120 `_) * add missing Perl build dependency for BLIS 0.8.0 (`#12146 `_) * use ``https://sources.easybuild.io`` as fallback source URL for UDUNITS (`#12049 `_, `#12156 `_, `#12182 `_) * correct the GCC version check to allow IBM VSX builds of GROMACS 2020.4 and 2020.5 (`#12159 `_) * add missing mkl-service dependency for Theano built with intel/2019b + enhance sanity check (`#12172 `_) * add patches to fix test problems with p4est 2.2 (`#12028 `_) * fix build of Bison using older system GCC (v4.x) (`#12203 `_) * fix lack of optimisation for SHAPEIT4 v4.1.3 (`#12206 `_) * add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6 (`#11801 `_, `#12208 `_) * fix source URL for libspatialite (`#12213 `_) * add ``archive`` fallback source URL to MAGMA easyconfigs (`#12214 `_) * fix checksum for patch in make 4.2.1 easyconfig using GCC/7.3.0-2.30 (`#12223 `_) * other changes: * replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a single easyconfig for BioPP v2.4.1 (using Bundle easyblock) (`#11609 `_) * add CESM-deps to whitelist in check for custom ``sanity_check_paths`` (`#11916 `_) * include '-4' in version for AMD-SecureRNG v2.2-4 (`#11934 `_, `#11935 `_) * switch to using python-parasail and tqdm dependencies in Bonito easyconfigs (`#11937 `_) * rename orca to plotly-orca (`#12015 `_) * remove duplicate extensions in R 3.5.x easyconfigs, and add test to detect such issues (`#12059 `_) * remove Python dependency from ecCodes v2.17.0 since it doesn't provide Python bindings (`#12084 `_) * update Java/1.8 wrapper to Java 1.8.0_281 (`#11928 `_, `#12088 `_) * update Bison (build) dependency for flex built with system compiler to v3.5.3 (`#12111 `_) * make symlinking of ``posix.so`` in test suite configuration conditional (`#12123 `_) * move make 4.3 easyconfigs to GCCcore toolchain (`#12166 `_) * move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore (`#12168 `_) * rename SNAP to SNAP-HMM and update easyconfig (`#12218 `_) .. _release_notes_eb432: EasyBuild v4.3.2 (December 10th 2020) ------------------------------------- bugfix/update release **framework** * add (experimental) support for specifying easyconfig files via an "easystack" file (`#3479 `_, `#3511 `_, `#3515 `_, `#3517 `_, `#3520 `_, `#3521 `_) * see also https://easybuild.readthedocs.io/en/latest/Easystack-files.html * add definition for new ``gobff`` toolchain using BLIS and LibFLAME (`#3505 `_) * various enhancements, including: * add support for toolchain options like ``extra_cxxflags`` to specify extra compiler options (`#2193 `_) * fix combination of ``--copy-ec`` and ``--from-pr`` (`#3482 `_) * enhance ``copy_files`` function: support single file target, error on empty input list, support verbose mode (`#3483 `_) * cache result of ``fetch_files_from_pr`` function (mainly to speed up framework test suite) (`#3484 `_) * add ``locate_files`` function to filetools module (`#3485 `_) * add support for ``%(module_name)s`` template value (`#3497 `_) * clarify input format for ``--cuda-compute-capabilities`` in ``eb --help`` output (`#3509 `_) * add support for skipping unit tests (test step) via ``--skip-test-step`` (`#3524 `_) * various bug fixes, including: * also ignore ``vsc.*`` imports coming from from ``pkg_resources/__init__.py`` (setuptools) in fake vsc namespace (`#3491 `_) * don't pass username in ``github_api_get_request`` when no GitHub token is available (`#3494 `_) * also inject ``-rpath`` options for all entries in ``$LIBRARY_PATH`` in ``RPATH`` wrappers (`#3495 `_) * avoid ``TypeError`` being raised by ``list_toolchains`` (`#3499 `_) * check if PR is already merged in ``--merge-pr`` (`#3502 `_) * graciously handle wrong PR id in ``fetch_pr_data`` (`#3503 `_) * fix regression in ``apply_regex_substitutions``: also accept list of paths to patch (`#3507 `_) * update installation procedure for EasyBuild in generated Singularity container recipes (`#3510 `_) * fix GitHub Actions workflow for test suite: run outside of repo checkout + also test bootstrap script with Python 3.9 (`#3518 `_) * bump cryptography from 2.9.2 to 3.2 for Python 2 in ``requirements.txt`` (`#3519 `_) * fix ``eb --help=rst`` when running with Python 3 (`#3525 `_) * other changes: * exclude test configurations with Lmod 7 and Python 3, except for Python 3.6 (`#3496 `_) * significantly speed up parsing of easyconfig files by only extracting comments from an easyconfig file when they're actually needed (`#3498 `_) * don't include ``file``/``ldd``/``readelf`` commands run during RPATH sanity check in ``--trace`` output (`#3508 `_) **easyblocks** * 2 new software-specific easyblocks: * code-server (`#2255 `_), Metagenome-Atlas (`#2219 `_) * minor enhancements, including: * add ``-fallow-argument-mismatch`` option when building CP2K 7.1 or older with GCC 10.x (`#2223 `_) * update TensorFlow easyblock for upcoming TensorFlow 2.4 (`#2225 `_) * add support for building Clang with OpenMP offload support (`#2229 `_) * enhance OpenMPI easyblock to catch any ``--with-ucx*`` configure options (`#2230 `_) * take into account ``preinstallopts`` and ``installopts`` in custom easyblock for NCL (`#2234 `_) * add support for ``withnvptx`` easyconfig parameter, to enable GPU offloading, in GCC easyblock (`#2235 `_) * take into account versions like ``4.x`` in OpenFOAM easyblock (`#2239 `_) * also add ``bin`` subdir to ``$PATH`` when installing a Python package (`#2244 `_) * various bug fixes, including: * fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK (`#2212 `_) * fix version check in Qt5 easyblock w.r.t. disabling features on old Linux kernel versions (`#2220 `_) * always define ``$FCCPP`` in QuantumESPRESSO easyblock (not just when using Intel compilers) (`#2221 `_) * allow wxPython to be installed as an extension (`#2227 `_, `#2275 `_) * only configure Python with ``--enable-optimizations`` when compiling Python with (recent) GCC compiler (`#2228 `_) * fix sanity check for Boost MT libraries (`#2231 `_) * fix hardcoded path in NVHPC easyblock to support multiple architectures (`#2233 `_) * fix ``CPASSERT`` test faults on RHEL8 in CP2K easyblock (`#2236 `_) * stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests (`#2238 `_, `#2271 `_) * append to module guesses in easyblocks for Chapel, icc, imkl and impi (rather than overwriting guesses from parent easyblock) (`#2242 `_) * weed out duplicates when determining paths to ``include-fixed`` subdirectory in GCC easyblock (`#2245 `_) * prepend all hardcoded ``/usr/*`` paths with sysroot in Python's setup.py installation script (`#2246 `_) * don't try to patch newer versions of Bazel where the patches won't apply (`#2249 `_) * fix setting of ``$RUNPARALLEL`` in HDF5 easyblock (`#2250 `_) * move ``--build`` and ``--host`` logic to ``run_configure_cmd`` in GCC easyblock (`#2252 `_) * set ``$UCX_TLS`` in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file (`#2253 `_, `#2258 `_) * enhance PyTorch easyblock to ensure it finds MKL (via ``$MKLROOT``) (`#2257 `_) * use integer division to determine number MPI ranks to use in WRF test step (`#2266 `_) * also specify ``locincpth`` and ``glibpth`` configure options for Perl based on ``--sysroot`` (`#2268 `_) * other changes, including: * add link to GCC mailing list thread confirming that binutils should not be configured with ``--with-sysroot=$EASYBUILD_SYSROOT`` when GCC is being configured like that (`#2215 `_) * pass paths to patch one by one to ``apply_regex_substitutions`` in GCC easyblock when ``--sysroot`` is set (`#2217 `_) * workaround for regression in ``apply_regex_substitutions`` introduced in EasyBuild v4.3.1 (which was fixed for v4.3.2) **easyconfigs** * add easyconfigs for new `gobff` toolchain: `gobff/2020.11` + `gobff/2020.06-amd` (`#11761 `_) * add easyconfigs for updates of common toolchains: `foss/2020b`, `fosscuda/2020b`, `intel/2020b`, `intelcuda/2020b` * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added example easyconfig files for 41 new software packages: * alsa-lib (`#11658 `_), assimp (`#11759 `_), BioServices (`#11602 `_), carputils (`#11270 `_), cctools (`#11799 `_), code-server (`#11778 `_), CRISPResso2 (`#11775 `_), elfutils (`#11783 `_), EMU (`#11641 `_), fgbio (`#11519 `_), Flink (`#11747 `_), FreeSASA (`#11699 `_), Geant4-data (`#11610 `_), geocube (`#11714 `_), IPM (`#11768 `_, `#11772 `_), libmicrohttpd (`#11783 `_), libStatGen (`#7982 `_), libzeep (`#11687 `_), LLDB (`#11822 `_), meshalyzer (`#11270 `_), meshtool (`#11270 `_), Metagenome-Atlas (`#11620 `_), MLxtend (`#11601 `_), MRChem (`#11604 `_), MRCPP (`#11579 `_), mxml (`#11769 `_), mxmlplus (`#11771 `_), nanocompore (`#11690 `_), neon (`#11797 `_), Open-Data-Cube-Core (`#11713 `_), OpenSees (`#11613 `_), PEST++ (`#11565 `_), pyFAI (`#11849 `_), pymca (`#11848 `_), RE2 (`#11718 `_), scikit-bio (`#11660 `_), SpaceRanger (`#11776 `_), SplAdder (`#11607 `_), SWAT+ (`#11615 `_), velocyto (`#11744 `_), WCT (`#11779 `_) * added additional easyconfigs for various supported software packages, including: * BBMap 38.87, Boost 1.74.0, CUDA 11.1.1, CellRanger 5.0.0.eb, CheckM 1.1.3, Clang 11.0.0, cuDNN 8.0.4.30, DMTCP 2.6.0, FDS 6.7.5, FFmpeg 4.3.1, GROMACS 2020.4, Geant4 10.6.2, Ghostscript 9.53.3, GitPython 3.1.9, GlobalArrays 5.8, HDF5 1.10.7, h5py 3.1.0, hypothesis 5.41.5, JasPer 2.0.16, LittleCMS 2.11, libedit 20191231, libyaml 0.2.5, MPFR 4.1.0, magma 2.5.4, matplotlib 3.3.3, NCCL 2.8.3, NLopt 2.6.2, Nextflow 20.10.0, netCDF-Fortran 4.5.3, OpenBLAS 0.3.12, OpenMolcas 20.10, Pillow 8.0.1, PnetCDF 1.12.1, PyYAML 5.3.1, packmol 20.2.2, protobuf 3.14.0, psycopg2 2.8.6, pybind11 2.6.0, pycocotools 2.0.2, Qt5 5.14.2, RAxML-NG 1.0.1, RSeQC 4.0.0, rioxarray 0.1.1, SCOTCH 6.1.0, SciPy-bundle 2020.11, SentencePiece 0.1.94, StringTie 2.1.4, SuperLU 5.2.2, scikit-learn 0.23.2, snakemake 5.26.1, tqdm 4.51.0, vsc-mympirun 5.2.5, x264 20201026 * minor enhancements, including: * add extension to R-bundle-Bioconductor 3.11: snpStats (`#11586 `_), SCANVIS (`#11638 `_) * add extensions to R 4.0.0: coloc, Exact, lmom, gld, DescTools (`#11587 `_); nlsem (`#11733 `_); mitools, survey, tableone, jstable (`#11841 `_) * add gxmapi extension (Python bindings) to GROMACS 2020.4 (`#11640 `_) * add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs (`#11654 `_) * enable NVPTX offload support in GCCcore 10.2.0 easyconfig (`#11720 `_) * various bug fixes, including: * prevent Minimac4 easyconfig from downloading libStatGen from GitHub (`#7982 `_) * limit build parallelism for RAxML-NG to avoid build failure (`#10363 `_) * fix ``source_urls`` in Geant4 easyconfigs (`#11596 `_) * add alternate checksum for extensions in R easyconfigs: KernSmooth (`#11600 `_), codetools (`#11616 `_, `#11736 `_) * fix BBMap version check in FusionCatcher v1.20 (`#11608 `_) * add patch for TensorFlow 2.3.1 to fix installation on Arm64 (`#11614 `_) * add patch for GCCcore 10.2 to fix ``__has_include`` regression (`#11627 `_) * change default ``bitmaptype`` for IRkernel to cairo (`#11645 `_) * set ``$JUPYTER_PATH`` to make Jupyter find the ipywidgets extension in recent IPython easyconfigs (`#11649 `_) * add missing dependencies + fix moduleclass in CheckM easyconfigs (should be bio) (`#11662 `_) * use Python 2 build dep for nodejs 12.19.0 (`#11679 `_) * use correct OS deps in UCX (`#11702 `_) * in-place update to magma 2.5.4 for PyTorch 1.2.0 (`#11723 `_) * in-place update to magma 2.5.4 for PyTorch easyconfigs using fosscuda/2019b toolchain (`#11726 `_) * add missing Java dep to Prokka (`#11732 `_) * add patch to fix possible memory leak in OpenBLAS 0.3.3+ (`#11745 `_) * do not treat warnings as errors in Java v1.8_191-b26-OpenJDK (POWER) (`#11755 `_) * add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check (`#11767 `_) * add missing gnuplot dependency in OpenFOAM easyconfigs (`#11770 `_, `#11800 `_) * consistently add Java as a dep for prokka 1.14.5 (`#11782 `_) * stick to http download URL in fetchMG easyconfig (https doesn't work) (`#11788 `_) * other changes: * rename XCfun to XCFun (`#11603 `_) * rename ambiguous Ray easyconfigs to Ray-assembler and Ray-project (`#11727 `_) * change 'rstudio' name to 'RStudio-Server' to agree with official name and better reflect what it provides (`#11764 `_) * rename Sumo to SUMO for consistency (`#11791 `_) .. _release_notes_eb431: EasyBuild v4.3.1 (October 29th 2020) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * further GCC toolchain fixes for aarch64 (`#3433 `_) * take into account ``--include-easyblocks-from-pr`` when uploading test reports (`#3446 `_) * add path to pkg-config files in sysroot to ``$PKG_CONFIG_PATH`` when ``--sysroot`` is specified (`#3451 `_) * add support for NVHPC compiler + toolchain (based on PGI) (`#3454 `_) * check for _VERSION and _PREFIX Cray environment variables with both software and module name (`#3460 `_) * allow including easyblocks from multiple PRs (`#3480 `_, `#3481 `_) * various bug fixes, including: * avoid ``UnicodeDecodeError`` in ``apply_regex_substitutions`` when patching files that include non-UTF-8 characters (`#3450 `_) * avoid appending lib stubs pattern to RPATH filter over and over again (`#3452 `_) * fix missing string template on error for incorrect extension ``sources`` value (`#3461 `_) * fix compatibility with Python 3.9 by renaming fancy root logger (`#3465 `_) * also remove empty checksums list specified in easyconfig file when using ``--inject-checksums`` (`#3466 `_) * avoid confusing error log message when determining impi version while trying to define value for ``%(mpi_cmd_prefix)s`` template (`#3474 `_) * unset ``$LD_LIBRARY_PATH`` when checking for OS dependencies with ``rpm`` & co (`#3477 `_) * don't change directory in ``download_repo`` function in ``tools.github`` (`#3486 `_) * take ``source_urls``, ``checksums``, ``patches`` into account when extension source is specified via ``sources`` (`#3487 `_) * other changes: * consider ``$EB_INSTALLPYTHON`` in ``eb`` command to specify ``python`` command to use for running EasyBuild (`#3428 `_) * use only the sub folder name for ``createSubmoduleDeps`` script (`#3464 `_) **easyblocks** * 2 new software-specific easyblocks: * CFDEMcoupling (`#1439 `_), NVHPC (`#2190 `_) * minor enhancements, including: * support having PyQt5 installed as part of Qt5 in QScintilla easyblock (`#2040 `_) * update TensorFlow easyblock to put Bazel build files in build directory + avoid unnecessary runtime patching (`#2166 `_) * update CBLAS easyblock for toolchains that include imkl (`#2175 `_) * add workaround for duplicate prefix path in Eigen CMake config (`#2176 `_) * enable ``CTEST_OUTPUT_ON_FAILURE`` for CMakeMake test step (`#2181 `_) * add XLA build support to TensorFlow easyblock (`#2182 `_) * also consider libfabric dep (``--with-ofi``) when setting default OpenMPI configure options (`#2184 `_) * make easyblock for installing CMake aware of ``--sysroot`` (`#2187 `_) * make OpenBLAS respect the parallelism set by easybuild (`#2191 `_) * handle option of building Michigan State University CCT3 & CCSD3A methods in GAMESS_US easyblock (`#2194 `_) * add support to RubyGem easyblock for installing zipped gems (`#2203 `_) * update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0) (`#2205 `_) * update Score-P easyblock to add support for NVHPC toolchain (`#2206 `_) * various bug fixes, including: * add ``torch/lib`` subdirectory in Python lib dir to ``$LD_LIBRARY_PATH`` for PyTorch installations (`#2183 `_) * update MUMmer easyblock to use ``apply_regex_substitutions`` and ``copy_file`` functions (`#2185 `_) * configure OpenMPI 4.x with ``--without-verbs`` when using UCX (`#2188 `_) * take into account that zlib may be listed in ``--filter-deps`` in custom easyblock for XML R package (`#2189 `_) * add sanity check commands to Clang easyblock and print warning for missing ncurses (`#2193 `_) * enhance OpenFOAM easyblock to add symlinks for libraries to ensure ``mpi`` versions have preference over ``dummy`` versions (`#2196 `_) * leverage installed OpenSSL/BoringSSL when cURL is used as a dependency for TensorFlow (`#2197 `_) * add ``-ffree-line-length-none`` to gfortran flags in Siesta easyblock (`#2204 `_) * respect ``--disable-mpi-tests`` in Siesta easyblock (`#2207 `_) * other changes, including: * set ``$EB_INSTALLPYTHON`` in module generated for EasyBuild rather than setting ``$EB_PYTHON``, to allow overriding Python command to be used for running EasyBuild with ``$EB_PYTHON`` (`#2109 `_) * remove unused custom easyblock for DIRAC (`#2192 `_, `#2198 `_) **easyconfigs** * added easyconfigs for 2 new toolchains: * fosscuda/2020a (`#11424 `_) and intelcuda/2020a (`#11425 `_) * added example easyconfig files for 75 new software packages: * Bsoft (`#6551 `_, `#11537 `_), causallift (`#11436 `_), CAVIAR (`#11158 `_), CCfits (`#11505 `_), Cereal (`#11506 `_), CFDEMcoupling (`#6465 `_), Check (`#11295 `_), chewBBACA (`#11418 `_), COMSOL (`#11513 `_), CUDAcore (`#11295 `_), Dalton (`#5808 `_), DIRAC (`#11414 `_), ESMValTool (`#6329 `_), eSpeak-NG (`#11236 `_), ExifTool (`#11521 `_), FabIO (`#11517 `_), festival (`#11236 `_), fetchMG (`#11283 `_), FHI-aims (`#11198 `_), Flexbar (`#11305 `_), FRUIT (`#6613 `_), FRUIT_processor (`#6631 `_), Gaussian (`#4247 `_), GBprocesS (`#11512 `_), GDRCopy (`#11295 `_), Genome_Profiler (`#6066 `_), groff (`#11200 `_), ILAMB (`#11309 `_), kedro (`#11436 `_), leidenalg (`#11407 `_), libav (`#6194 `_), libmo_unpack (`#6329 `_), libobjcryst (`#11321 `_), makeinfo (`#11368 `_), mauveAligner (`#11395 `_), MBROLA (`#11236 `_), MDSplus-Java (`#10705 `_), MDSplus-Python (`#10705 `_), MyCC (`#11283 `_), nanomax-analysis-utils (`#11517 `_), Nek5000 (`#6408 `_), NVHPC (`#11391 `_), OPERA-MS (`#11410 `_), ORFfinder (`#7031 `_), phonemizer (`#11236 `_), Pingouin (`#11280 `_), Pint (`#11151 `_), pydantic (`#11151 `_), pyobjcryst (`#11321 `_), PyOpenCL (`#11517 `_), pyspoa (`#11438 `_), QtPy (`#11517 `_), Qtconsole (`#11517 `_), rasterio (`#11468 `_), rasterstats (`#11468 `_), ReMatCh (`#6067 `_), Ruby-Tk (`#6613 `_), SBCL (`#11413 `_), scikit-uplift (`#11432 `_), SDL (`#6202 `_), SDL2 (`#6203 `_), SDL2_image (`#6203 `_), SDL_image (`#6202 `_), SeqKit (`#11538 `_), silx (`#11517 `_), SiNVICT (`#11404 `_), sonic (`#11236 `_), speech_tools (`#11236 `_), Statistics-R (`#11274 `_), SUMO (`#11435 `_), tidybayes (`#11335 `_), treatSens (`#11431 `_), tsne (`#11283 `_), wandb (`#11450 `_), WisecondorX (`#11399 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2, cURL 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0, HMMER 3.3.1, Horovod 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 1.1.0, JupyterLab 2.2.8, LLVM 11.0.0, libarchive 3.4.3, libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 1.3.2, libunwind 1.4.0, libxcb 1.13, MAFFT 7.471, MDSplus 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, medaka 1.1.3, mpifileutils 0.10.1, NASM 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 2.7.7, nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0, PyGEOS 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, Python 3.8.6, pandas 1.1.2, phonopy 2.7.1, picard 2.22.1, pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, ReFrame 3.2. re2c 2.0.3, SAMtools 1.11, SCons 4.0.1, SQLite 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, spglib-python 1.16.0, spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, torchvision 0.7.0, UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc mympirun 5.2.0 X11 20201008, XGBoost 1.2.0, XZ 5.2.5, Xerces-C++ 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5 * minor enhancements, including: * use more EasyBuild installed dependencies for TensorFlow 2.2.0 (`#11224 `_) * add additional extensions to R 4.0.0 easyconfig (`#11340 `_, `#11430 `_, `#11487 `_) * add additional extensions to Bioconductor 3.11 bundle (`#11341 `_, `#11488 `_) * make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (`#11355 `_) * add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (`#11387 `_, `#11568 `_) * build LibTIFF with ``-fPIC`` (`#11527 `_) * update Java/1.8 wrapper to also support aarch64 (`#11545 `_) * various bug fixes, including: * add Python 3 as build dep for Xvfb 1.20.8 easyconfigs (`#10745 `_) * patch out bug in collective primitive in TensorFlow 2.2.0 (`#11175 `_) * add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (`#11200 `_) * add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (`#11273 `_) * add libtirpc as a build dep for HDF to fix installation on RHEL8 (`#11279 `_) * fix build problems with make 4.2.1 on RHEL8 (`#11282 `_, `#11371 `_) * change ``$LIBS`` in Ghostscript 9.27 easyconfig to include location of zlib library to link with (`#11291 `_) * remove ``--no-dist-info`` configuration option for SIP in recent PyQt5 easyconfigs (`#11307 `_) * make sure correct zlib is used in recent Ghostscript easyconfigs (`#11319 `_) * remove GLog and GFlags from PyTorch 1.2.0 (`#11327 `_), 1.3.1 (`#11325 `_), 1.4.0 (`#11322 `_) and 1.6.0 (`#11323 `_) * use PyTorch easyblock for PyTorch 1.3.1 (`#11325 `_) * add missing git build dependency for OpenImageIO 2.0.12 (`#11328 `_) * fix HDF 4.2.14 easyconfigs for RHEL8 (`#11330 `_) * add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems (`#11334 `_) * fix dependency on Bowtie of v0.x in seq2HLA easyconfigs (`#11339 `_) * fix installation of Hadoop v2.10.0 on RHEL8 (`#11358 `_) * add patch to fix installation of Sailfish v0.10.1 on RHEL8 (`#11364 `_) * add patch to fix installation of FuSeq v1.1.2 on RHEL8 (`#11365 `_) * fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (`#11385 `_, `#11386 `_) * add patch for LAME configure script to make it check for correct ncurses symbol (`#11388 `_) * add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (`#11390 `_) * fix Multiwfn 3.6 installation on RHEL8 (`#11402 `_) * fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 (`#11409 `_) * fix broken worker easyconfigs (`#11412 `_) * add ncurses runtime dependency to Clang easyconfigs (`#11415 `_, `#11416 `_, `#11419 `_, `#11472 `_) * fix installation of Bioconductor 3.11 bundle on aarch64 (`#11417 `_) * add patch to libunwind fixing a failure on POWER (`#11421 `_) * fix infinite loop build bug on ppc64le for R 4.0.0 (`#11428 `_) * fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (`#11434 `_) * fix PyVCF easyconfig, only supports Python 2 (`#11437 `_) * add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS (`#11443 `_, `#11444 `_, `#11445 `_) * add missing DB dependency (required for DB_File) to easyconfigs for Perl (`#11451 `_, `#11452 `_) * fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (`#11453 `_) * use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (`#11454 `_) * add missing UnZip dependency for Python 3.8.2 (`#11458 `_) * add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (`#11464 `_) * allow Kent_tools to build when MySQL installed at the OS level (`#11471 `_) * add missing ``moduleclass`` to easyconfigs for: * Arlequin 3.5.2.2 (`#11473 `_), MEGAHIT 1.2.8 (`#11474 `_) and 1.2.9 (`#11475 `_), PyCUDA 2019.1.2 (`#11476 `_) * fix source for SQLite 3.31.1 (`#11483 `_) * fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 (`#11498 `_) * fix checksum in NAMD 2.12 easyconfigs + add source URL (`#11515 `_) * add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (`#11523 `_) * backport fixes for Score-P v6.0 (`#11540 `_) * add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (`#11561 `_) * add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 (`#11575 `_) * other changes: * update README on constructing source file for MATLAB (`#6341 `_) * remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (`#11301 `_) * make CI error messages less confusing ("is" -> "should be") (`#11314 `_) * remove extensions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (`#11429 `_) * cache M4 source tarball to avoid test failures because of download problems (`#11469 `_) * rename jupyterhub to JupyterHub (`#11571 `_) .. _release_notes_eb430: EasyBuild v4.3.0 (September 13th 2020) -------------------------------------- feature release **framework** * various enhancements, including: * add script to create ``sources`` entries for git submodules (`#3369 `_, `#3436 `_) * add templates for CUDA compute capabilities (`#3382 `_) * ``%(cuda_compute_capabilities)s``, ``%(cuda_sm_comma_sep)s``, ``%(cuda_sm_space_sep)s`` * add EasyBuild configuration option ``--generate-devel-module`` (`#3388 `_) * to allow disabling generating of "devel" modules via ``--disable-generate-devel-module`` * set up a minimal build environment when using system compiler (`#3399 `_) * by default, ``$CC`` is set to ``gcc`` and ``$CXX`` is set to ``g++`` when using ``system`` toolchain * minimal build environment can be customized via ``--minimal-build-env`` configuration option * add ``--sysroot`` configuration option to specify alternative location of system root (`#3419 `_) * this is useful when installing software in a Gentoo Prefix environment (for example) * various bug fixes, including: * allow including easyblocks from multiple locations, by combining ``--include-easyblocks`` and ``--include-easyblocks-from-pr`` (`#3311 `_) * also escape backslashes in ``quote_py_str()`` (`#3386 `_) * use one argument ``module swap`` statements in Tcl modulefiles (required by Modules 4.2.3+) (`#3397 `_) * fix copying of (non-existing) file with ``apply_patch`` (`#3400 `_) * create symlink from ``lib64`` to ``lib`` subdir in installation directories to avoid that GCC prefers ``/lib64`` system directories (`#3401 `_) * fix default value for ``lib64_fallback_sanity_check`` build option (`#3402 `_) * correctly determine commit status in ``--merge-pr`` (`#3406 `_) * stop installing ccache wrapper for Fortran compiler (`#3409 `_) * fix issues with applying PR patch in ``--from-pr`` (`#3414 `_) * make ``RPATH`` wrapper script more robust by using ``python -E -s -S`` to run ``rpath_args.py`` (`#3422 `_) * don't inject ``-Wl,-rpath`` options when ``-x c++-header`` compiler option is used (`#3424 `_) * fix lack of ``-mno-recip`` on aarch64 by tweaking GCC options used when ``precise`` toolchain option is enabled (`#3425 `_) * make sure ``self.start_dir`` is set in ``ExtensionEasyBlock`` (`#3426 `_, `#3435 `_) * exclude local variables from typo check in easyconfig files (`#3427 `_) * other changes: * stick to cryptography 2.9.2 when using Python 2.7 to avoid broken test suite in CI (`#3392 `_) * automatically enable ``--ignore-locks`` with ``--fetch`` (`#3404 `_) * switch to status badge based on tests run in GitHub Actions CI in README (`#3415 `_) * make ``flake8`` code style checks pass (`#3416 `_, `#3417 `_) * limit Travis to only test with Python 2.6 + Lmod 7 (`#3418 `_) * ignore deprecation warning raised for cryptography when using Python 3.5 produced by output of test suite (`#3423 `_) **easyblocks** * 2 new software-specific easyblocks: * pybind11 (`#2115 `_), PyTorch (`#2104 `_) * minor enhancements, including: * update MATLAB easyblock to use new binary installer for versions >= 2020a (`#2058 `_) * add ``use_pip_requirement`` custom easyconfig parameter to PythonPackage easyblock to allow providing a requirements file to the ``pip`` command, as a source (`#2064 `_) * update CP2K easyblock for recent versions (>= 7.0) (`#2069 `_) * add ``multi_deps`` support into custom easyblock for QScintilla (`#2077 `_) * update Mothur easyblock for v1.44.0 and higher (`#2084 `_) * update MotionCor2 easyblock to add support for v1.3.2 (`#2100 `_) * update Tinker easyblock to handle skipping of tests depending on version and link with ``fftw_omp`` (`#2102 `_) * launch test & sanity check commands through ``mpirun`` for netcdf4-python if MPI support is enabled (`#2106 `_) * check for installation of pip & setuptools in Python 3.4+ (`#2108 `_) * update QuantumESPRESSO easyblock to support version 6.6 (`#2112 `_) * allow NAMD to be built on POWER, and also use the CUDA arch info (`#2113 `_, `#2123 `_) * update Libint easyblock for versions >= 2.6.0 + add custom easyconfig parameter to enable Fortran support (`#2116 `_) * update TensorFlow easyblock to use system/EasyBuild installed libraries (`#2117 `_, `#2165 `_, `#2163 `_, `#2172 `_) * add support in NAMD easyblock to pass additional C++ compiler options for building Charm++ component with + wrap them in single quotes (`#2118 `_) * automatically add required ``-G Ninja`` option when using CMakeNinja easyblock + add ``generator`` custom easyconfig parameter for CMakeMake (`#2120 `_) * make several easyblocks aware of ``--sysroot`` EasyBuild configuration option: binutils (`#2147 `_, `#2159 `_), CMakeMake (`#2152 `_), GCC (`#2143 `_), Perl (`#2142 `_), Python (`#2148 `_, `#2149 `_) * make Mesa easyblock aware of aarch64 (`#2153 `_) * enhance sanity check in custom Doxygen easyblock to catch broken installation (`#2171 `_) * various bug fixes, including: * make TensorFlow easyblock ignore the ``PKG_REVISION`` identifier if NCCL version if it exists (`#2085 `_) * remove version check against the ``version.txt`` file in CUDA easyblock (`#2097 `_) * add ``lib`` symlink in tbb installation directory when building from source (`#2103 `_) * handle GNUInstallDirs special cases in CMakeMake easyblock (`#2105 `_, `#2124 `_) * patch ELPA's ``manual_cpp`` script to fix hardcoded ``/usr/bin/python`` (`#2107 `_) * make TensorFlow easyblock also set ``$GCC_HOST_COMPILER_PREFIX`` to specify binutils location (`#2110 `_) * ensure stand-alone Python package being installed is in view when running ``pip check`` by loading fake module first (`#2114 `_) * be more patient when running interactive configure script for WRF (`#2119 `_) * make sure ``self.start_dir`` is set to a full path before constructing installation command in RPackage easyblock (`#2125 `_) * correctly check whether ``modinc`` easyconfig parameter is set to ``True`` in CP2K easyblock (`#2138 `_) * update PSI easyblock to correctly find Python and enable PCMSolver/CheMPS2 (`#2141 `_) * fix running GROMACS tests when using ``eb --rpath`` (`#2144 `_, `#2154 `_) * remove existing Python installation directory if both ``eb --rpath`` and ``--enable-optimizations`` configuration option are used (`#2146 `_) * ensure ``libQt5Core.so`` is compatible with older Linux kernels by disabling ``renameat2`` and ``getentropy`` features (`#2151 `_) * solve issue where pybind11 picks up on the system Python instead of one provided by a module (`#2158 `_) * fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be ``linux-g++``) (`#2160 `_) * fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (`#2162 `_) * explicitly enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) * fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (`#2168 `_) * unset ``$COLUMNS`` if it is set to ``0`` before running Perl's configure script (`#2169 `_) * other changes: * filter out Python in SLEPc configure (`#2101 `_) * switch to status badge based on tests run in GitHub Actions CI in README (`#2126 `_) * fix code style issues to make ``flake8`` checks pass (`#2128 `_ - `#2137 `_, `#2140 `_, `#2145 `_, `#2155 `_) * limit test configurations in Travis CI to only Python 2.6 (`#2139 `_) **easyconfigs** * added easyconfigs for 2 new toolchains: * gomkl/2020a and iomkl/2020a (`#11036 `_) * added example easyconfig files for 49 new software packages: * almosthere (`#11152 `_), arcasHLA (`#10867 `_), BioPP (`#11113 `_), Bracken (`#10829 `_), BUFRLIB (`#11140 `_), Calib (`#11111 `_), CellRanger-ATAC (`#11186 `_), edlib (`#10470 `_, `#11246 `_), flatbuffers (`#11109 `_), gengetopt (`#11117 `_), graphite2 (`#11168 `_), HeFFTe (`#10990 `_), hierfstat (`#11249 `_), immunedeconv (`#11136 `_), ioapi (`#10959 `_), itpp (`#10958 `_), LiBis (`#11059 `_), libosmium (`#11024 `_), limix-bgen (`#11152 `_), minibar (`#10470 `_, `#11246 `_), misha (`#11127 `_), MOABS (`#10747 `_), moonjit (`#11163 `_), NGLess (`#11128 `_), nsync (`#11109 `_), openCARP (`#11117 `_), OpenForceField (`#11048 `_), OpenMMTools (`#11046 `_), OpenMS (`#10994 `_), PennCNV (`#10986 `_), plantcv (`#10968 `_), PlasmaPy (`#10732 `_), Portcullis (`#11038 `_), PycURL (`#11169 `_), PyGEOS (`#11110 `_), pySCENIC (`#11115 `_), Reapr (`#9296 `_), RnBeads (`#11142 `_), sf (`#11248 `_), SLiM (`#11172 `_), stars (`#11215 `_, `#11248 `_), Sumo (`#11071 `_), Telescope (`#10943 `_), tensorflow-probability (`#10312 `_), texlive (`#11168 `_), tidymodels (`#11010 `_), Trycycler (`#11207 `_), umi4cPackage (`#11127 `_), variant_tools (`#11169 `_) * added additional easyconfigs for various supported software packages, including: * Bazel 3.4.1, Bonito 0.2.2, binutils 2.35, CP2K 7.1, Clang 10.0.1, ccache 3.7.11, ctffind 4.1.14, datamash 1.5, ELPA 2020.05.001, Emacs 26.3, Flye 2.8.1, GCC(core) 10.2.0, googletest 1.10.0, HDF 4.2.15, Horovod 0.19.5, imageio 2.9.0, JUBE 2.4.0, Julia 1.5.1, Kent_tools 401, Libint 2.6.0, libxsmm 1.16.1, MDSplus 7.96.8, MDTraj 1.9.4, MariaDB 10.4.13, Meson 0.55.1, MotionCor2 1.3.2, NAMD 2.14, NCO 4.9.3, OpenFOAM 8, OpenMPI 4.0.5, OptiX 6.5.0, Pandoc 2.10, Perl 5.32.0, PostgreSQL 12.4, PyCUDA 2019.1.2, PyFR 1.9.0, PyTorch 1.6.0, PyZMQ 18.1.1, patchelf 0.12, pocl 1.5, pycocotools 2.0.1, pyproj 2.6.1.post1, QuantumESPRESSO 6.6, RDKit 2020.03.3, rgdal 1.5, Salmon 1.3.0, Spark 3.0.0, scikit-image 0.17.1, scipy 1.4.1, snpEff 5.0, sympy 1.6.2, TINKER 8.7.2, tqdm 4.47.0, Unicycler 0.4.8, VMD 1.9.4a43 * minor enhancements, including: * also build Python libraries for ParaView 5.8.0 (`#10927 `_) * add extensions to recent Bioconductor easyconfigs: FlowSorted.Blood.EPIC (`#11021 `_), DRIMSeq + stageR (`#11053 `_) * add extensions to recent R easyconfigs: AICcmodavg + biomod2 (`#11030 `_), qqman (`#11052 `_), poLCA (`#11081 `_), coxed (`#11094 `_), testit + data.tree (`#11135 `_), celestial + fasterize (`#11206 `_) * add Config::Simple extension to Perl 5.30.x easyconfigs (`#11051 `_) * update TensorFlow v2.1.0 (`#11109 `_) and v2.0.0 (`#11233 `_) easyconfigs to provide more dependencies via EasyBuild * add CUDA compute capabilities to torchvision-0.5.0 (`#11241 `_) * various bug fixes, including: * patch to fix exporting images with PyQtGraph v0.10.0 (`#10848 `_) * add missing Python dependency to PETSc 3.11.1 (`#10907 `_) and PETSc 3.12.x (`#10908 `_) easyconfigs * use CMakeMake easyblock for installing magma to avoid C++11 related failures on POWER (`#10929 `_) * fix source URL for Graphviz v2.40.1 (`#10944 `_) * fix ``lapack.h`` for use with C++ in OpenBLAS 0.3.9 easyconfigs (`#10960 `_) * add missing build dep on M4 for 2019b versions of netCDF-Fortran (`#10972 `_) * update easyconfig for PyTorch 1.4 to use custom easyblock and run on POWER (`#11000 `_) * create symlinks to incorrectly named directories in OpenBabel-3.1.1 so ``$BABEL_LIBDIR`` and ``$BABEL_DATADIR`` work properly (`#11004 `_) * add missing Python build dep to recent ELPA easyconfigs (`#11011 `_) * use ``is_generic_easyblock`` from filetools in easyconfigs test suite (`#11020 `_) * fix sources in Portcullis v1.2.2 easyconfigs (`#11038 `_) * add patch for FFTW 3.3.8 to avoid use of ``-no-gcc`` when building with Intel compilers, to fix installation on CentOS 8 (cfr. `#10932 `_) (`#11050 `_) * add missing Python build dep for BEDTools 2.29.x (`#11054 `_) * add missing SciPy-bundle and Kent_tools (for bedPartition command) dependencies to FLAIR (`#11057 `_) * add patch to fix bug in LiBiS v20200428 easyconfig (`#11059 `_) * use FFTW provided via EasyBuild for ScaFaCoS (`#11060 `_) * fix undefined reference to ``qfloat16::mantissatable`` in Qt5.14.1 (`#11063 `_) * add alternative checksum for rstantools 2.0.0 extension (`#11081 `_) * update checksums for R 3.6.0 packages and add patch for ppc (`#11088 `_) * install scikit-learn 0.23.1 as a bundle and include required threadpoolctl extension (`#11089 `_) * update pybind11 easyconfigs to use custom easyblock to install with pip (`#11091 `_) * add recent six as extension to archspec installed on top of Python 3.7.4 (`#11092 `_) * add missing Seaborn dependency to LiBis easyconfig (`#11095 `_) * add missing dependencies for OpenPIV + switch to PythonBundle easyblock and include progressbar2 as extension (`#11096 `_) * add missing argparse dep to TEtranscripts easyconfig (`#11097 `_) * add missing pkg-config build dep in Octave 5.1.0 easyconfigs (`#11100 `_) * don't statically link MUSCLE, to avoid requiring that glibc-static is installed in OS (`#11102 `_) * add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs (`#11104 `_) * add patch to h5py 2.8.0 (`#11119 `_) and 2.9.0 (`#11118 `_) easyconfigs to avoid MPI_Init on ``import h5py`` * add patch to support libbfd 2.34 API change in Score-P 6.0 (`#11123 `_) * use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (`#11143 `_, `#11260 `_) * add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with ``foss*/2019b`` toolchain (`#11156 `_) * add missing pocl dependency in R 3.6.0 (`#11157 `_) * update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix aggressive RPATH stripping (`#11178 `_) * disable generating of man pages in recent libdrm easyconfigs to avoid installation failure if docbook-xsl is not installed (`#11182 `_) * add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with ``--rpath`` (`#11183 `_) * fix failing ``make check`` for MPFR 4.x (`#11187 `_) and GMP (`#11188 `_) when installing with ``eb --rpath`` * add pkg-config as a build dependency for libglvnd (`#11189 `_) * add missing libiconv dep in recent Doxygen easyconfigs (`#11191 `_, `#11257 `_) * enhance Java/11 wrapper to also support for aarch64/Arm (`#11192 `_) * add pkg-config as a build dependency to Ghostscript 9.52, needed on aarch64/arm (`#11194 `_) * add patch for pycrypto extension in recent Python easyconfigs to remove hardcoded ``/usr/include`` which causes problems when ``eb --sysroot`` is used (`#11202 `_) * fix installation of R v3.6.3 and v4.0.0 with foss/2020a on Arm (aarch64) (`#11213 `_) * update PyTorch 1.4 easyconfigs to use custom easyblock (and do less downloading during installations) (`#11219 `_) * other changes: * don't require custom ``sanity_check_paths`` for CUDA bundle easyconfigs (`#10936 `_) * move intervaltree and sortedcontainers to main Python easyconfigs (`#10969 `_, `#10970 `_) * disable qtwayland in Qt5 v5.14.1 (`#11107 `_) * remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 easyconfigs (`#11019 `_) * use pip to install h5py 2.10.0 (`#11044 `_) * stop testing easyconfig PRs with Travis, only use GitHub Actions from now on (`#11008 `_, `#11055 `_) * switch to Kent_tools built from source as dep for FusionCatcher (`#11057 `_) * fall back to using PR target branch when determining "merge base" between PR branch & target branch fails in test suite (`#11069 `_) * rename gtest to googletest (`#11082 `_) * rename sdsl-lite to SDSL (to use one single name) (`#11084 `_) * stop using ``remove_usr_bin`` patch in TensorFlow easyconfig, no longer required with updated TensorFlow easyblock (`#11087 `_) * extend timeout for libxc-4.3.4 to avoid failing tests (`#11126 `_) * move GitHub Actions status badge to top of README (`#11138 `_) * fix code style issues in test (`#11146 `_) * enable ``flake8`` on CI and fix issues (`#11147 `_) * prefer gc GitHub site for source downloads (`#11208 `_) * prefer ``https`` over ``ftp`` in ``source_urls`` of IgBLAST easyconfig (`#11244 `_) .. _release_notes_eb422: EasyBuild v4.2.2 (July 8th 2020) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for using ``sources`` and ``git_config`` for extensions in ``exts_list`` (`#3294 `_) * add support for software minver template (like ``%(pyminver)s``, etc.) (`#3344 `_, `#3345 `_) * add support for updating dictionary or tuple easyconfig parameters with ``self.cfg.update`` (`#3356 `_) * various bug fixes, including: * fix crash in ``--avail-easyconfig-constants`` when using ``--output-format=rst`` + ensure sorted output (`#3341 `_) * always take into account ``builddependencies`` when generating template values, also when we're not iterating over ``builddependencies`` (`#3346 `_) * fix running command as ``easybuild`` user in generated Singularity definition file (`#3347 `_) * allow ignoring ``versionsuffix`` in ``--try-update-deps`` (`#3350 `_, `#3353 `_) * retain order of paths when generating ``prepend_path`` statements for module file (don't sort them alphabetically) (`#3367 `_) * also put easyblocks used by extensions in ``reprod`` directory (`#3375 `_) * also copy template values in ``EasyConfig.copy`` method to ensure they are defined when installing extensions (`#3377 `_) * skip lines that start with ``module-version`` when determining whether a module exists in ``ModulesTool.exist`` (`#3379 `_) **easyblocks** * 3 new software-specific easyblocks: * LLVM (`#2065 `_), Scipion (`#1847 `_), XALT (`#1942 `_) * minor enhancements, including: * use ``wclean -platform`` instead of ``wcleanPlatform`` for OpenFOAM v2006 & newer (`#2088 `_) * various bug fixes, including: * only build OpenCV with IPP support on x86_64 systems (`#2056 `_) * make sure ``CFLAGS`` and ``MYCFLAGS`` are used in Lua easyblock (`#2062 `_) * also accept ``exist_lic`` as valid value for ``license_file`` in IntelBase easyblock (`#2067 `_) * fix minor bug in shared libs handling and correctly setup SuiteSparse variables in Trilinos easyblock (`#2071 `_) * make sure ``PythonBundle`` uses correct ``python`` command in extensions filter + also add ``lib64/python*/site-packages`` to ``$PYTHONPATH`` (if it exists) (`#2075 `_, `#2081 `_) * fix build environment for WRF by patching shebang in compile script (`#2079 `_) * fix order of ``intel64/lib`` paths in generated module for impi (and drop ``intel64/lib/release_mt``) (`#2080 `_) * set ``$XDG_CACHE_HOME`` to avoid abuse of ``$HOME/.cache/pip`` when installing DOLFIN (`#2082 `_) * make VMD easyblock Python 3 compatible (`#2083 `_) * rename include-fixed subdirectory in GCC installation to avoid problems after OS upgrade (`#2087 `_, `#2093 `_, `#2094 `_) * use glob pattern to determine name of Mathematica installation script (`#2089 `_) * use ``mpirun`` for sanity check commands in LAMMPS easyblock (`#2096 `_) **easyconfigs** * added easyconfigs for 2 new toolchains: * golf/2020a (`#10672 `_) * intel/2020.06, based on intel/2020a but with impi 2018 update 5 (`#10864 `_) * added example easyconfig files for 36 new software packages: * AmrPlusPlus (`#9919 `_), arrow (`#10882 `_), attrdict (`#10827 `_), Cartopy (`#10685 `_), dm-tree (`#10775 `_), dotNET-SDK (`#10661 `_), FLAIR (`#10860 `_), fastqsplitter (`#10706 `_), GLFW (`#10709 `_), git-extras (`#10440 `_), hl7apy (`#10728 `_), hyperopt (`#10735 `_), IgBLAST (`#10889 `_), IntelDAAL (`#9848 `_), ichorCNA (`#10595 `_), MARS (`#10691 `_), MITObim (`#10897 `_), MUST (`#10849 `_), mhcnuggets (`#9743 `_), PAUP (`#10830 `_), Percolator (`#10665 `_), PyBerny (`#10885 `_), poetry (`#10884 `_), pycocotools (`#10806 `_), python-hl7 (`#10673 `_), SHAPEIT4 (`#10814 `_), SYMPHONY (`#10058 `_), SunPy (`#10676 `_), sdsl-lite (`#10691 `_), TEtranscripts (`#10909 `_, `#10921 `_), Tombo (`#10646 `_), tensorboardX (`#10774 `_), Unidecode (`#10828 `_), WHAM (`#10736 `_), XALT (`#9792 `_), Xvfb (`#10512 `_) * added additional easyconfigs for various supported software packages, including: * Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, Blitz++ 1.0.2, Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10, dask 2.18.1, Elk 6.3.2, GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6, geopandas 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0, IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, MATIO 1.5.17, MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 2.10.5, NiBabel 3.1.0, Nipype 1.4.2, ncbi-vdb 20.10.7, numba 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006, PDT 3.25.1, PRSice 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2, Pysam 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1, ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 1.3.959, SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, Seaborn 0.10.1, Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, StringTie 2.1.3, scikit-allel 1.2.1, scikit-learn 0.23.1, snpEff 4.3t, Valgrind 3.16.1, VarScan 2.4.4, vsc-mympirun 5.1.0, WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0 * minor enhancements, including: * add extensions to R 4.0.0 easyconfig: drgee + stdReg (`#10833 `_), copCAR (`#10911 `_), ngspatial (`#10913 `_), drugCombo (`#10914 `_) * add extensions to R-bundle-Bioconductor 3.11 easyconfig: BSgenome.Cfamiliaris.UCSC.canFam3 (`#10840 `_), SingleR (`#10904 `_) * include extra extension and support for MPI in MAFFT v7.453 and v7.470 (`#10853 `_) * add Array::Transpose to Perl (`#10878 `_) * various bug fixes, including: * fix dependencies and configuration of CoinUtils ecosystem (`#10450 `_) * fix Togl configure patch so that it completely ignores ``TCL_SRC_DIR`` and ``TK_SRC_DIR`` (`#10662 `_) * change Xerces-C++ to official CMakeMake build (fixes missing links to curl) (`#10664 `_) * add ``-fPIC`` to ``toolchainopts`` in easyconfig for Lua 5.3.5 with system toolchain (`#10671 `_) * remove hardcoded X86 target in LLVM easyconfigs (`#10677 `_) * switch to https ``homepage`` and ``source_urls`` in libGLU easyconfigs (`#10686 `_) * add patch for h5py 2.10.0 to avoid triggering ``MPI_Init`` at import (`#10687 `_) * add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (`#10692 `_) * update UDUNITS ``source_urls`` to https sources (`#10693 `_) * add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (`#10695 `_, `#10697 `_) * add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (`#10710 `_) * add M4 builddependency to SuiteSparse 2019b easyconfigs (`#10720 `_) * make sure WHAM is built with correct compiler (`#10736 `_) * define ``MAX_JOBS`` in easyconfigs of PyTorch from v1.1.0 to v1.4.0 (`#10772 `_) * add dm-tree and lz4 as dependencies to Ray v0.8.4 (`#10775 `_) * fix source URL in recent ant easyconfigs (`#10790 `_) * bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in Bioconductor 3.11 bundle, since sources for old versions have disappeared (`#10791 `_) * add patch to Armadillo easyconfigs using the foss toolchain to prevent it from picking up MKL if installed system-wide (`#10812 `_) * add missing kerneltree extension in FLAIR easyconfig (`#10860 `_) * fix source URLs in Eigen 3.2.* (`#10872 `_) and 3.3.* (`#10869 `_) easyconfigs * refer to issue in GitHub repo in configparser patch, since Bitbucket repo is disappearing (`#10873 `_) * switch to github.com source URL for MetaPhlAn (`#10874 `_) * switch to GitHub sources for ScientificPython 2.9.4 (`#10875 `_) * switch to GitHub source URL for HPDBSCAN (`#10876 `_) * download x265 3.2/3.3 sources from ``bitbucket.org/multicoreware/x265_git`` (`#10905 `_) * fix download URL for libatomic in gc 7.6.12 easyconfigs (`#10915 `_) * fix ``sanity_check_paths`` in CFITSIO-3.48-GCCcore-9.3.0.eb easyconfig (`#10917 `_) * add missing dependencies for geopandas 0.7.0 (`#10923 `_) * other changes: * rename OpenPyXL 2.6.4 easyconfig to openpyxl (`#10916 `_) .. _release_notes_eb421: EasyBuild v4.2.1 (May 20th 2020) -------------------------------- bugfix/update release **framework** * various enhancements, including: * also mention CPU architecture (x86_64, POWER) in comment for test reports (`#3281 `_) * add support for enhancing existing sanity check in easyconfigs, as opposed to overwriting paths/commands (`#3288 `_) * clean up locks when EasyBuild session is cancelled with a signal like ``SIGTERM`` (`#3291 `_, `#3321 `_) * add ``find_glob_pattern`` function to ``filetools`` module (`#3297 `_) * add constants for common OS dependencies (``OS_PKG_IBVERBS_DEV``, ``OS_PKG_OPENSSL_DEV``, ...) (`#3309 `_, `#3334 `_) * flesh out ``get_mpi_cmd_template`` function from ``Mpi.mpi_cmd_for`` method (`#3312 `_) * add variable ``moddependpaths`` to specify extra ``$MODULEPATH`` entry to consider for loading dependency modules (`#3324 `_) * allow copying of tweaked easyconfigs when using ``--try-*`` with ``--copy-ec`` (`#3332 `_) * various bug fixes, including: * make ``ModulesTool.exist`` more robust w.r.t. module wrappers, aliases, defaults, etc. (`#3216 `_, `#3337 `_) * clean up rst output of ``--list-toolchains`` (`#3246 `_) * cast CPU arch name provided by archspec to a regular string (`#3286 `_) * get ``pr_title`` and ``pr_descr`` build_options in ``new_pr_from_branch`` instead of ``new_pr`` (and commit_msg in both) (`#3298 `_) * make ``pypi_source_urls`` more robust by using ``HTMLParser`` rather than ``xml.etree.ElementTree`` (`#3303 `_, `#3329 `_) * fix broken test for ``--include-easyblocks-from-pr`` (`#3304 `_) * don't use ``distutils.dir_util`` in ``copy_dir`` (`#3310 `_) * print trace message for sanity check command before running it (`#3316 `_) * fix problems with processing of easyconfigs using a Cray* toolchain when there are no actual external modules (`#3319 `_) * make ``test_find_eb_script`` more robust in case ``$EB_SCRIPT_PATH`` is already set (`#3320 `_) * fix several small problems with ``--try-update-deps`` (experimental feature) (`#3325 `_, `#3326 `_, `#3330 `_) * add ``--disable-job`` in ``eb`` command used in jobs, to prevent infinite job cycle (`#3328 `_) * avoid empty entries in ``$LD_LIBRARY_PATH`` and other path-like environment variables (`#3333 `_) * other changes: * fix code style issues in ``easybuild.tools`` + add ``flake8`` linting test (`#3282 `_) * introduce ``contextmanager`` for disabling templating and reduce resolving errors (`#3287 `_) * add ``change_into_dir`` named argument to ``extract_file`` + print deprecation warning if it's not specified (`#3292 `_) * improve ``install_eb_dep.sh`` script to install EasyBuild dependencies in CI environment (`#3314 `_) **easyblocks** * add generic easyblock for installing Go packages: ``GoPackage`` (`#2042 `_) * minor enhancements, including: * update ``config.guess`` for all R packages, required installing R + extensions on Linux/POWER systems (`#1949 `_) * add support for ``preinstallopts`` and install in subdirectory to ``Tarball`` generic easyblock (`#1989 `_, `#2049 `_) * rewrite ``GROMACS`` easyblock to install all four variations (single/double precision, with/without MPI) in the same directory (`#1991 `_) * add custom ``subdir_version`` easyconfig parameter for FLUENT (`#2021 `_) * use updated ``config.guess`` in ``GCC`` easyblock (`#2033 `_, `#2059 `_) * add extra question pattern to support installing CPLEX 12.10 (`#2038 `_) * add support for building NWChem on top of external GlobalArrays + also define ``$LAPACK_LIB`` (required for NWChem 7.x) (`#2043 `_) * execute minimal test in sanity check commands in ``impi`` easyblock (`#2045 `_) * update for ``MotionCor2`` easyblock for v1.3.1 (`#2046 `_) * fixes + enhancements for ``PETSc`` easyblock (`#2048 `_) * various bug fixes, including: * use correct version in ``ELPA`` preprocessor flag used for QuantumESPRESSO v6.x (`#2027 `_) * generically find the arch folder and add top-level bin/lib symlinks in ``PDT`` & ``TAU`` easyblocks (`#2029 `_) * fix typo in ``LAMMPS`` easyblock preventing disabling the ``USER-INTEL`` package via ``configopts`` (`#2031 `_) * let ``CMakeMake`` remove ``easybuild_obj`` build directory if it already exists (`#2032 `_) * include own lib dir in ``RPATH`` before system lib dirs in ``binutils`` easyblock (`#2044 `_) * clean ``$CPATH`` before building ROOT to avoid clash between external LLVM loaded as a dependency and internal LLVM used by ROOT (`#2047 `_) * don't let ``extract_file`` change directory in various easyblocks (`#2051 `_) * make ``postinstallcmds`` available to Mathematica easyconfigs + add bin/Executables to ``$PATH`` (`#2052 `_) * fix the extra dirs added to PATH in ``FreeSurfer`` easyblock (`#2053 `_) * correct download url for test data in ``WPS`` easyblock (`#2055 `_) * fix typo in warning in ``TensorFlow`` easyblock (`#2057 `_) * fix failing sanity check under ``--module-only`` in ``GCC`` easyblock (`#2059 `_) * other changes: * add configure options for CubeLib/CubeWriter dependencies in ``Score-P`` easyblock (`#2030 `_) * remove local ``find_glob_pattern`` in ``Blender`` & ``ROOT`` easyblocks, use function provided by ``filetools`` instead (`#2037 `_) **easyconfigs** * added easyconfigs for new common toolchains: foss/2020a (`#10483 `_, `#10492 `_), intel/2020a (`#10494 `_) * added example easyconfig files for 66 new software packages: * Alpha (`#9994 `_), antiSMASH (`#10589 `_), Arlequin (`#10620 `_), artic-ncov2019 (`#10459 `_), augur (`#10405 `_), AutoMap (`#10419 `_), Bio-EUtilities (`#10037 `_), CaSpER (`#10593 `_), cdbfasta (`#10547 `_), cddlib (`#10429 `_), CoCoALib (`#10429 `_) dftd3-lib (`#10351 `_), DoubletFinder (`#10603 `_), E-ANTIC (`#10429 `_), FastViromeExplorer (`#10571 `_), FIX (`#8870 `_), FusionCatcher (`#10134 `_), geopandas (`#10322 `_), goalign (`#10469 `_), gotree (`#10459 `_), gretl (`#10413 `_), harmony (`#10604 `_), HDF-EOS (`#10534 `_), HDF-EOS5 (`#10536 `_), HMMER2 (`#10588 `_), HyPo (`#10642 `_), king (`#10365 `_), libdeflate (`#10459 `_), libfabric (`#10616 `_), libgit2 (`#10453 `_), libuv (`#10444 `_), mbuffer (`#10524 `_), MDAnalysis (`#10545 `_), MEM (`#10605 `_), MESS (`#10597 `_), metaerg (`#10037 `_), MinCED (`#10037 `_), MitoZ (`#7735 `_), nauty (`#10429 `_), nifti2dicom (`#10598 `_), NLMpy (`#10029 `_), ntCard (`#10502 `_), NTL (`#10431 `_), pIRS (`#10508 `_), popscle (`#10550 `_), ProtHint (`#10549 `_), protozero (`#10495 `_), pysndfx (`#10452 `_), PyVCF (`#10564 `_), PyWavelets (`#10501 `_), rampart (`#10459 `_), rickflow (`#10641 `_), RNA-Bloom (`#10502 `_), root_numpy (`#10424 `_), rstudio (`#10619 `_), ScaFaCoS (`#10537 `_), Scythe (`#10524 `_), SDSL (`#10642 `_), SHAP (`#10379 `_), SNPomatic (`#10524 `_), SoX (`#10452 `_), swissknife (`#10037 `_),) Taiyaki (`#10573 `_), TCLAP (`#10598 `_), torchaudio (`#10516 `_), wtdbg2 (`#10524 `_) * added additional easyconfigs for various supported software packages, including: * ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4, CPLEX 12.10, CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 2.17.0, expat 2.2.9, FFmpeg 4.2.2, FriBidi 1.0.9, GATK 4.1.5.0, GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 6.2.0, GROMACS 2020.1, GTK+ 3.24.17, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2, gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1, IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1, libarchive 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 2.0.4, librsvg 2.48.4, libsigsegv 2.12, lrslib 7.0a, MEME 5.1.1, MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 1.3.1, MultiQC 1.8, matplotlib 3.2.1, NGS-Python-2.10.4, NGS 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1, Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1, OpenMPI 4.0.3, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PLUMED 2.6.0, PMIx 3.1.5, PROJ 7.0.0, Perl 5.30.2, Pillow 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 5.14.1, R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3, rioxarray 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 2.0.10, SIONlib 1.7.6, SQLite 3.31.1, SRA-Toolkit 2.10.4, Salmon 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, StringTie 2.1.1, SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2, tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12, wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, zstd 1.4.4 * minor enhancements, including: * add additional extensions for recent versions of R (`#10359 `_, `#10585 `_, `#10586 `_, `#10621 `_) and R-bundle-Bioconductor (`#10585 `_, `#10596 `_, `#10621 `_) * add additional extensions for recent versions of Perl (`#10412 `_, `#10546 `_, `#10623 `_) * include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(`#10458 `_) * include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (`#10464 `_) * add alternate checksum for EMBOSS (`#10607 `_) * various bug fixes, including: * fix incorrect checksums for Amber patches (`#8870 `_) * add patches to fix installation of R 3.6.2 on POWER (`#9830 `_) * add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) * add Perl as a build dependency for recent Autoconf/Automake easyconfigs (`#10408 `_, `#10426 `_) * fix source_urls in ICU easyconfigs (`#10417 `_) * disable ``USER-INTEL`` package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (`#10418 `_) * fix undefined reference to ``qfloat16::mantissatable`` in Qt5-5.13.1-GCCcore-8.3.0 (`#10425 `_) * get rid of double '-' in versionsuffix of torchtext easyconfig (`#10472 `_) * fix broken Mako easyconfigs (`#10480 `_, `#10627 `_) * move builddependencies to dependencies in OTF2 and Score-P easyconfigs (`#10496 `_) * add missing cURL dep for LAMMPS (`#10527 `_) * add Python 2 build dependency for OpenPGM (`#10539 `_) * use ``OS_PKG_IBVERBS_DEV`` constant for OS dependency in PyTorch 1.4.0 easyconfigs (`#10540 `_) * add missing Bison build dep in Graphviz easyconfigs (`#10541 `_) * use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (`#10559 `_) * add missing PyVCF dependency for BAMSurgeon (`#10564 `_) * remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (`#10565 `_) * fix ITK v5.0.1 easyconfig w.r.t. locale and location of libjpeg-turbo library (`#10592 `_) * add patch to fix missing ``const`` qualifiers for ncurses (`#10606 `_) * fix OS dependency for rstudio for Debian-based systems (`#10608 `_) * fix Rmath paths in easyconfig for FastQTL v2.184 (`#10612 `_) * add symlink for Arlequin commands + fix sanity check commands (`#10620 `_) * fix recent binutils easyconfigs using system toolchain for Fedora 32 / GCC 10 (`#10633 `_) * replace '/path/to' with actual installation prefix in FuSeq scripts (`#10640 `_) * other changes: * check sdist with different Python versions in CI (`#10388 `_) * use Bison 3.3.2 as build dep for flex 2.6.4 (`#10403 `_) * mention ``http://`` Pfam website rather than ``ftp://`` in load message of BiG-SCAPE easyconfig (`#10439 `_) * archive old Singularity configs (`#10591 `_) * Singularity is not well suited to install via EasyBuild because it requires admin privileges to enable setuid * stop using old hpcugent URL for cloning framework/easyblocks repos in CI (`#10635 `_) * use ``SYSTEM`` constant for toolchain in easyconfigs already use ``system`` toolchain (`#10638 `_) .. _release_notes_eb420: EasyBuild v4.2.0 (April 14th 2020) ---------------------------------- feature release **framework** * add support for ``--try-update-deps`` (experimental feature), to upgrade dependencies based on available easyconfigs (`#2599 `_) * adding locking to prevent two parallel builds of the same installation directory (`#3009 `_) * for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html * significantly speed up ``-D/--dry-run`` by avoiding useless '``module show``' (`#3203 `_) * add support for creating an index & using it when searching for easyconfigs (`#3210 `_) * for more information, see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html * additional GitHub integration features: * add support for targeting easyblocks and framework repositories in ``--new-pr`` (`#1876 `_, `#3189 `_) * add support for ``--include-easyblocks-from-pr`` (`#3206 `_) * for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html * various other enhancements, including: * add a contrib/hooks dir with some examples of hooks used (`#2777 `_) * also mention working directory + input passed via stdin (if any) in trace output of ``run_cmd`` (`#3168 `_) * probe external modules for missing metadata that is not provided via extermal module metadata file (`#3174 `_) * also update ``$CMAKE_PREFIX_PATH`` and ``$CMAKE_LIBRARY_PATH`` in generated module file (`#3176 `_) * optionally call ``log.warning`` in ``print_warning`` (`#3195 `_) * add an option to ``git_config`` to retain the ``.git`` directory (`#3197 `_) * allow use of ``SYSTEM`` as ``--try-toolchain`` option (`#3213 `_) * mention CPU arch name in comment for uploaded test report, if it's known by ``archspec`` (`#3227 `_) * make ``--merge-pr`` take into account ``--pr-target-branch`` (`#3236 `_) * make ``--check-contrib`` print a warning when ``None`` is used for checksums (`#3244 `_) * update ``install-EasyBuild-develop.sh`` script and create script for 2020a merge sprint (`#3245 `_) * add template for ``mpi_cmd_prefix`` (`#3264 `_) * update ``copy_dir`` to include option to merge directories (`#3270 `_) * support template name for CUDA version (`#3274 `_) * various bug fixes, including: * use correct module for ``errors_found_in_log`` (`#3119 `_) * fix ``EasyConfig.update`` code to handle both strings and lists as input (`#3170 `_) * fix removing temporary branch on ``--check-github`` (`#3182 `_) * fix shebang even if first line doesn't start with '``#!``' (`#3183 `_) * make bootstrap script work with Python 3 (`#3186 `_) * read patch files as bytestring to avoid ``UnicodeDecodeError`` for patches that include funky characters (`#3191 `_) * fix online check in ``--check-github``: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) * don't crash when GitPython is not installed when using Python 3 (`#3198 `_) * fix ``os_name_map`` for RHEL8 (`#3201 `_) * don't add shebang to binary files (`#3208 `_) * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#3219 `_) * don't filter out ``None`` values in to_checksums, leave them in place (`#3225 `_) * fix defining of ``$MPI_INC_*`` and ``$MPI_LIB_*`` environment variables for impi version 2019 and later (`#3229 `_) * use correct target account/repo when creating test report & posting comment in PR (`#3234 `_) * reorganize ``EasyBlock.extensions_step`` to ensure correct filtering of extensions (`#3235 `_) * also support ``%(installdir)s`` and ``%(builddir)s`` templates for extensions (`#3237 `_) * unset ``$GITHUB_TOKEN`` in Travis after installing token, to avoid failing ``test_from_pr_token_log`` (`#3252 `_) * fix reporting when skipping extensions (`#3254 `_) * avoid API rate limit errors on online check in ``--check-github`` (`#3257 `_) * show easyconfig filenames for parallel build (`#3258 `_) * make ``EasyConfig.dump`` aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (`#3261 `_) * fix use of ``--copy-ec`` with a single argument, assume copy to current working directory (`#3262 `_) * fix posting of comment in PR with ``--upload-test-report`` (`#3272 `_) * take into account dependencies marked as external modules when composing template values like ``%(pyver)s`` (`#3273 `_) * other changes: * increase timeout & use ``api.github.com`` for connectivity check in ``check_github`` (`#3192 `_) * restore ``flake8`` default ignores (`#3193 `_) * enable tracking of test suite coverage using coveralls (`#3204 `_) * make tests use ``easybuilders/testrepository`` rather than ``hpcugent/testrepository`` after it was moved (`#3238 `_) * improve raised error in ``remove_dir`` and deprecate ``rmtree2`` (`#3228 `_) **easyblocks** * 7 new software-specific easyblocks: * BerkeleyGW (`#1951 `_), CMake (`#1936 `_), ELSI (`#1883 `_), LAMMPS (`#1964 `_, `#1975 `_, `#1978 `_, `#1982 `_, `#1997 `_), libdrm (`#1983 `_), Mesa (`#1892 `_, `#2006 `_), SEPP (`#1998 `_) * minor enhancements, including: * make ParMETIS easyblock compatible with custom ``configopts`` (`#1774 `_) * update Trinity easyblock for v2.9.0 (`#1906 `_) * disable ROCM and Android workspace explicitly in TensorFlow easyblock (`#1944 `_) * update QuantumESPRESSO easyblock for version 6.5 (`#1947 `_) * update Siesta easyblock to support MaX-1.0 release (`#1954 `_) * update Ferret easyblock for versions >= 7.5.0 (`#1956 `_) * update XCrySDen easyblock to support Togl dependency (`#1959 `_) * pass value for ``TARGET`` specified in ``buildopts`` to ``testopts`` and ``installopts`` in OpenBLAS easyblock (`#1960 `_) * fix netCDF(-Fortran) support in Siesta easyblock (`#1967 `_, 1971) * add ``NCDF_PARALLEL`` and METIS support to Siesta easyblock (`#1973 `_) * add support for ``use_pip_extras`` custom easyconfig parameter in ``PythonPackage`` easyblock (`#1980 `_) * update Open Babel easyblock for version 3.0.0 (`#1992 `_) * allow differing names for TensorFlow wheel (`#1995 `_) * make MATLAB runtime available from MATLAB (`#2008 `_) * various bug fixes, including: * fix linking of Hypre to external BLAS/LAPACK + support building (only) static/shared library (`#1885 `_) * fix MPI-CXX dependency of PETSc (`#1917 `_) * limit amount of parallelism in TensorFlow easyblock (`#1934 `_) * support GCCcore and gcc4.8 (if that dir exists) in function ``get_tbb_gccprefix`` in tbb easyblock (`#1943 `_) * restore default ``flake8`` warnings (`#1950 `_) * remove tests from ``build_step`` and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) * add optional ``runtest`` to the catch for ``FATAL ERRORS`` to OpenBLAS easyblock (`#1958 `_) * ensure right '``python``' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) * make sure ``lib/python*/lib-dynload`` exists in Python installation (`#1966 `_) * in version 6.0 of TensorRT, ``libnvinfer.a`` is renamed ``libnvinfer_static.a`` (`#1970 `_) * handle ``configopts`` without configure args in CMake easyblock (`#1974 `_) * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#1976 `_) * don't insist that pylibdir always exists in OpenCV easyblock (`#1977 `_) * also set ``$TRINITY_HOME`` environment variable in Trinity easyblock (`#1979 `_) * fix sanity check for OpenFOAM-Extend >= 4.1 (`#1981 `_) * fix pattern matching in regex subst for ``I_MPI_ROOT`` in impi easyblock (`#1986 `_) * use ``remove_dir`` instead of deprecated ``rmtree2`` in various easyblocks (`#1993 `_) * fix "``AttributeError: module 'git' has no attribute 'Git'``" that may occur when using Python 3 (`#1994 `_) * don't sanity check for ``QtWebEngine`` in Qt easyblock when building for POWER (`#2000 `_) * fix installation of TensorFlow in some environments, by setting ``$PYTHONNOUSERSITE`` (& more) (`#2002 `_, `#2020 `_) * make sure libxml2 is built with XZ provided as dependency (`#2005 `_) * look for Python version directories with suffixes in ROOT easyblock (`#2010 `_) * enable TK, FLTK and OPENGL configure options in VMD easyblock (`#2013 `_) * update the contributing docs (`#2014 `_) * fix numexpr easyblock to allow (correctly) installing it as extension (`#2022 `_) * other changes: * simplify various CMakeMake-based easyblocks by enhancing ``CMakeMake`` (w.r.t. ``CMAKE_BUILD_TYPE``, shared vs static libs, ``-fPIC``) (`#1929 `_) * enable out of tree build by default in ``CMakeMake`` easyblock (`#1933 `_) * force building Clang without CUDA when it is not found as a proper dependency (`#1968 `_) **easyconfigs** * added example easyconfig files for 114 new software packages: * ABRA2 (`#10272 `_), ABRicate (`#10310 `_), ADIOS (`#10036 `_), aNCI (`#9929 `_), any2fasta (`#10310 `_), apex (`#10269 `_), archspec (`#9898 `_), ArviZ (`#10366 `_), autopep8 (`#9626 `_), BAMSurgeon (`#10330 `_), BatMeth2 (`#10323 `_), BiG-SCAPE (`#10352 `_), BinSanity (`#10001 `_), Bonito (`#10269 `_), BSMAPz (`#10283 `_), BSseeker2 (`#10039 `_), BUStools (`#9838 `_), Cbc (`#10052 `_), Cgl (`#10048 `_), CGmapTools (`#10288 `_), Clp (`#10033 `_), CoinUtils (`#9937 `_), dtcwt (`#9695 `_), ELSI (`#9857 `_), EnsEMBLCoreAPI (`#8734 `_), fastq-pair (`#9894 `_), FigureGen (`#10076 `_), Fiona (`#10321 `_), FuSeq (`#10004 `_), GenomeTools (`#9797 `_), GraphMap2 (`#10299 `_), GRASP (`#9896 `_), Groovy (`#9809 `_), gsport (`#9821 `_), gubbins (`#9689 `_), igv-reports (`#9977 `_), inferCNV (`#9686 `_), iVar (`#10291 `_), joypy (`#10212 `_), JupyterLab (`#9752 `_), kma (`#10259 `_), LAMMPS (`#10371 `_), lancet (`#10271 `_), libBigWig (`#10006 `_), libGridXC (`#9858 `_), libPSML (`#5859 `_), LtrDetector (`#10343 `_), manta (`#5104 `_), medImgProc (`#10228 `_), MedPy (`#9748 `_), Mini-XML (`#10036 `_), mkl_fft (`#9887 `_), Monocle3 (`#9825 `_), MoreRONN (`#10255 `_), motionSegmentation (`#10228 `_), NanoComp (`#10212 `_), NanoFilt (`#10212 `_), nanoget (`#10212 `_), nanomath (`#10212 `_), NanoPlot (`#10212 `_), ngspice (`#9922 `_), ntEdit (`#9836 `_), ntHits (`#9833 `_), occt (`#9939 `_), OCNet (`#9955 `_), OpenAI-Gym (`#10347 `_), OpenPIV (`#9959 `_), OpenPyXL (`#10115 `_), orca (`#9518 `_), Osi (`#10361 `_), PartitionFinder (`#9983 `_), pauvre (`#10212 `_), polymake (`#9904 `_), pretty-yaml (`#10041 `_)), PRSice (`#9988 `_), pycodestyle (`#9626 `_), pydot (`#9899 `_), pygraphviz (`#9969 `_), pylift (`#10051 `_), PyMC3 (`#10279 `_), pyparsing (`#9983 `_), PyRe (`#10095 `_), python-weka-wrapper3 (`#9704 `_), PyTorch-Geometric (`#9995 `_), qcat (`#10244 `_), RAxML-NG (`#9990 `_), Ray (`#10302 `_), rclone (`#7934 `_), Red (`#9856 `_), rstanarm (`#9964 `_), scikit-build (`#9762 `_), scVelo (`#9805 `_), SECAPR (`#9721 `_), segmentation-models (`#10211 `_), SentencePiece (`#10192 `_), SEPP (`#10047 `_), Shapely (`#10309 `_), Singular (`#10030 `_), SLATEC (`#7529 `_), spatialreg (`#9767 `_), split-seq (`#9749 `_), spoa (`#9705 `_), SSN (`#9955 `_), STEAK (`#10337 `_), stpipeline (`#9736 `_), SVG (`#9905 `_), Togl (`#9868 `_), torchtext (`#10193 `_), units (`#9682 `_), UQTk (`#10279 `_), WildMagic (`#10044 `_), Winnowmap (`#10005 `_), xtb (`#9993 `_), Zip (`#9972 `_) * added additional easyconfigs for various supported software packages, including: * ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34, CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8, DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1, GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020, GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1, gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1, Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166, ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045, LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453, MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0, Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1, Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11, PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1, pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3 Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0, SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0, SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0, TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2, tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4 * minor enhancements, including: * add easyconfig for Java 11.0.6 on ``ppc64le`` and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_) * add additional extensions for R: ``HiddenMarkov`` (`#9685 `_), ``lmerTest`` (`#9853 `_), ``VSURF`` + ``Rborist`` (`#10355 `_) * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_) * build shared libs and install header files for Ghostscript (`#9785 `_) * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (`#9880 `_, `#9891 `_) * add Perl extensions: ``Term::ReadLine::Gnu`` (`#9901 `_), ``URI::Escape`` and ``Set::IntervalTree`` (`#10049 `_) * add dat directory to aNCI (`#9929 `_) * add patch to create a symlink from ``libsvm.so.$(SHVER)`` to ``libsvm.so`` in LIBSVM easyconfigs (`#10045 `_) * build SUNDIALS with '``pic``' (`#10278 `_) * add ``BSgenome.Hsapiens.UCSC.hg38`` + ``MEDIPS`` extensions to R-bundle-Bioconductor v3.10 (`#10298 `_) * fix checksums for ``mkl-dnn`` and ``tbb`` extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_) * update ``Java/1.8`` wrapper to ``Java/1.8.0_241.eb`` (`#10305 `_) * various bug fixes, including: * use CMake for building double-conversion (`#9659 `_) * update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (`#9694 `_) * add alternate checksum for OpenMolcas 18.09 (`#9701 `_) * use Github to download releases for MariaDB-connector-c (`#9702 `_) * add ``-DOMPI_SKIP_MPICXX`` in ``configopts`` for MathGL, to avoid using mpicxx during build (`#9703 `_) * make installing independent of build folder in pybind11 easyconfig (`#9738 `_) * add Lua as a dependency to gnuplot (`#9773 `_) * stick to ``http://`` source URLS for ISL in GCCcore easyconfigs, since ``https://`` doesn't work (`#9784 `_) * add alternative checksums for ``farver``/``fracdiff``/``pkgmaker``/``rngtools``/``doRNG``/``cobs`` extensions in R 3.6.2 easyconfigs (`#9789 `_) * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_) * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_) * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_) * add missing ``sanity_check_commands`` to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_) * don't overwrite ``configopts`` in BLAST+ easyconfigs, append to it (`#9875 `_) * add alternate checksum for ``LaplacesDemon`` in R 3.6.x easyconfigs (`#9879 `_, `#10382 `_) * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_) * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_) * fix NCIPLOT build flags (`#9915 `_) * add missing patch to iccifort libxc easyconfigs (`#9918 `_) * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#9925 `_) * re-enable building utils in Siesta 4.1-MaX-1.0 release (`#9936 `_) * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_) * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_) * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_) * patch GCC ``lisanitizer`` for glibc 2.31 (`#9966 `_) * add Zip as build dependency for recent Bazel versions (`#9972 `_) * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_) * fix source URLs for ParMGridGen easyconfigs (`#10019 `_) * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_) * fix sources for LS-PrePost 4.6 (`#10236 `_) * security update for vsc-mympirun 4.1.9 (`#10185 `_) * configure libwebp to also install ``libwebpmux`` (`#10274 `_) * ensure that CVS easyconfigs are included in source tarball produced by '``python setup.py sdist``' (`#10326 `_) * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_) * fix source_urls for tbb: use (new) official '``oneapi-src``' GitHub repository (`#10361 `_) * update checksums and homepage in tbb easyconfigs (`#10285 `_) * other changes: * use new custom easyblock in recent CMake easyconfigs (`#9871 `_, `#9923 `_) * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_) * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_) * use ``https://`` in ``homepage``/``source_urls`` of ``zlib-1.2.11.eb`` (`#10018 `_) * add ``-GCCcore-9.2.0`` versionsuffix for ``intel/2020.00`` components (`#10083 `_) * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_) * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_) .. _release_notes_eb412: EasyBuild v4.1.2 (March 16th 2020) ---------------------------------- bugfix release .. note:: This release includes a bug fix for the leaking of your GitHub token in the EasyBuild (debug) log file. **We strongly encourage that you revoke the GitHub tokens you are using currently, via** https://github.com/settings/tokens, **and to replace them using a new token (using** ``eb --install-github-token --force`` **).** More information in https://github.com/easybuilders/easybuild-framework/pull/3248 . **framework** * fix gitdb dependency on Python 2.6 in test configuration (`#3212 `_) * fix broken test for --review-pr by using different PR to test with (`#3226 `_) * censor authorization part of headers before logging ReST API request (`#3248 `_) **easyblocks** *(no changes)* **easyconfigs** *(no changes)* .. _release_notes_eb411: EasyBuild v4.1.1 (January 16th 2020) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add ``check_log_for_errors`` function (in ``easybuild.tools.run``) to detect and handle multiple errors (`#3118 `_) * implement support for ``eb --show-ec`` to show contents of specified easyconfig file (`#3132 `_) * also update ``$XDG_DATA_DIR`` (share/) and ``$GI_TYPELIB_PATH`` environment variables (lib*/girepository-*) in generated module files (`#3133 `_) * add support for ``--copy-ec`` to copy easyconfig file to specified location (`#3142 `_) * mention ``--disable-*`` option in ``--help`` output for boolean options enabled by default (`#3151 `_) * add ``--cuda-compute-capabilities`` configuration option (`#3161 `_) * various bug fixes, including: * ignore imports from ``vsc`` namespace made from pkgutil.py (`#3120 `_) * only actually change permissions using ``os.chmod`` in ``adjust_permissions`` if the current permissions are not correct already (`#3125 `_) * use ``shutil.copyfile`` to just copy file contents if target path exists and is owned by someone else (`#3127 `_) * fix or avoid warnings that commonly arise in build log (`#3129 `_) * disable buffering in ``asyncprocess.Popen`` using ``bufsize=0``, to fix ``run_cmd_qa`` missing output (`#3130 `_) * update pip & install wheel package in generated Singularity container recipes (`#3136 `_) * avoid crash in ``modify_env`` & unset ``unset_env_vars`` when using (older versions) of Python 3.5 & 3.6 by using ``list(...)`` (`#3140 `_) * take into account that lib64 could be a symlink to lib (or vice versa) in ``get_software_libdir`` function (`#3141 `_) * only parse docstring if it exists in ``gen_easyblock_doc_section_rst`` function (`#3144 `_) * only add useful entries for ``$CPATH``, ``$(LD_)LIBRARY_PATH`` and ``$PATH`` (non-empty directories) (`#3145 `_, `#3152 `_) * fix ``--list-software=detailed`` when using Python 3 by leveraging ``sort_looseversions`` function from ``py2vs3`` module (`#3146 `_) * ensure subdirectories in software install directory have correct search (exec) permission (`#3147 `_) * take into account that a checksum value may be a tuple of valid checksum in ``EasyBlock.check_checksums`` (`#3153 `_) * other changes: * bump to Lmod 8.2.9 in GitHub CI config (`#3115 `_) * update copyright statements for 2020 (`#3149 `_) * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#3162 `_) **easyblocks** * new software-specific easyblock for cryptography (to fix missing ``-pthread`` for all versions) (`#1874 `_) * minor enhancements, including: * update WPS easyblock for v3.6 & newer (`#1315 `_) * update FSL easyblock to support FSL v6.0.2 & newer (`#1860 `_) * add ``setup_cmake_env`` function in CMakeMake easyblock which can be leveraged in other easyblocks, and use it for OpenFOAM (`#1869 `_) * remove obsolete configure options for Python + build with optimizations/LTO enabled for recent Python versions (`#1876 `_) * update WPS easyblock for recent versions: set ``$WRF_DIR`` to point to location of WRF installation (`#1886 `_) * make sure ``$LIBLAPACK_MT`` is set before using it in ESMF easyblock (`#1887 `_) * remove useless ``PATH`` entries + add ``PKG_CONFIG_PATH`` in imkl easyblock (`#1900 `_) * enhance tbb easyblock to support building on POWER (`#1912 `_) * enhance TensorFlow easyblock to pick up on ``--cuda-compute-capabilities``, and issue a warning if no CUDA compute capabilities are specified (`#1913 `_) * add custom easyconfig parameter ``build_type`` to generic CMakeMake easyblock (`#1915 `_, `#1922 `_) * various bug fixes, including: * fix for conda packages that rely on particular versions of Python (`#1836 `_) * fix path for intel and netCDF lib directories in NCL easyblock (`#1862 `_) * fix CUDA 10.1 installation on POWER (`#1871 `_) * change Bazel easyblock to prefer using Java dependency rather than included JDK (fix for POWER9) (`#1875 `_) * remove optarch warning in GROMACS for Cray toolchains (`#1879 `_) * also fix ``$WM_COMPILE_OPTION`` in OpenFOAM rc scripts to make debug builds work correctly (`#1880 `_) * limit MPI ranks used for running WRF test cases to max. 4 + include contents of rsl.error.0000 output file in case test failed (`#1884 `_) * update ``$PYTHONPATH`` + add ``python -c 'import mrtrix3'`` as sanity check command for recent MRtrix versions (`#1889 `_) * update sanity check in SAMtools easyblock for version 1.10 (`#1890 `_) * make sure ``$PYTHONNOUSERSITE`` it set when performing sanity check for (bundles of) Python package(s) (`#1891 `_) * fix install dir subdir for WPS v4.0+ that is considered for ``$PATH`` and ``$LD_LIBRARY_PATH`` (`#1895 `_) * impi: don't rebuild libfabric if the source code is not present (`#1896 `_) * also copy component patches to self.cfg in Bundle generic easyblock (`#1897 `_) * skip patch step in Bundle generic easyblock (per-component patches are still applied) (`#1898 `_) * derive easyblock for iccifort only from icc easyblock (not ifort), to avoid adding include subdir to ``$CPATH`` (`#1899 `_) * add ``export LANG=C`` to preinstallopts instead of install_script path in CUDA easyblock (`#1902 `_) * stop setting updating ``$CPATH`` and ``$LIBRARY_PATH`` for GCC and GCCcore, not required (`#1903 `_) * remove ``$LIBRARY_PATH`` entries in iccifort easyblock, already known to icc et al (`#1904 `_) * use major/minor version of Python command being used if ``req_py_majver``/``req_py_minver`` are not specified (`#1907 `_) * define ``$EB_PYTHON`` in module for EasyBuild installation, to make sure correct Python version is used at runtime (`#1908 `_) * fix Python easyblock to allow configuring build of Python v3.8 (``Setup.dist`` script was renamed to ``Setup``) (`#1909 `_) * fix netCDF easyblock for version 4.4.0 (`#1911 `_) * correct comment about when we set ``RUNPARALLEL`` in HDF5 easyblock (`#1914 `_) * do not sanity check on MATLAB compiler, since it requires a separate license (`#1916 `_) * build HDF5 without MPI C++ extension to avoid breaking linkage for C software that requires HDF5 (`#1918 `_, `#1919 `_) * override ``set_pylibdirs`` method in ``VersionIndependentPythonPackage`` to hard set ``self.pylibdir`` to 'lib' (`#1924 `_) * other changes: * increase timeout for interactive installation command in CUDA easyblock to 1000 sec. (`#1878 `_) * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#1882 `_) * stop requiring Python dep for SWIG, just configure with ``--without-python`` if Python is not a dependency (`#1894 `_) * update copyright statements for 2020 (`#1905 `_) * make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (`#1923 `_) **easyconfigs** * added example easyconfig files for 27 new software packages: * Autoconf-archive (`#9658 `_), breseq (`#9603 `_), CrossMap (`#9483 `_), CSBDeep (`#9560 `_), CNT-ILP (`#9323 `_), cytoolz (`#9453 `_), Faber (`#9553 `_), Fiji (`#8748 `_), GARLI (`#9404 `_), Globus-CLI (`#9565 `_), GtkSourceView (`#9526 `_), gradunwarp (`#9648 `_), gsettings-desktop-schemas (`#9529 `_), HyPhy (`#9405 `_), horton (`#7449 `_), IGMPlot (`#9438 `_), LEMON (`#9323 `_), Meld (`#9530 `_), mhcflurry (`#9554 `_), NCIPLOT (`#9419 `_), ncl (`#9632 `_), OpenSlide (`#9499 `_), openslide-python (`#9499 `_), pythran (`#9488 `_, `#9594 `_), Qualimap (`#9411 `_), TinyDB (`#9555 `_), TreeShrink (`#9381 `_) * added additional easyconfigs for various supported software packages, including: * Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2, GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10, lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1, pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2, WPS 4.1, WRF 4.1.3 * added easyconfigs for ``intel/2020.00`` toolchain (`#9575 `_) * minor enhancements, including: * add POWER9 support to CUDA 10.1 easyconfigs (`#9442 `_) * build CMake in parallel (`#9543 `_) * use NCCL for GPU ops in Horovod 0.18.2 easyconfig (`#9562 `_) * update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (`#9585 `_) * various bug fixes, including: * fix remote launch of broker and workers for SCOOP (`#9366 `_) * fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using ``foss/2018b``) (`#9388 `_) * add missing 'wheel' extensions to Spark 2.4.0 easyconfig using ``intel/2018b`` toolchain (`#9424 `_) * add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (`#9454 `_) * fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (`#9455 `_) * fix CMake 3.15.3 build on Power (+ enable building in parallel) (`#9469 `_) * fix source URLs in xorg-macros easyconfigs (`#9477 `_, `#9578 `_) * add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (`#9479 `_) * remove (wrong) ``GI_TYPELIB_PATH`` and ``XDG_DATA_DIRS`` in various easyconfigs (`#9528 `_, `#9577 `_, `#9615 `_) * use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (`#9546 `_) * fix lpsymphony extension for R-bundle-Bioconductor (`#9548 `_) * add correct 'old-versions' source URL to all Mesa easyconfigs (`#9569 `_) * add missing SHA256 checksums for Armadillo (`#9572 `_) * also define ``$AUGUSTUS_BIN_PATH`` and ``$AUGUSTUS_SCRIPTS_PATH`` in generated module file for AUGUSTUS (`#9579 `_) * add SSL OS dependencies for GDAL 3.0.0 (`#9586 `_) * add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (`#9587 `_) * patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (`#9590 `_) * patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (`#9591 `_) * fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (`#9601 `_) * use absolute path for extraction to allow relocating the build dir for g2log-1.0 (`#9604 `_) * add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (`#9611 `_) * add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (`#9621 `_) * update ctffind website (`#9622 `_) * make sure we use easybuild Clang in pocl easyconfigs (`#9624 `_) * make ``postinstallcmds`` independent of current working directory in OpenCV 3.1.0 easyconfigs (`#9628 `_) * update ``source_urls`` to include old releases folder in libsodium easyconfigs (`#9632 `_) * fix source URLs for ant v1.10.5 - v1.10.7 (`#9633 `_) * update URLs to new location of libxc (`#9635 `_) * add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (`#9644 `_) * update source URLs in QCA 2.1.0 easyconfigs (`#9647 `_) * fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI (`#9649 `_) * fix tesseract 4.1.0 dependencies (`#9650 `_) * make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (`#9652 `_) * use ``True`` (boolean value) rather than ``'True'`` (string value) for boolean easyconfig parameters (`#9657 `_) * fix pyfits easyconfig by adding missing d2to1 extension (`#9687 `_) * other changes: * disable running of ``sudo apt-get update`` in GitHub CI config, since it's failing (and we don't really need it) (`#9492 `_) * require that ``sanity_pip_check`` is enabled in new/changed easyconfigs (`#9516 `_, `#9576 `_) * update copyright statements for 2020 (`#9598 `_) * allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (`#9634 `_) .. _release_notes_eb410: EasyBuild v4.1.0 (December 4th 2019) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * performance improvements: * skip validation when copying EasyConfig object for extension (`#3071 `_) * correctly specify that ActiveMNS & co are singleton classes when using Python 3 (`#3073 `_) * don't call out to prohibitively expensive ``getRootLoggerName`` in ``getLogger``, just use 'root' instead (`#3074 `_) * fix inconsistent module path usage that leads to repeated reloading in HMNS (`#3099 `_) * add support for specifying different dependency version based on processor architecture (`#3047 `_) * support use of glob patterns for paths to files with external modules metadata (`#3075 `_) * take into account that external modules may not be visible directly (due to module hierarchy) (`#3083 `_) * add support for including 'extensions' statement in Lua modules with Lmod 8.2.8+ (`#3085 `_, `#3107 `_, `#3110 `_) * add support for ``--sync-pr-with-develop`` (`#3087 `_) * add support for ``--new-branch-github``, ``--new-pr-from-branch``, ``--sync-branch-with-develop``, ``--update-branch-github`` (`#3103 `_) * fix typo in docstring for ``new_branch_github`` (`#3106 `_) * various bug fixes, including: * correctly handle ``iccifortcuda`` toolchain with standalone ``iccifort`` in ``det_toolchain_compilers`` (`#3055 `_) * init git repo with ``git.repo.clone()`` instead of ``copy_dir()`` (`#3062 `_) * fix regular expression so depends-on statements are recognized correctly in Tcl module files (`#3065 `_) * update GitPython to latest version that supports Python 2.6 in requirements.txt to fix broken ``test_new_update_pr`` (`#3066 `_) * imply ``--disable-pre-create-installdir`` with ``--inject-checksums`` (`#3069 `_) * handle patches in extensions more like normal patches (`#3067 `_) * take into account that ``platform.linux_distribution`` and ``platform.dist`` was removed in Python 3.8 (`#3078 `_) * always include mandatory easyconfig parameters in dumped easyconfig (`#3081 `_) * hide backup module file when using Lmod 6.x (fixes `#9302 `_) (`#3089 `_) * add better error message when mandatory key is missing from a dictionary easyconfig parameter (`#3092 `_) * also create symlinks for default modules in class module folders (`#3093 `_) * fix semantics of ``--set-default-module``: only set default for specified easyconfigs, not for the ones that are installed as dependencies via ``--robot`` (`#3094 `_) * fix various issues in extracting comments from original easyconfig file and including them again in dumped easyconfig (`#3095 `_) * don't use ``%(version)s`` template in ``exts_default_options`` in dumped easyconfig (`#3096 `_) * fix generated module statements in case only a single version is listed in ``multi_deps`` (`#3097 `_) * fix broken ``test_show_system_info`` on macOS due to 'Python' binary (`#3105 `_) * take into account that dependency version could be a dict rather than a string value in template_constant_dict (`#3111 `_) * other changes: * deprecate running EasyBuild with Python 2.6 via new ``check_python_version()`` function (`#3076 `_) * deprecate support for using Lmod 6.x (`#3077 `_) * trim set of test configurations in Travis CI (`#3086 `_) * flesh out ``env_vars_external_module`` from ``Toolchain._simulated_load_dependency_module`` (`#3088 `_) **easyblocks** * new software-specific easyblock for cuDNN, to allow setting ``cudnnarch`` (`#1855 `_) * refactored software-specific easyblock for Xmipp, based on Scons (`#1837 `_) * minor enhancements, including: * add ``prebuildopts`` to Bazel build command (`#1838 `_) * add support to Toolchain generic easyblock for defining $EB* environment variables for toolchain components that use an external module (`#1849 `_) * add support for running 'pip check' during sanity check in generic PythonPackage easyblock (`#1853 `_) * various bug fixes, including: * clean up ``/tmp/cuda-installer.log`` in CUDA easyblock, to avoid segfault in cuda-installer (`#1835 `_) * minor fix to name of Gctf binary (`#1840 `_) * move BLAS toolchain existence check earlier in SuperLU easyblock (`#1842 `_) * fixes for TensorFlow easyblocks w.r.t. Bazel build options & ``__init__`` in top-level google-protobuf package dir (`#1843 `_) * fix support for sequential version in MUMPS easyblock (`#1845 `_) * change default value of ``files_to_copy`` to None in MakeCp generic easyblock + code cleanup & use ``change_dir``, ``copy_dir``, ``copy_file`` and ``mkdir`` function from ``filetools`` (`#1848 `_) * prepend ``-L$EBROOTZLIB/lib`` to ``LDFLAGS`` in SCOTCH easyblock (`#1850 `_) * improve configuration in netCDF and netcdf4_python easyblocks (`#1852 `_) * fix CUDA header paths for TensorFlow versions < 1.14 (`#1854 `_) * handle incorrect regex better in generic CmdCp easyblock (`#1861 `_) * add missing docstrings in cmakeninja easyblock (`#1867 `_) * other changes: * add GitHub Actions workflow to run easybuild-easyblocks test suite (`#1844 `_) **easyconfigs** * added example easyconfig files for 46 new software packages: * Amara (`#9340 `_), anvio (`#9387 `_), Arriba (`#9226 `_, `#9244 `_), attr (`#7824 `_), bibtexparser (`#9284 `_), bwa-meth (`#9217 `_), CITE-seq-Count (`#9237 `_), CoordgenLibs (`#9374 `_), dtcmp (`#9052 `_), fatslim (`#9193 `_), GromacsWrapper (`#9177 `_), GULP (`#9243 `_), hdf5storage (`#9195 `_), ITSTool (`#7260 `_), kim-api (`#8786 `_), kwant (`#9238 `_), libarchive (`#9052 `_), libcircle (`#9052 `_), libxml2-python (`#7260 `_), lifelines (`#9215 `_), lwgrp (`#9052 `_), maeparser (`#9374 `_), MaxQuant (`#9281 `_), MethylDackel (`#9216 `_), MoviePy (`#9205 `_), mpifileutils (`#9052 `_), mpiP (`#9059 `_), nanofilt (`#8502 `_), NOVOPlasty (`#9326 `_), openkim-models (`#8786 `_), parallel-fastq-dump (`#9218 `_), pasta (`#9348 `_), pyqstem (`#9277 `_), python-Levenshtein (`#9237 `_), RapidJSON (`#9373 `_), RDFlib (`#9346 `_), RQGIS3 (`#9125 `_), Short-Pair (`#9376 `_), SpliceMap (`#9375 `_), TRIQS-cthyb (`#9230 `_), TRIQS-dft_tools (`#9230 `_), TRIQS-tprf (`#9230 `_), UMI-tools (`#9237 `_), VarDict (`#7283 `_), Xmipp (`#9257 `_), XSD (`#9347 `_) * added additional easyconfigs for various supported software packages, including: * awscli 1.16.290, BLIS 0.6.0, Bazel 1.1.0, Biopython 1.75, Blender 2.81, bokeh 1.4.0, CONCOCT 1.1.0, CUDA 10.2.89, Catch2 2.11.0, CellRanger 3.1.0, CheckM 1.0.18, dask 2.8.0, deepTools 3.3.1, FastANI 1.2, Flye 2.6, GDCM 3.0.4, GTDB-Tk 0.3.2, Glade 3.8.6, Hadoop 2.9.2, h5py 2.10.0, hypothesis 4.44.2, IPython 7.9.0, Kaiju 1.7.2, Kraken 1.1.1, libsodium 1.0.18, MEGAHIT 1.2.8, Mesa 19.2.1, MetaBAT 2.14, matplotlib 3.1.1, metaWRAP 1.2.2,cNCCL 2.4.8, NGS 2.10.0, NiBabel 2.5.1, netCDF 4.7.1, networkx 2.4, numba 0.46.0, OpenCV 3.4.7, OpenCoarrays 2.8.0, OpenEXR 2.4.0, OpenFOAM v1906, OpenImageIO 2.0.12, ParaView 5.6.2, Pillow 6.2.1, PyTorch 1.3.1, PyYAML 5.1.2, Pysam 0.15.3, picard 2.21.1, prokka 1.14.5, protobuf 3.10.0, R-keras 2.2.5.0, Racon 1.4.7, SCOTCH 6.0.9, SRPRISM 3.1.1, Salmon 0.14.2, SciPy-bundle 2019.10, Subread 2.0.0, scikit-image 0.16.2, scikit-learn 0.21.3, TRIQS 2.2.1, TensorFlow 1.15.0, TensorFlow 2.0.0 w/ fosscuda/2019b, Tkinter 3.7.4, ToFu 1.4.1, tbb 2019_U9, Xerces-C++ 3.2.2, Xmipp 3.19.04, yaff 1.6.0 * added easyconfigs for ``intelcuda/2019a`` toolchain (`#9271 `_) * minor enhancements, including: * tweak Java 1.8 wrapper to use different Java version on POWER systems (`#9081 `_) * add jupyter_nbextensions_configurator extension to IPython 7.7.0 easyconfigs (`#9133 `_) * add additional extensions to R 3.6.0 easyconfigs (`#9184 `_, `#9275 `_) * add additional extensions to R-bundle-Bioconductor 3.9 easyconfig (`#9185 `_, `#9349 `_, `#9410 `_) * enhance sanity check in cutadapt 1.18 easyconfigs + consistently use PythonBundle & ``use_pip`` (`#9219 `_) * update cuDNN 7.6.4.38 easyconfigs to support both x86_64 and ppc64le (`#9331 `_) * tweak NCCL 2.4.8 easyconfig to support x86_64 and ppc64le (`#9336 `_) * define ``$SPARK_HOME`` in generated module file for Spark 2.4.0 (`#9408 `_) * add sanity check command for matplotlib 3.x with Python 3 to check import from mpl_toolkits (`#9413 `_, `#9414 `_) * various bug fixes, including: * explicitly set ``SYSCONFDIR`` configure option in TurboVNC easyconfig (`#9137 `_) * patch pigz Makefile so zlib provided by EasyBuild is picked up (`#9138 `_) * add libjpeg-turbo as dependency to recent LibTIFF easyconfigs, to avoid picking up LibTIFF installed in system (`#9146 `_) * add freetype as dependency to OpenImageIO, to avoid picking up freetyype installed in system (`#9147 `_, `#9152 `_) * fix definition of ``fosscuda/2019b`` to make sure it works with hierarchical MNS (`#9178 `_) * add missing setuptools_scm extension required to build dateutil extension in Python 3.7.0 easyconfigs (`#9209 `_) * add Python as build dependency for recent Bazel versions (`#9223 `_, `#9299 `_, `#9342 `_) * fix homepage & description in Bioconductor easyconfigs (`#9225 `_) * fix checksum in Stacks 2.41 easyconfig after sneaky re-release (`#9232 `_) * apply fixes to ImageJ 1.51k easyconfig (`#9245 `_) * consistently use patch for OpenCV 3.4.7 (`#9279 `_) * use protobuf 3.10.0 as build dep for TensorFlow 2.0.0 w/ fosscuda/2019b + use nodocs variant of git as build dep (`#9298 `_) * add Jasper dependency to Qt5 v.5.13.1 (`#9313 `_) * fix Python 3.7.2 required OpenSSL version for old OS to the one provided on the same toolchain (`#9324 `_) * add missing extensions required by Sphinx & pytest to easyconfigs for Python 3.7.2 and 3.7.4 (`#9329 `_) * update TensorFlow v1.14.0 + v2.0.0 CUDA patch to handle compiler wrappers like ccache (`#9333 `_) * patch binutils 2.31.1 and 2.32 to fix compatibility with RHEL8 (`#9335 `_) * add missing extensions in TensorFlow 2.0.0 easyconfigs (+ update to tensorboard/tensorflow-estimator 2.0.1) (`#9338 `_) * fix logic to determine location of scripts dir + ensure right compiler flags are used in KAT easyconfigs (`#9360 `_) * add missing GCCcore-6.3.0_fix-sanitizer_linux.patch in GCCcore 6.4.0 easyconfig (`#9362 `_) * fix linker errors when linking with libhts.a for MetaBAT 2.12.1 (`#9379 `_) * add egg-info file via patch in VTK v8.2.0, for Pytho 2.7.15, 3.7.2, 3.7.4 (`#9386 `_) * promote binutils to a runtime dependency for Python in GCCcore based builds (`#9402 `_) * fix archive URL typo for ncdf4 (`#9407 `_) * fix problems with mpl_toolkits namespace for matplotlib easyconfigs using Python 2 (`#9415 `_, `#9416 `_, `#9417 `_) * other changes: * ignore commented out lines in easyconfig files when checking for http:// URLs (`#9224 `_) * add GitHub Actions workflow to run easybuild-easyconfigs test suite (`#9231 `_, `#9255 `_) * archive old patches for Xmipp 3.1 (`#9256 `_) * speed up easyconfigs test suite by avoiding re-parsing and re-ordering of easyconfigs (`#9236 `_) * only run easyconfigs test suite with Python 2.7 & 3.6 + Lmod 7 in Travis CI (`#9297 `_) * archive ACML easyconfigs (`#9367 `_) * update CMake build in Eigen 3.3.7 to use more recent toolchain (`#9398 `_) .. _release_notes_eb401: EasyBuild v4.0.1 (October 15th 2019) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add '``parallel``' to list of config templates (`#3036 `_) * add GitHub Actions workflow to run easybuild-framework test suite (`#3039 `_) * add '``retest``' as a reason to ``--close-pr``, to close/re-open PRs to trigger re-test in Travis (`#3040 `_) * define ``$EB_SCRIPT_PATH`` in '``eb``' wrapper script, and consider it before location of '``eb``' determined via ``$PATH`` in ``get_paths_for`` function (`#3046 `_) * add support for ``--remove-ghost-install-dirs`` configuration option, and warn about (potential) ghost install dirs by default when ``--force``/``--rebuild`` is used (`#3050 `_) * various bug fixes, including: * update bootstrap script to support installing EasyBuild v4.0 (`#3017 `_) * fix broken ``test_download_repo`` due to archiving of easyconfigs (`#3019 `_, `#3023 `_) * avoid that ``--inject-checksums`` introduces list of patches for extensions as a single long line (`#3025 `_, `#3034 `_) * enhance regex in ``fix_shebang`` method to fix more Python/Perl shebangs + avoid patching binary files (`#3029 `_) * delete test gist that is created by ``--check-github`` (`#3031 `_) * disable templates when defining easyconfig parameters in ``EasyConfig.set_keys()`` (`#3037 `_) * avoid setting GC3Pie's max_in_flight to ``None`` if ``--job-max-jobs`` is not specified (`#3038 `_) * fix use of ``obtain_file`` method for extensions (`#3042 `_) * error out if some GC3Pie job failed (`#3044 `_) **easyblocks** * one new generic easyblock: ``CMakeNinja`` (`#1829 `_) * new software-specific easyblock for Gctf (`#1827 `_), MotionCor2 (`#1819 `_) * minor enhancements, including: * update OpenFOAM easyblock for changes in version 1906 w.r.t. wamke rules (`#1772 `_) * add ``%(cudaarch)s`` template variable so that it can be used in sources (`#1797 `_) * update Boost easyblock for versions >=1.71.0 (`#1814 `_) * update RepeatMasker easyblock for version 4.0.9 (`#1815 `_) * add ``--verbose`` flag to '``pip install``' when running EB in debug mode (`#1822 `_) * update TensorFlow easyblock to support TensorFlow 2.0 (`#1823 `_) * add support in TensorFlow easyblock to run a custom test script as smoke test (`#1824 `_) * add support for installing QScintilla on top of PyQt5 (`#1825 `_) * update VEP easyblock to make installation compatible with ``Bio::EnsEMBL::XS`` (`#1828 `_) * various bug fixes, including: * enhance TensorFlow easyblock to support installing TF 1.14.0 with CUDA and MPI support (`#1811 `_, `#1816 `_) * avoid ``UnicodeDecodeError`` when reading '``configure``' script and checking for '``Generated by GNU Autoconf``' in ``ConfigureMake`` (`#1817 `_, `#1821 `_) * don't require '``python``' command to install libxml2 without Python bindings (`#1818 `_) * make sure "``generic=True``" actually turns on generic build in GCC easyblock (`#1826 `_) * fix compatibility of Trilinos easyblock with Python 3 (`#1831 `_) **easyconfigs** * added example easyconfig files for 58 new software packages: * ADOL-C (`#9098 `_), ALFA (`#9106 `_), ASTRID (`#9088 `_), Annif (`#8536 `_), bnpy (`#8989 `_), bpp-core (`#9064 `_), bpp-phyl (`#9064 `_), bpp-seq (`#9064 `_), Clang-Python-bindings (`#9084 `_), CPB (`#5869 `_), Centrifuge (`#8714 `_), Chromaprint (`#9047 `_), Con3F (`#8755 `_), DeepSurv (`#8096 `_), Essentia (`#9054 `_), FastRFS (`#9088 `_), GAT (`#5871 `_), Gaia (`#9049 `_), Gctf (`#9097 `_), GenomeMapper (`#5872 `_), Infomap (`#9091 `_), kpcalg (`#8740 `_), libglvnd (`#9111 `_, `#9130 `_), libsamplerate (`#9046 `_), libssh (`#8865 `_), libzip (`#9073 `_), MetaboAnalystR (`#8773 `_), Metaxa2 (`#8939 `_), MotionCor2 (`#8942 `_), NFFT (`#9085 `_), PhyML (`#9103 `_), PlaScope (`#8714 `_), PyCharm (`#9100 `_), pbcopper (`#8928 `_), pbmm2 (`#8929 `_), phylokit (`#9088 `_), phylonaut (`#9088 `_), phyx (`#9090 `_), pycma (`#8834 `_), Q6 (`#9069 `_), Qt5Webkit (`#9120 `_), ROME (`#9050 `_, `#9062 `_), rioxarray (`#9007 `_), SVDquest (`#9088 `_), savvy (`#9124 `_), sciClone (`#7806 `_), shapAAR (`#8983 `_), shrinkwrap (`#9124 `_), Structure (`#5866 `_), trimAl (`#9063 `_), thurstonianIRT (`#9080 `_), TurboVNC (`#9110 `_, `#9111 `_, `#9128 `_), Tracer (`#8970 `_), TagLib (`#9048 `_), TRIQS (`#8835 `_), THetA (`#8875 `_), vcfnp (`#5862 `_), WebSocket++ (`#8842 `_) * added additional easyconfigs for various supported software packages, including: * Armadillo 9.700.2, arpack-ng 3.7.0, BLASR 5.3.3, Bazel 0.26.1 + Bazel 0.29.1, Cufflinks 20190706, DL_POLY_Classic 1.10, FFmpeg 4.2.1, Go 1.13.1, Horovod 0.18.1, IOR 3.2.1, Julia 1.2.0, LLVM 9.0.0, Mesa 19.1.7, Molden 6.1, Mono 6.4.0.198, NCO 4.8.1, , Net-core 3.0.0, Nim 1.0.0, OpenFOAM 2.2.x, PGI 19.7, PLUMED 2.5.2, PMIx 3.1.4, PostgreSQL 11.3, psycopg2 2.8.3, QGIS 3.4.12, QScintilla 2.11.2, Qt5 5.13.1, ReFrame 2.19, Rust 1.37.0, Spack 0.12.1, TAMkin 1.2.6, TensorFlow 1.14.0 w/ fosscuda/2019a, TensorFlow 2.0.0 w/ foss/2019a, UCX 1.6.1, VEP 96.0, xarray 0.13.0 * added easyconfigs for ``fosscuda/2019a`` toolchain (`#9066 `_) * minor enhancements, including: * add EBImage extension to easyconfig for R-bundle-Bioconductor 3.9 (`#8982 `_) * add check for ``http://`` URLs in easyconfig files added/changed in PRs (`#9012 `_) * add bbmle/emdbook/SOAR/rasterVis/tictoc extensions to R 3.6.0 easyconfigs (`#9037 `_) * updated PyQt5 5.12.1 easyconfig to also build sip files + minor readability changes (`#9071 `_) * enabled ``SQLITE_ENABLE_COLUMN_METADATA``, which is needed for GDAL (and QGIS) (`#9118 `_) * also install include/GL/internal/ for recent Mesa installations (`#9129 `_) * various bug fixes, including: * add ncurses as dependency to lftp (`#8646 `_) * add patch for gettext 0.19.8* to avoid picking up global git config that could break the installation (`#8957 `_) * fix source URLs in GlimmerHMM easyconfigs (`#8980 `_) * add patch for PyTorch 1.2.0 to use version of torchvision that is compatible with PyTorch 1.2.0 (`#8986 `_) * clarify the comment regarding the optarch setting in ITK-5.0.1 (`#8991 `_) * fix homepage & description in easyconfig file for YAPS (`#8993 `_) * add patch for PyTorch 1.2.0 to fix failing softmax test on Intel Sandy Bridge (`#9010 `_) * fix permissions for TRF (`#9034 `_) * ICU needs Python 2.7+ to build, so add that as builddependency (`#9053 `_) * fix urls for Anaconda and Miniconda (`#9087 `_) * use a cuDNN version that has support for the CUDA version in ``fosscuda/2019a`` (CUDA 10.1) in PyTorch, TensorFlow and Theano easyconfigs (`#9112 `_) * other changes: * make sources in CUDA 10.1.105 use ``%(cudaarch)s`` template value (to use different source on POWER systems) (`#8136 `_) * update ``Java/1.8`` wrapper to ``Java/1.8.0_221`` (`#9038 `_) * allow divergent Java dep version as long as it's indicated by versionsuffix (`#9041 `_) .. _release_notes_eb400: EasyBuild v4.0.0 (September 20th 2019) -------------------------------------- feature release (incl. backwards-incompatible changes) **framework** * **fixed compatibility with Python 3.5+** (`#2708 `_, `#2713 `_, `#2714 `_, `#2719 `_, `#2721 `_, `#2723 `_, `#2729 `_, `#2743 `_, `#2744 `_, `#2751 `_, `#2756 `_, `#2759 `_, `#2761 `_, `#2762 `_, `#2765 `_, `#2766 `_, `#2767 `_, `#2768 `_, `#2774 `_, `#2775 `_, `#2778 `_, `#2780 `_, `#2785 `_, `#2787 `_, `#2789 `_, `#2791 `_, `#2792 `_, `#2794 `_, `#2800 `_, `#2801 `_, `#2805 `_, `#2806 `_, `#2895 `_, `#2932 `_, `#2982 `_, `#2992 `_, `#3007 `_, `#3011 `_) * supported Python versions: 2.6, 2.7, 3.5, 3.6, 3.7 * some functionality from the Python standard library should be imported from the new ``easybuild.tools.py2vs3`` package * see :ref:`py2_py3_compatibility` & :ref:`eb4_relocated_functions_classes_constants` * **ingested relevant code from** ``vsc-base`` & ``vsc-install`` (`#2708 `_, `#2713 `_, `#2714 `_, `#2763 `_, `#2790 `_, `#2993 `_) * ``vsc-base`` & ``vsc-install`` are no longer required as dependencies * the functionality that was provided by these packages is now (mostly) available from the ``easybuild.base`` package * any import statements from the '``vsc``' namespace will result in an error * see also :ref:`eb4_changes_ingested_vsc_base` and :ref:`eb4_relocated_functions_classes_constants` * ``setuptools`` **is longer required** (neither for installing or using EasyBuild) (`#2836 `_, `#2837 `_, `#2984 `_, `#2986 `_, `#2988 `_) * see also :ref:`eb4_no_required_deps` * this required moving some classes and constants, see :ref:`eb4_relocated_functions_classes_constants` * **the** '``dummy``' **toolchain is deprecated and replaced by the** '``system``' **toolchain** (`#2877 `_, `#3001 `_) * if '``dummy``' is still used as a toolchain in easyconfig files, a warning will be printed * use "``toolchain = SYSTEM``" instead * for more information, see :ref:`system_toolchain` * **a warning is printed when local variables in easyconfig file don't follow the recommended naming scheme** (`#2938 `_, `#2968 `_) * see also :ref:`easyconfig_files_local_variables` * **names of software installation directories are independent of module naming scheme by enabling** ``--fixed-installdir-naming-scheme`` **by default** (`#2999 `_) * see :ref:`eb4_changes_fixed_installdir_naming_scheme` for more information * various other small enhancements, including: * use requests instead of urllib2 for 403 errors (`#2695 `_) * use pip requirements file in Travis (`#2874 `_) * add support for ``--fix-deprecated-easyconfigs`` (`#2881 `_, 2898, `#2938 `_) * add ``-L$EBROOTIMKL/lib/intel64`` to ``$LDFLAGS`` for MKL (`#2930 `_) * handle dict-type checksums in check_checksums_for (`#2974 `_) * allow that ``icc`` & ``ifort`` are not actual dependencies in ``iccifort`` toolchain module (`#2995 `_) * define mapping for ``iccifort``->``intel`` for ``iccifort`` compiler-only toolchain for HMNS (`#2996 `_) * also consider concatenation of compiler module names to determine details of toolchain compiler component (`#2997 `_) * update metadata for Cray-provided external modules (`#3013 `_) * various bug fixes, including: * update the PyPI trove classifiers in setup.py (`#2875 `_) * reverse lists for ``$LDFLAGS`` and ``$CPPFLAGS`` (`#2931 `_) * enhance/fix to_template_str function to do a better job at using template values in dumped easyconfigs (`#2948 `_) * also take into account ``--filter-deps`` when finalizing parsed dependencies to fix problem with dependency filters using version ranges (`#2983 `_) * fix broken ``--from-pr`` tests due to archiving of easyconfigs (`#2985 `_) * fixes required to avoid breaking Cray support (`#3008 `_) * fixes for ``--read-only-installdir``: avoid crash with ``ModuleRC`` easyblock + also make log file in installdir read-only (`#3012 `_) * other changes: * add check to ensure that ``--robot`` argument specifies an existing directory (`#2086 `_) * remove old scripts that are no longer useful (+ minor fixes to others) (`#2897 `_) * use '``command -v``' to avoid requiring '``which``' in '``eb``' command (`#2979 `_) * add ``modluafooter`` & ``modtclfooter`` at the end of the generated module file (`#3003 `_) * print warning when '``eb``' command is not found in ``$PATH`` and for empty robot search path (`#3006 `_) **easyblocks** * fixes due to backwards-incompatible changes in easybuild-framework v4.0.0 * use ``is_system_toolchain()`` rather than checking toolchain name against DUMMY_TOOLCHAIN_NAME constant (`#1690 `_, `#1728 `_) * fix compatibility of various easyblocks with Python 3 (`#1640 `_, `#1644 `_, `#1648 `_, `#1721 `_, `#1794 `_, `#1808 `_, `#1795 `_, `#1796 `_, `#1807 `_, `#1809 `_) * new software-specific easyblocks for ``OpenMPI`` (`#1789 `_, `#1801 `_), ``iccifort`` (`#1799 `_) and ``numexpr`` (`#1803 `_, `#1804 `_) * various other enhancements, including: * removed checks for Boussinesq and sonic solvers for OpenFOAM 7, since those have been deprecated (`#1733 `_) * update Paraver easyblock to support recent versions (`#1790 `_) * various bug fixes, including: * update the PyPI trove classifiers (`#1723 `_) * make the plugins build use the correct Tcl library version in VMD easyblock (`#1786 `_) * use ``*_MT libs`` for BLAS/LAPACK only if ``openmp`` is enabled in Trilinos easyblock (`#1791 `_) * filter out empty entries in ``$CPATH`` or ``$C_INCLUDE_PATH`` when building Perl, since that breaks the build (`#1800 `_) * set ``$XDG_CACHE_HOME`` in TensorFlow easyblock to avoid that ``pip`` (ab)uses ``$HOME/.cache`` (`#1802 `_) * don't load modules for dependencies in ``CrayToolchain.prepare_step`` (`#1805 `_) * other changes: * drop requirement for setuptools as runtime dependency (`#1689 `_) * enable '``check_ldshared``' in generic PythonPackage easyblock by default for recent Python versions (`#1788 `_) * stop trying to use ``setuptools.setup`` in ``setup.py``, always use ``distutils.core.setup`` instead (`#1793 `_) **easyconfigs** * fixes due to changes in easybuild-framework v4.0.0 * use ``SYSTEM`` toolchain rather than deprecated ``dummy`` toolchain (`#8369 `_, `#8711 `_, `#8822 `_) * fix names of local variables (`#8682 `_-`#8688 `_, `#8690 `_, `#8695 `_-`#8702 `_, `#8709 `_, `#8710 `_, `#8715 `_, `#8717 `_, `#8718 `_, `#8720 `_-`#8732 `_, `#8822 `_) * enable ``--local-var-naming-check=error`` for easyconfigs tests (`#8784 `_) * stick to '``dummy``' toolchain for now in easyconfig for latest EasyBuild 3.x (`#8829 `_) * fix compatibility with Python 3: also run easyconfigs tests with Python 3.5, 3.6 and 3.7 (`#7778 `_, `#7836 `_, `#8293 `_) * added easyconfigs for new common toolchains: ``foss/2019b`` (`#8567 `_), ``intel/2019b`` (`#8681 `_) * ``iccifort`` is now installed as a single entity (no more separate ``icc``/``ifort`` installations from ``intel/2019b`` onwards) (see also `#8879 `_) * ``versionsuffix`` has been stripped down for toolchain components (GCC/binutils/OpenBLAS versions are no longer included) * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added example easyconfig files for 28 new software packages: * AGFusion (`#8840 `_), Bonmin (`#8855 `_), causalml (`#8871 `_), ClonalFrameML (`#6082 `_), Control-FREEC (`#8794 `_), corner (`#8886 `_), CVXPY (`#8662 `_), cytosim (`#8368 `_), dill (`#8885 `_), Dsuite (`#8713 `_), GDCHART (`#8679 `_), gifsicle (`#8664 `_), guenomu (`#8677 `_), JsonCpp (`#8841 `_), libxml++ (`#8896 `_), LOHHLA (`#7227 `_), Longshot (`#8830 `_), MDBM (`#8850 `_), nglview (`#8860 `_), ownCloud (`#6804 `_), ptemcee (`#8884 `_), pubtcrs (`#7500 `_), pyiron (`#8860 `_), qpth (`#8665 `_), QtKeychain (`#6804 `_), rgdal (`#8826 `_), smallgenomeutilities (`#8507 `_), umis (`#8812 `_) * added additional easyconfigs for various supported software packages, including: * Blosc 1.17.0, bokeh 1.3.4, cURL 7.66.0, csvkit 1.0.4, dask 2.3.0, Extrae 3.7.1, FSL 6.0.1, GLibmm 2.49.7, git 2.23.0, IPython 7.7.0, numexpr 2.7.0, OSU-Micro-Benchmarks 5.6.2, OpenBLAS 0.3.7, OpenSSL 1.1.1d, ParaView 5.5.2, Paraver 4.8.1, Perl 5.30.0, PnetCDF 1.10.0, Porechop 0.2.4, PyTables 3.5.2, PyTorch 1.2.0, Python 2.7.16 + 3.7.4, parallel 20190622, phonopy 2.2.0, QIIME2 2019.7, Qiskit 0.12.0, REMORA 1.8.3, scikit-image 0.15.0, spglib-python 1.14.1.post0, torchvision 0.3.0, X11 20190717 * various additional minor enhancements, including: * add several extensions to R 3.6.0 easyconfigs (`#8843 `_, `#8881 `_) * add pRoloc to R-bundle-Bioconductor v3.9 (`#8882 `_) * clean up OpenMPI 3.1.* and 4.* easyconfigs to use custom OpenMPI easyblock (`#8889 `_, `#8890 `_) * update numexpr easyconfigs to use custom easyblock for numexpr (`#8901 `_) * switch to ``PythonBundle`` & enable use_pip in old dask easyconfig files (`#8922 `_) * update ``CrayCCE``, ``CrayGNU``, ``CrayIntel`` and ``CrayPGI`` toolchains to 19.06 (`#8944 `_) * various bug fixes, including: * make TensorFlow 1.7.0 work for AMD CPUs (`#6256 `_) * make sure that right Python wrapper is used in VTK8 (`#7296 `_) * update the PyPI trove classifiers (`#8298 `_) * add missing checksum for matplotlib v3.0.3 (`#8643 `_) * add patch to ``plugins/Make-arch`` to use the correct Tcl library version in VMD (`#8820 `_) * fix issue where '``print_qiime_config.py -t``' sanity check command fails for QIIME 1.9.1 because of missing subdir in ``$PYTHONPATH`` (`#8838 `_) * update homepage info in likwid (`#8846 `_) * disable threading in ``preprocessCore`` extension included with Bioconductor 3.9 to work around conflict with OpenBLAS's threading (`#8847 `_) * add ``-lrt`` patch to PyTorch 1.1.0 easyconfig (`#8852 `_) * fix incorrect escaping in SIP configure options in PyQt5 easyconfigs (`#8856 `_) * add missing Autotools build dep for fastq-tools (`#8858 `_) * add missing deps for zlib, bzip2, and XZ for angsd (`#8867 `_) * apply patch to R package uroot in R 3.6.0 (`#8872 `_) * consider archive source URL for all extensions in R-tesseract easyconfig (`#8897 `_) * add pkg-config build dep for tesseract v4.0.0 (`#8898 `_) * fix ``source_urls`` in byacc easyconfig files (`#8899 `_, `#8908 `_) * add missing cairo dependency to PRINSEQ easyconfig file (`#8902 `_) * configure OpenMPI 1.10.x with ``--without-ucx`` to avoid problems when ``ucx-devel`` is installed in the OS (`#8903 `_) * add GDAL 3.0.0 for Python 2.7.15 and fix the Python 3.7.2 version (`#8912 `_) * fix homepage & description in scikit-image easyconfigs (`#8916 `_) * add faulthandler patches to Python 3.7.0 easyconfigs (`#8832 `_) * other changes: * archive ancient CUDA 5.0.35 easyconfigs with creative way of determining sources (`#7796 `_) * remove ancient easyconfigs from archive (`#8542 `_) * archive easyconfigs using deprecated toolchains (`#8557 `_, `#8558 `_, `#8585 `_) * archive ancient versions of GC3Pie/GCC/OpenMPI/ORCA (`#8586 `_) & CPLEX (`#8765 `_) * rename SALMON to SALMON-TDDFT to fix name clash with Salmon (`#8613 `_) * bump AnnotationDb version in bundle for Bioconductor 3.9 (`#8854 `_) * stop trying to use ``setuptools.setup`` in ``setup.py``, always use ``distutils.core.setup`` instead (`#8866 `_, `#8892 `_, `#8894 `_) * archive easyconfigs using ancient ``Cray*`` toolchains (`#8945 `_) .. _release_notes_eb394: EasyBuild v3.9.4 (August 23rd 2019) ----------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for specifying checksum via dict providing a filename-to-checksum mapping (`#2946 `_) * enhance 'completed' message with how much time was needed for the installation (`#2956 `_) * add support for specifying tuple of alternative checksums (`#2958 `_) * support using '``system``' as alias for '``dummy``' toolchain + ``SYSTEM`` constant (`#2960 `_) * ensure '``docurls``' easyconfig parameter value is a list of string values, not a single string value (`#2963 `_) * automatically enable ``--ignore-osdeps`` when using ``--check-contrib`` or ``--check-style`` (`#2965 `_) * various bug fixes, including: * escape '``+``' in search queries + handle invalid search queries better (`#2967 `_) * also consider extension patches when determining for which easyconfig a given patch file is intended in ``--new-pr``/``--update-pr`` (`#2969 `_) * unset ``$CDPATH`` early on if it is defined (`#2970 `_) * create specified temporary log directory if it doesn't exist yet in ``init_logging`` (`#2972 `_) * don't indicate first multi_deps version as default in module help text when ``multi_deps_load_default=False`` (`#2973 `_) * other changes: * deprecate toolchains older than ``gompi/2016a`` and ``foss/2016a`` (`#2951 `_) **easyblocks** * new software-specific easyblock for MSM (`#1770 `_, `#1775 `_, `#1776 `_) * minor enhancements, including: * allow specifying the license file directly in MATLAB easyblock (`#1712 `_) * enhance CPLEX easyblock to also build Python bindings (`#1738 `_) * workaround for XCrySDen for Tcl 8.6 (`#1749 `_) * update WIEN2k easyblock to support version 19.1 (`#1758 `_) * resolve custom ``%(cudaarch)s`` template value for CUDA sources (`#1766 `_) * enhance sanity check for Blender to make sure that Cycles render engine is available (`#1779 `_) * various bug fixes, including: * only check for qtwebengine in custom easyblock for Qt(5) if glibc is sufficiently recent (`#1771 `_) * correctly define ``comp.src`` in Bundle easyblock, to fix compatibility with easyblocks that leverage ``self.src`` (`#1777 `_) * fix ``Bundle.check_checksums`` to checksums for extensions are also checked (`#1778 `_) **easyconfigs** * added example easyconfig files for 36 new software packages: * ArrayFire (`#8461 `_), BRAKER (`#8437 `_), bwidget (`#8477 `_), Catch2 (`#8703 `_), core-counter (`#8749 `_), CubeGUI (`#6328 `_), CubeLib (`#6328 `_), CubeWriter (`#6328 `_), dagitty (`#8606 `_), enaBrowserTool (`#8795 `_), GEMMA (`#8270 `_), GeneMark-ET (`#8437 `_), GenomeThreader (`#8437 `_), ieeg-cli (`#8793 `_, `#8811 `_), Judy (`#8543 `_), Julia (`#8578 `_), libaio (`#8543 `_), libtirpc (`#8792 `_), magick (`#8545 `_), MSM (`#8556 `_), MSPC (`#8531 `_), mygene (`#8809 `_), OpenMolcas (`#7699 `_), PhiPack (`#8750 `_), plc (`#8796 `_), plotly.py (`#8756 `_), pymemcache (`#8663 `_), PySCF (`#8736 `_), qcint (`#8736 `_), Qiskit (`#7592 `_), QuaZIP (`#8672 `_), re2c (`#8543 `_), SeqAn3 (`#8651 `_), snippy (`#8635 `_), spaln (`#8437 `_), V8 (`#8676 `_) * added additional easyconfigs for various supported software packages, including: * ASE 3.18.0, BEDTools 2.28.0, Bowtie 1.2.3, bzip2 1.0.8, CPLEX 12.9, CUDA 10.1 update 2, cyvcf2 0.11.5, EIGENSOFT 7.2.1, GC3Pie 2.5.2, GCC(core) 9.2.0, GPAW 19.8.1, GlobalArrays 5.7, IMB 2019.3, imageio 2.5.0, jemalloc 5.2.0, nodejs 10.15.3, PyTorch 1.1.0, pybedtools 0.8.0, Quandl 3.4.8, R 3.6.0 w/ intel/2019a, R-bundle-Bioconductor 3.9, Salmon 0.14.1, Scalasca 2.5, Score-P 6.0, Stacks 2.41, TensorFlow 1.14.0, ToFu 1.4.0, WIEN2k 19.1, Wannier90 3.0.0, XCrySDen 1.5.60 * minor enhancements, including: * add patch and dependencies to easyconfig for Qt5 5.12.3 to fix Xlib support & enhance the installation (`#8544 `_) * update nodejs to version 10.15.3 and build libnode and libv8 shared libs (`#8546 `_) * add extensions to R 3.6.0 easyconfig: ``MIIVsem`` (`#8565 `_), ``medflex`` (`#8680 `_), ``Rserve``/``spls`` (`#8758 `_), ``Boruta``/``CovSel``/``ctmle``/``BayesPen`` (`#8805 `_) * include PyQtWebEngine bindings in easyconfig for PyQt5 5.12.1 using Python 3.7.2 (`#8572 `_) * switch GLX backend to Gallium in Mesa-19.0.1 (`#8594 `_) * various bug fixes, including: * fix typo in description in GroopM easyconfig file (`#8346 `_) * add missing bugfix patch to easyconfig for OpenMPI 3.1.4 (`#8566 `_) * downgrade AtomPAW to last supported version in ABINIT 8.10.3 (`#8571 `_) * switch easyconfig for glew 2.1.0 to ``ConfigureMake`` easyblock (`#8595 `_) * fix checksum for source tarball in ``foss/2018b`` easyconfig of NAMD v2.13 (`#8602 `_) * update URL for bzip2 easyconfigs (`#8614 `_) * add patch for M4 1.4.17 to fix installation on top of glibc 2.28 (`#8666 `_) * add patch for Bison 3.0.4 to fix installation on top of glibc 2.28 (`#8675 `_) - avoid needless requirement for matplotlib < 3.0.0 in MultiQC easyconfigs (`#8691 `_) * fix checksum in OpenMPI 1.8.8 easyconfigs (`#8692 `_) * add alternative checksums for ``nlme``/``mgcv``/``foreign``/``boot`` extensions in R 3.5.1 and 3.6.0 easyconfigs (`#8564 `_, `#8762 `_) * add missing core-counter dependency for worker 1.6.8 (`#8749 `_) * add missing pkg-config build dependency in various easyconfigs for (`#8763 `_, `#8775 `_, `#8777 `_, `#8776 `_, `#8764 `_, `#8787 `_, `#8816 `_) * add patch to Python 3.7.2 easyconfig to fix faulthandler segfault (`#8781 `_) * set ``$CPLUS_INCLUDE_PATH`` in easyconfigs for older matplotlib versions (`#8785 `_) * patch out removed glibc 2.28 header from GCC libsanitizer (`#8789 `_) * include ``sysmacros.h`` directly to work around removal from glibc header in numactl easyconfig (`#8790 `_) * adapt gzip's bundled gnulib for glibc 2.28 (`#8791 `_) * add libtirpc and depend on it in easyconfig for libdap 3.20.3 (`#8792 `_) * add missing YAML extension to Perl 5.28.0 easyconfig (required by BioPerl scripts) (`#8806 `_) * other changes: * remove broken easyconfigs for ciftify due to non-trivial missing dependencies (`#8560 `_) .. _release_notes_eb393: EasyBuild v3.9.3 (July 8th 2019) ---------------------- bugfix/update release **framework** * various enhancements, including: * add a URL whatis line to generated module files (`#2933 `_) * various bug fixes, including: * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#2928 `_) * honor ``--tmp-logdir`` when determining location of temporary log file (`#2937 `_) **easyblocks** * minor enhancements, including: * also install docs and demos in Rosetta easyblock (`#1745 `_) * update HEALPix easyblock to work with latest version of HEALPix' ``configure.sh`` (`#1752 `_) * make HPCG log pattern more generic, it changed in 3.1 (`#1753 `_) * allow bootstrapping GCC with profile-guided optimizations (`#1756 `_) * only require vsc-base for EasyBuild 2.x and 3.x in EasyBuildMeta easyblock (`#1757 `_) * extend question patterns with '``https``' URL entry in Modeller easyblock for recent versions (`#1762 `_) * ``modextrapaths`` implemented on easyblock level, ``sanity_check_step``, ``gcc_target`` added in HEALPix easyblock (`#1763 `_) * update OpenBLAS easyblock to be aware of POWER9 support in OpenBLAS 0.3.6 (`#1765 `_) * various bug fixes, including: * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#1751 `_) * fix scripts installation path in SNPhylo easyblock (`#1759 `_) * be more patient when running interactive ``Allwmake.firstInstall`` command for recent OpenFOAM-Extend versions (`#1761 `_) * also add ``--without-go`` configure option for SWIG as we "disable everything by default" (`#1754 `_) * don't assume cmake arguments when configure_cmd is set in CMakeMake easyblock (`#1750 `_) **easyconfigs** * added example easyconfig files for 25 new software packages: * Arb (`#8137 `_), AtomPAW (`#8506 `_), ciftify (`#8457 `_), cysignals (`#8459 `_), deal.II (`#8440 `_), FastQTL (`#8449 `_), FLINT (`#8137 `_), gdbgui (`#8488 `_), gearshifft (`#8482 `_), jbigkit (`#8442 `_), lavaan (`#8539 `_), libRmath (`#8449 `_), OR-Tools (`#8364 `_, `#8523 `_), p4est (`#8440 `_), ppl (`#8459 `_), pplpy (`#8459 `_), PRISMS-PF (`#8440 `_), PyAPS3 (`#8398 `_), pyEGA3 (`#8418 `_), ReFrame (`#8481 `_), S4 (`#8487 `_), SALMON (`#8478 `_), TM-align (`#8510 `_), UnZip (`#8474 `_), XTandem (`#8517 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.10.3, CFITSIO 3.47, GDB 8.3, GROMACS 2019.3, HEALPix 3.50, HPCG 3.1, Nilearn 0.5.2, OpenBLAS 0.3.6, Xerces-C++ 3.2.0 * minor enhancements, including: * update easyconfig for CFITSIO 3.45 with https and sanity check (`#8472 `_) * add AtomPAW and Wannier90 support to ABINIT 8.10.2 easyconfig (`#8506 `_) * add '``resample``' extension to R 3.5.1 + 3.6.0 easyconfigs (`#8538 `_) * various bug fixes, including: * fix source URLs for Mesa 17.{2,3} with fosscuda toolchain (`#8446 `_) * add in Boost dependency to canu-1.8 easyconfigs using ``foss`` toolchain (`#8470 `_) * stick to Ubuntu Trusty when testing with Python 2.6 in Travis (`#8483 `_) * fix incorrect order of extensions for Python-2.7.14 easyconfigs (``pycparser`` and ``cffi`` must come before ``cryptography``) (`#8495 `_) * suppress installation of ``libbfd`` and ``libopcode`` for GDB (`#8496 `_) * fix KronaTools easyconfigs to make sure symlinks in bin are not broken (`#8508 `_) * make additional configopts in PETSc easyconfigs work after uncommenting (`#8522 `_) * add ``pkg-config`` build dep to easyconfig for pocl 1.2 (`#8528 `_) * download correct source tarball for Net-core 2.1.8 (`#8530 `_) * fix '``Permission denied``' error when running '``cp -a``' for ANTs 2.3.1 installation by first removing the ``.git`` subdirectories causing them (`#8535 `_) * fix checksum for boot 1.3-22 extension in R 3.6.0 easyconfig (`#8537 `_) .. _release_notes_eb392: EasyBuild v3.9.2 (June 9th 2019) -------------------------------- bugfix/update release **framework** - various enhancements, including: - enhance (experimental) support for generating Singularity container recipes/images (`#2884 `_, `#2900 `_, `#2902 `_, `#2903 `_, `#2907 `_, `#2909 `_, `#2910 `_, `#2913 `_, `#2915 `_) - add support for specifying container configuration via ``--container-config`` (``--container-base`` option has been removed) - add support for providing custom template for container recipe via ``--container-template-recipe`` - add support for '``sif``' Singularity 3.x container image format - add support for specifying non-image based Singularity bootstrap agents - install default set of OS packages in container recipes starting from scratch - configure Lmod and update Lmod spider cache in generated Singularity container recipes - configure EasyBuild via environment variables (to allow overriding configuration settings via options to '``eb``' command) - also consider ``/tmp/easybuild/sources`` in source path (to allow seeding in sources in container build environment) - updated documentation is available at https://easybuild.readthedocs.io/en/latest/Containers.html - various bug fixes, including: - make sure that easyconfig file for EasyBuild version being bootstrapped is found in robot search path (`#2899 `_) - remove interpreter options when fixing script shebang (`#2905 `_, `#2906 `_) - fix crash on iterated installation when using Cray toolchains (`#2914 `_) - disable checking of read/exec permissions when checking for availability of '``sudo``' command (`#2918 `_) - other changes: - stick to vsc-base < 2.9.0 in bootstrap script to avoid requiring '``future``' dependency (`#2892 `_) **easyblocks** - new software-specific easyblock for ELPA (`#1621 `_) - minor enhancements, including: - allow Boost to build both Python 2 and Python 3 libraries (`#1718 `_) - update CPLEX sanity check: convert tool was removed in CPLEX 12.8 (`#1737 `_) - don't try to patch ``CROSSTOOL`` script for recent Bazel versions (since it's no longer there) (`#1741 `_) - various bug fixes, including: - fix version check on using '``-log``' option to '``Allwmake``' in OpenFOAM easyblock (`#1739 `_) - fix GROMACS easyblock for list-type ``configopts`` (`#1740 `_) - fix configure step for GROMACS version < 4.6 (`#1742 `_) **easyconfigs** - added example easyconfig files for 17 new software packages: - adjustText (`#8354 `_), cowsay (`#8380 `_), fxtract (`#8426 `_), google-java-format (`#8373 `_), libtar (`#8379 `_), mkl-service (`#8390 `_), msprime (`#8371 `_), pygrib (`#8395 `_), pyhdf (`#8394 `_), pyproj (`#8395 `_), PyStan (`#8410 `_), Racon (`#8358 `_), rapidtide (`#8256 `_), SingleM (`#8428 `_), smafa (`#8420 `_), SVDetect (`#8399 `_), Unicycler (`#8376 `_) - added additional easyconfigs for various supported software packages, including: - BLAST+ 2.9.0, Boost.Python 1.70.0, DIAMOND 0.9.24, EMAN2 2.3, ecCodes 2.12.5, GDAL 3.0.0, ImageMagick 7.0.8-46, Libint 2.5.0, matplotlib 2.2.4, NLopt 2.6.1, OrfM 0.7.1, PGI 19.4, PostgreSQL 11.3, R 3.6.0, R-bundle-Bioconductor 3.8, Rust 1.35.0, STAR 2.7.1a - minor enhancements, including: - use CMake rather than configure script for libxc 4.3.4 (`#8361 `_, `#8453 `_) - add '``cobs``' extension to R 3.5.1 easyconfigs (`#8389 `_) - add sanity check command to PSI4 1.2.1 easyconfigs to ensure that '``import psi4``' works (`#8393 `_) - include the provided backports patch in QuantumESPRESSO-6.4.1 (`#8405 `_) - add ``Logger::Simple``, ``Scalar::Util::Numeric``, ``YAML``, ``Object::InsideOut`` extensions to Perl 5.28.1 easyconfig (`#8432 `_) - update Java 1.8 to 1.8.0_212 (`#8443 `_) - various bug fixes, including: - add missing build dependency on gettext to ATK/2.28.1 for fosscuda/2018b (`#8402 `_) - add patch to fix OpenBLAS v0.3.1 matrices multiplication issue (`#8396 `_) - make Eigen a build dependency for nanopolish (`#8448 `_) - other changes: - clean up ELPA 2018.11.001 easyconfig to use custom easyblock for ELPA (`#8360 `_) - remove unused checksum for ``ballgown`` extension in Bioconductor 3.7 easyconfigs (`#8363 `_) .. _release_notes_eb391: EasyBuild v3.9.1 (May 20th 2019) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add function to determine whether specified easyblock is generic or not (`#2838 `_) * add support to ``apply_regex_substitutions`` function to skip creation of backup (`#2844 `_) * add support for ``%(pymajver)s`` (& co) (`#2850 `_) * add support for '``fix_python_shebang_for``' and '``fix_perl_shebang_for``' easyconfig parameters (`#2878 `_) * add ``multi_deps`` information to generated module, help and whatis sections (`#2882 `_) * add support for '``eb --missing``' ('``eb -M``') (`#2883 `_) * see also https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#getting-an-overview-of-missing-installations-missing-m * various bug fixes, including: * only call '``scontrol release``' when there's at least one job submitted (`#2834 `_) * fix small bug in ``find_eb_script`` + various minor issues with tests (related to environment in which tests are run) (`#2835 `_) * list build dependencies *before* runtime dependencies, so dependencies listed via ``multi_deps`` are loaded first in toolchain environment (`#2839 `_) * allow setting parallel to ``0`` or ``False`` to disable adding the ``-j`` argument (`#2842 `_) * be more careful when using single quotes for Tcl syntax (`#2847 `_) * append to existing ``.modulerc`` file rather than overwriting it (if ``--force`` is used) (`#2848 `_) * correctly resolve template values used for extensions (`#2852 `_) * update template values after updating iterative easyconfig parameters (`#2854 `_) * add top-level directories of hierarchical module naming scheme to ``$MODULEPATH`` before loading dependencies (`#2857 `_) * inject dependencies specified via ``multi_deps`` before normal build dependencies (`#2861 `_) * include Python version(s) in PR titles auto-generated by ``--new-pr`` (`#2863 `_, `#2880 `_) * update ``HierarchicalMNS`` for GCCcore toolchain (`#2870 `_) * bump iteration index counter at the correct time (`#2886 `_) * don't specify ``--ntasks-per-node`` when submitting Slurm jobs (`#2887 `_) * fix order of easyconfig parameters in output generated by '``eb --avail-easyconfig-params --output-format rst``' (`#2888 `_) * other changes: * lower required version in Slurm job backend to 16.05 (`#2833 `_) * add Lmod 8 to test suite (`#2849 `_) * deprecate useless 'skip_lower' named argument in template_constant_dict, always define ``*lower`` templates (`#2856 `_) * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#2876 `_) **easyblocks** * one new generic easyblock: ``CMakeMakeCp`` (`#1725 `_) * new software-specific easyblock for Blender (`#1595 `_), Lua (`#1396 `_), OpenBLAS (`#1693 `_, `#1697 `_) * OpenBLAS easyblock also supports installation on POWER systems * minor enhancements, including: * enhance VMD easyblock to also build Surf & Stride + pick up netCDF for VMD >= 1.9.3 (`#1314 `_) * update CGAL easyblock to support CGAL 4.12 & newer (`#1679 `_) * update QuantumESPRESSO easyblock for v6.4.1 (`#1692 `_) * enhance Advisor & VTune easyblocks, since no license is required starting with version 2019 update 3 (`#1694 `_, `#1695 `_) * handle new multi-deps Python setup with ``$EBPYTHONPREFIXES`` for Tensorflow (`#1702 `_) * make CHARMM easyblock pick up on ``prebuildopts`` and ``runtest`` (`#1707 `_) * change default value for ``'use_pip``' to None, so we can discriminate from '``use_pip``' being set to False explicitly (`#1709 `_) * make PythonPackage aware of ``(pre)testopts`` (`#1715 `_) * enable GPU offloading in Clang if CUDA is included as a dep (`#1716 `_) * add support to Clang easyblock for also building libc++ and RTTI (`#1717 `_) * rebuild internal libfabric for impi 2019.x & more recent (`#1730 `_) * update Q&A patterns in SAS easyblock for version 9.4 + add support for custom license file path (`#1731 `_) * various bug fixes, including: * only install mkl-dnn by default with TensorFlow on x86-64 systems (`#1666 `_) * make sure ``ldconfig`` can be found before using it in CUDA easyblock (`#1684 `_) * use temporary directory for pip cache (rather than ``$HOME/.cache/pip``) in ``PythonPackage`` easyblock (`#1687 `_) * allow oversubscription when testing FFTW on top of OpenMPI >= 3.0 (`#1688 `_) * make sure ``$HOME/.cache/pip`` isn't used while installing Tkinter (`#1691 `_) * set default ``exts_filter`` in ``PythonBundle``, so already installed extensions in a bundle can be skipped (`#1701 `_) * instruct Bazel to not use ``$HOME/.cache/bazel`` in TensorFlow easyblock (`#1704 `_) * also set ``$XDG_CACHE_HOME`` during installation of Python, to ensure that '``pip``' that comes along with it doesn't touch ``$HOME/.cache/pip`` (`#1705 `_) * use ``-fp-model precise`` if FMA instructions are missing in GROMACS easyblock (`#1706 `_) * make sure Perl install dir follows a standard format (`#1708 `_) * attach ``source_urls`` directly to sources for components in generic ``Bundle`` easyblock (`#1711 `_) * avoid that ``--no-build-isolation`` option is specified multiple times in ``PythonPackage`` easyblock (`#1713 `_) * fix prefix in impi compiler wrappers (`#1727 `_) * only embed zlib in binutils if it is listed a build dependency (`#1732 `_) * other changes: * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#1724 `_) **easyconfigs** * added easyconfigs for new toolchains: * ``fosscuda/2019a`` (`#8063 `_), ``gimkl/2018b`` (`#8287 `_), ``gomkl/2018b`` (`#8216 `_), ``gomkl/2019a`` (`#8218 `_), intelcuda/2019a (`#8069 `_) * added example easyconfig files for 52 new software packages: * ADDA (`#8207 `_), AMD-LibM (`#7164 `_), AMD-RNG (`#7165 `_), AMD-SecureRNG (`#7165 `_), ARGoS (`#8039 `_, `#8104 `_), ARWEN (`#8213 `_), Canvas (`#7716 `_), cdsapi (`#7970 `_), charmm (`#8202 `_), emcee (`#7989 `_), FlexiDot (`#8228 `_, `#8275 `_), FreeImage (`#8039 `_), Hello (`#7704 `_), HLAminer (8094), hypothesis (`#8307 `_), imgaug (`#8229 `_), INTEGRATE (`#8193 `_, `#8304 `_), INTEGRATE-Neo (`#8094 `_), IRkernel (`#8050 `_, `#8099 `_), JiTCODE (`#7148 `_, `#8327 `_), libFLAME (`#7163 `_), libpsml (`#5859 `_), LibSoup (`#8116 `_), libutempter (`#6426 `_), LS-PrePost (`#8070 `_), LUSCUS (`#7191 `_, `#8105 `_, `#8285 `_), memory-profiler (`#8255 `_), metaWRAP (`#7896 `_), Net-core (`#7716 `_), netMHC (`#8094 `_), Nextflow (`#8195 `_), nvtop (`#8024 `_), openpyxl (`#8121 `_), py-cpuinfo (`#8245 `_), pyFFTW (`#8198 `_), PyQtGraph (`#7525 `_, `#8253 `_), R-tesseract (`#7933 `_), RBFOpt (`#8178 `_), rnaQUAST (`#8040 `_), RStan (`#7996 `_), scikit-multilearn (`#8142 `_), simpy (`#8177 `_, `#8250 `_), SMARTdenovo (`#7630 `_), socat (`#8305 `_), SymEngine (`#7148 `_, `#8327 `_), unixODBC (`#8074 `_), VAtools (`#7938 `_), VirtualGL (`#8008 `_), WebKitGTK+ (`#8118 `_, `#8241 `_), xmlf90 (`#5858 `_), YAPS (`#7976 `_), zingeR (`#7264 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.70.0, cairo 1.16.0, CGAL 4.14, Clang 8.0, cutadapt 2.1, dask 1.1.4, ELPA 2018.11.001, FFmpeg 4.1.3, GCC 9.1.0, GEOS 3.7.2, GLib 2.60.1, gmsh 4.2.2, GROMACS 2019.2, GTK+ 3.24.8, h5py 2.9.0, hwloc 1.11.12, Hypre 2.15.1, Mathematica 12.0.0, matplotlib 3.0.3, Mesa 19.0.1, NBO 7.0, NCL 6.6.2, NCO 4.7.9, NiBabel 2.4.0, numba 0.43.1, OpenMPI 3.1.4, OrthoFinder 2.3.3, PCMSolver 1.2.3, PETSc 3.11.1, PROJ 6.0.0, PyQt5 5.12.1, PyTorch 1.0.1, PyYAML 5.1, Qt5 5.12.3, QuantumESPRESSO 6.4.1, R 3.5.1 (w/ intel/2018b), RNAIndel 1.0.0, Ruby 2.6.3, scikit-learn 0.20.3, SLEPc 3.11.0, sympy 1.4, Tkinter 3.7.2, Vim 8.1.1209, VTK 8.2.0, wrf-python 1.3.1, wxPython 4.0.4, wxWidgets 3.0.4, xarray 0.12.1, zstd 1.4.0 * minor enhancements, including: * enable auto-download of VMD 1.9.3 + add patches for Surf and Stride (`#7305 `_) * add mlegp extension in R 3.5.1 easyconfigs (`#7814 `_) * add pkg-config file to bzip2 easyconfigs (`#8200 `_) * allow use of '``use_pip = False``' in easyconfigs if pip doesn't work (`#8220 `_) * various bug fixes, including: * fix checksums for nlme extensions in R easyconfigs (`#7814 `_, `#8054 `_) * add missing XZ dependency for Pysam > 0.12 (`#7971 `_) * define ``$GRACE_HOME`` in Grace easyconfigs, so that font dir can be located (`#8048 `_) * ``$XDG_DATA_DIRS`` must be set for GTK+ (`#8089 `_) * add missing FriBidi dependency for Pango 1.43.0 (`#8103 `_) * add (back) custom ``sanity_check_paths`` in recent Pango easyconfigs (`#8106 `_) * fix missing extensions in cutadapt 1.16 easyconfigs (`#8130 `_) * add missing cURL dependency for recent SAMtools versions (`#8131 `_) * add singledispatch extension to Python 2.7.15 easyconfig using ``GCCcore/8.2.0`` toolchain (`#8164 `_) * add missing X11 dependency for Gdk-Pixbuf 2.38.1 (`#8222 `_) * make sure ``hdf5r`` picks up HDF5 dependency in R 3.5.1 easyconfigs (`#8223 `_) * enable zstd compression in GRASS 7.6.0 easyconfig (`#8224 `_) * add missing ICU dependency on ICU for Harfbuzz 2.4.0 (`#8226 `_) * disable AVX512 DGEMM kernels in OpenBLAS 0.3.5 (`#8227 `_) * fix homepage/description in OrthoFinder easyconfig (`#8234 `_) * add ``Parallel::ForkManager`` extension to Perl 5.28.x easyconfigs (`#8247 `_) * replace LibUUID dependencies with util-linux (`#8258 `_) * add jemalloc & pkg-config as build deps for Salmon 0.12.0 (`#8264 `_) * fix MAJIQ easyconfig by fixing order of extensions + avoid numpy test hang (`#8272 `_) * fix shebang in GLib Python script + clarify runtime dependency on Python (`#8277 `_) * add pkg-config and expat as (build) dependency for DBus (`#8283 `_) * define ``$GI_TYPELIB_PATH`` in GTK+ and Pango easyconfigs (`#8246 `_, `#8286 `_) * add pkg-config build dep to PROJ 6.0.0 easyconfig (`#8309 `_) * fix source URLS in recent libcerf easyconfigs (`#8332 `_, `#8243 `_) * make zlib a real dependency rather than a build dep in recent binutils easyconfigs (>= 2.28) (`#8340 `_) * add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs (`#8341 `_) * set ``$XDG_CACHE_HOME`` to $TMPDIR before '``pip install``' in Arrow 0.12.0 easyconfigs (`#8347 `_) * other changes: * remove xbitmaps dependency from motif (`#7530 `_) * require custom ``sanity_check_paths`` in easyconfigs touched in PRs when generic easyblock is used (`#8101 `_, `#8123 `_) * use CMake built with GCCcore toolchain when installing Eigen 3.3.4+ (`#8261 `_) * fix Python classifiers in ``setup.py``, should be (only) Python 2.6 & 2.7 (`#8299 `_) * use custom easyblock for OpenBLAS in OpenBLAS 0.3.x easyconfigs (`#8345 `_, `#8339 `_) .. _release_notes_eb390: EasyBuild v3.9.0 (April 12th 2019) ---------------------------------- feature release **framework** * various enhancements, including: * add ``(pre)testopts`` easyconfig parameters (`#2793 `_) * add support for ``multi_deps`` easyconfig parameter (`#2741 `_, `#2810 `_, `#2811 `_, `#2812 `_, `#2813 `_, `#2825 `_, `#2826 `_, `#2827 `_, `#2828 `_) * various bug fixes, including: * fix argument name in ``close_pr`` (`#2752 `_) * fix undefined variable '``prefix``' in ``Compiler._set_compiler_vars`` (`#2757 `_) * fix test account for GitHub-related tests (`#2760 `_) * make sure read permissions are always set in ``permissions_step`` (`#2770 `_) * make test for ``dep_graph`` function robust against changing order of lines in resulting dot file (`#2772 `_) * fix problem with ``import_available_modules`` when running from easybuild-framework directory (`#2786 `_) * prepend location of test easyblocks to ``$PYTHONPATH`` to ``test_generate_software_list``, rather than append (`#2788 `_) * use pid in backup name candidate to reduce risk of two processes colliding (`#2796 `_) * automatically enable ``--ignore-osdeps`` when using ``--preview-pr`` (`#2799 `_) * use temporary checkout of repository as robot path for ``--new-pr`` and ``--update-pr`` to determine locations for patch files (`#2803 `_) * avoid relying on order in which keys are processed in ``to_dependency`` (`#2804 `_) * fix yeb format to work with PyYAML 5 (`#2809 `_) * fix typo in error message for use of unknown easyconfig parameter (`#2817 `_) * enhance ``log_file_format`` to fix problem when ``%(name)s`` template value is used for log directory (`#2818 `_) * iterate over subdirectories in order in ``find_egg_dir_for`` of bootstrap script, to ensure oldest vsc-install is picked (`#2819 `_) * replace ``-Wl,--enable-new-dtags`` compiler option with ``-Wl,--disable-new-dtags`` in RPATH wrapper script (`#2821 `_) * updated ``COMPILER_F77`` for PGI >= 19.1 (`#2823 `_) * added ``FFTW_STATIC_LIBS_MT`` to ``FFTW_MAP_CLASS``, otherwise ``FFTW_STATIC_LIBS_MT`` are incorrectly defined (`#2822 `_) * sort available version list when selecting/generating easyconfig (`#2732 `_) * other changes: * use ``assertEqual`` rather than ``assertEquals`` (which is deprecated) (`#2746 `_) * test with Tmod 4.1.4 (packaged in RHEL8) in Travis CI (`#2747 `_) * replace deps by hidden deps instead of removing them from the lists (`#2748 `_) * ensure non-zero exit code for all test subsuites (+ fix trivial style issues) (`#2773 `_) * silence printed deprecation warnings for easyconfigs/toolchains while running (easyconfigs) test suite (`#2781 `_) * avoid printing of messages/warnings in framework test suite (`#2782 `_) * enable silent mode for ``--new-pr`` and ``--update-pr`` (`#2802 `_) * update Travis config to reflect that PyYAML 5.x is no longer compatible with Python 2.6 (`#2807 `_) **easyblocks** * new software-specific easyblock for TensorRT (`#1627 `_) * minor enhancements, including: * make sure CMake doesn't pick up on system Boost in CMakeMake generic easyblock (`#1618 `_) * modified ``ConfigureMake`` and ``CMakeMake`` generic easyblocks to allow changing ``configure_cmd``, ``build_cmd`` and ``install_cmd`` to fit various needs (`#1628 `_, `#1658 `_) * update ANSYS easyblock to deal with changed versioning scheme (`#1631 `_) * add extra path to builddir for SNPhylo >= 20160204 (`#1632 `_) * add better support for TensorRT to TensorFlow (`#1634 `_) * add support for newer versions of wxPython to wxPython easyblock (`#1635 `_) * update OCaml easyblock to support OPAM 2.x (`#1638 `_) * update sanity check in TensorFlow easyblock for TensorFlow 1.13.x (`#1642 `_) * make ``ConfigureMake``, ``MesonNinja`` and ``SCons`` generic easyblocks aware of pretestopts (`#1645 `_) * add support for installing Python packages with '``pip``' without using ``--ignore-installed`` (`#1647 `_) * add support to ``CMakeMake`` easyblock to specify compilers using absolute file path (`#1652 `_, `#1655 `_) * stop checking for deprecated ``pgf77`` in sanity check of PGI easyblock (`#1653 `_) * accommodate version 10.1 in CUDA easyblock (`#1654 `_) * install ``sitecustomize.py`` with Python to support Python package installations for multiple Python versions in a single directory (`#1657 `_) * enhance SAMtools easyblock to also install ``libhts.a`` and include/htslib (when applicable) (`#1661 `_) * tweak ``PythonPackage`` & ``PythonBundle`` to update ``$EBPYTHONPREFIXES`` rather than ``$PYTHONPATH`` for multi-Python installations + make ``sanity_check_step`` aware of multi_deps (`#1664 `_, `#1678 `_) * replace ``-openmp`` with ``-fopenmp`` when building TINKER with Intel compilers (+ modernize easyblock) (`#1668 `_) * make sure Meson is configured with ``-Dlibdir=lib`` so it doesn't install libraries in ``lib/x86_64-linux-gnu`` on Debian/Ubuntu multiarch systems (`#1673 `_) * allow for external libfabric via ``ofi_libfabric`` parameter in impi easyblock (`#1676 `_) * pass down compiler names and options to Qt5 5.8 & more recent via corresponding ``QMAKE_*`` configuration options (`#1677 `_) * various bug fixes, including: * create symlinks to ``.modulerc`` in symlinked module directories (`#1636 `_) * add missing import in FFTW easyblock (`#1641 `_) * fix finding of Python 3 include subdir + ``libpython*.so`` in OpenBabel easyblock (`#1633 `_) * add ``no_qa`` pattern for interactive installation command for ABAQUS (`#1637 `_) * make serial, smpar and dm+sm builds of WRF work and pass tests (`#1646 `_) * configure CP2K with correct ``DATA_DIR`` value rather than relying on ``$CP2K_DATA_DIR`` environment variable (`#1650 `_) * CP2K fixes: only call configure_LAPACK/ScaLAPACK when imkl is not used, prefer using 2^2 MPI processes for tests (`#1651 `_) * also take into account custom easyconfig parameters from ``CMakeMake`` in BamTools easyblock (`#1656 `_) * make sure Perl scripts are installed in the right location (`#1660 `_) * make sure setenv is used for CUDA_PATH etc. (`#1663 `_) * cleanup ``sanity_check_paths`` in numpy & scipy easyblocks (`#1665 `_, `#1667 `_) * always set ``self.pylibdir`` in ``PythonPackage.set_pylibdirs()``, which is important when installing Python packages for multiple Python versions via ``multi_deps`` (`#1671 `_) * fix custom definition of ``load_module`` method in LAPACK module (`#1675 `_) * other changes: * replace '``except OSError, err:``' pattern with '``except OSError as err:``' (for compatibility with Python 3.x) (`#1639 `_) * clean up Java easyblock to use ``filetools`` functionality (`#1649 `_) **easyconfigs** * added easyconfigs for new toolchains: ``intel/2019.02`` (`#7598 `_), ``intel/2019.03`` (`#7846 `_) * added example easyconfig files for 68 new software packages: * ACT (`#7928 `_), aiohttp (`#7728 `_), at-spi2-atk and at-spi2-core (`#7658 `_), Bader (`#7804 `_), barrnap (`#7738 `_), BCEL (`#7937 `_), biscuit (`#5868 `_), bitarray (`#7772 `_), BlobTools (`#7565 `_, `#7583 `_), bmtagger (`#7890 `_), bsddb3 (`#7642 `_), CheckM (`#7712 `_), Cheetah (`#7952 `_), CONCOCT (`#7891 `_), cyvcf2 (`#8031 `_), DAS_Tool (`#7741 `_), ExaBayes (`#7801 `_), FastANI (`#7992 `_), fastp (`#7693 `_), Flask (`#7734 `_), giflib (`#7663 `_), Giza (`#7843 `_), glew (`#7685 `_), gpustat (`#8025 `_), GRASS (`#7489 `_), GTDB-Tk (`#7995 `_), HPCX (`#7725 `_), IntelPython (`#7920 `_), KNIME (`#7554 `_), KronaTools (`#7721 `_), KyotoCabinet (`#7955 `_), Leptonica (`#7932 `_), libepoxy (`#7655 `_), libpsl (`#7666 `_), MAGMA (`#7829 `_), MATLAB-Engine (`#7758 `_), MaxBin (`#7767 `_), MetaBAT (`#7746 `_, `#7931 `_), MinPath (`#7763 `_), ncdu (`#7505 `_), NGSadmix (`#7524 `_), NIMBLE (`#7564 `_), PCAngsd (`#7727 `_), pizzly (`#7724 `_), Ploticus (`#7545 `_), pocl (`#7681 `_), POT (`#8011 `_), ProjectQ (`#7576 `_), pullseq (`#7740 `_), pyBigWig (`#7600 `_), Pyke3 (`#8034 `_), PyRETIS (`#8041 `_), RDKit (`#7973 `_), RNAIndel (`#8009 `_), scikit-optimize (`#7613 `_), SciPy-bundle (`#7922 `_), sep (`#8032 `_), slidingwindow (`#7909 `_), SPLASH (`#7843 `_), SqueezeMeta (`#7771 `_), SRPRISM (`#7890 `_), taxator-tk (`#7894 `_), TensorRT (`#7584 `_), tesseract (`#7932 `_), Transrate (`#5108 `_), VCF-kit (`#7786 `_, `#7882 `_), VV (`#7297 `_) * added additional easyconfigs for various supported software packages, including: * AFNI 19.0.01, Arrow 0.7.1, BLAST+ 2.8.1, CUDA 10.1.105, GCC(core) 8.3.0, GTK+ 3.22.30, Java (OpenJDK) 11(.0.2), Meson 0.50.0, MultiQC 1.7, Nim 0.19.2, Ninja 1.9.0, netCDF 4.6.2, netCDF-Fortran 4.4.5, PCRE 8.43, Perl 5.28.1, PGI 19.1, Python 3.7.2, RELION 3.0.4, Ruby 2.6.1, SCons 3.0.4, SQLite 3.27.2, SuiteSparse 5.4.0, TINKER 8.6.1, TensorFlow 1.13.1, X11 20190311 * minor enhancements, including: * add various extensions to R 3.5.1 easyconfigs: ``asnipe`` (`#7572 `_), ``liquidSVM`` (`#7597 `_), ``oddsratio``/``mltools``/``h2o`` (`#7744 `_), ``mlegp`` (`#7814 `_), ``bartMachine``/``lqa`` (`#7865 `_), ``PresenceAbsence``/``GUTS``/``GenSA`` (`#7905 `_), ``parsedate`` (`#7935 `_), ``circular`` (`#7975 `_) * add ``ujson`` extension in recent Python easyconfigs (`#7517 `_) * run various checks on easyconfigs that are touched in pull requests and involve Python packages (`#7754 `_) * add ``cpanminus`` extension to recent Perl easyconfigs (`#7866 `_) * also install ANTs scripts (and set ``$ANTSPATH`` as required by those scripts) (`#7940 `_) * add missing ``configopts`` in GATE 8.1 easyconfig to enable Davis feature (`#8000 `_) * various bug fixes, including: * add patch for Mesa 18.1.1 to detect MIT-SHM (`#7536 `_) * add proper description to MINC-2.4.03 (`#7551 `_) * add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (`#7629 `_) * add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs (`#7696 `_) * fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) (`#7743 `_) * use ``https://`` in most recent XZ easyconfigs (`#7782 `_) * add patch for OpenMPI 3.1.x to fix ib-query '``Invalid argument``' error (`#7789 `_) * build OpenBLAS with ``-fno-tree-vectorize`` (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (`#7790 `_, `#7793 `_) * extra patch for TensorFlow 1.12.0 to remove ``-B/usr/bin`` from ``linker_bin_path_flag`` in ``cuda_configure.bzl`` (`#7800 `_) * fix easyconfig for STAR-Fusion 1.5.0 (`#7802 `_) * fix checksums for boot/nlme extensions in R easyconfigs (`#7814 `_, `#8054 `_) * add patch for OpenMPI 3.x to fix UCX memory leak (`#7535 `_, `#7824 `_) * replace ``ncurses-devel`` OS dependency in CMake easyconfigs using ``dummy`` toolchain with proper ncurses dependency (`#7834 `_) * use ``PythonBundle`` for ``snakemake-5.2.4-foss-2018b-Python-3.6.6.eb`` (+ fix moduleclass) (`#7842 `_) * use correct ``buildopts`` + add missing zlib dependency in StringTie 1.3.5 easyconfig (`#7845 `_) * update GStreamer to not enable dw and fix some missing dependencies (`#7889 `_) * add missing XZ dependency to most recent Pysam easyconfigs (`#7897 `_) * expat: add configure option ``--without-docbook`` to avoid docbook2X dependency (`#7930 `_) * fix source URLs for mawk (`#7960 `_) * fix LWM2, OTF2, OPARI2, and Score-P download URLs (`#7994 `_) * use ``https://`` in homepage & source_urls for OpenMPI and hwloc easyconfigs (`#8013 `_, `#8014 `_, `#8015 `_ and `#8016 `_) * add missing bokeh dependency for dask 1.0.0 (+ add dask-jobqueue) (`#8029 `_) * fix checking of binutils build dep in easyconfig tests (`#8038 `_) * other changes: * avoid use of ``.items()`` in R (bundle) easyconfigs, to fix compatibility with EasyBuild running on top of Python 3 (`#7791 `_) * trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (`#7795 `_, `#7798 `_) * use ``%(pyshortver)s`` template in (old) SIP easyconfigs (`#7797 `_) * add PyTorch to whitelist for not having '``use_pip``' enabled (`#7844 `_) * don't use local variable '``pylibdir``' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 (`#7848 `_) * use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains (`#7864 `_) * prefer ``https://`` over ``ftp://`` for source_urls in recent GROMACS easyconfigs (`#7948 `_) * rename arrow to Arrow for old easyconfig (`#8007 `_) .. _release_notes_eb381: EasyBuild v3.8.1 (January 29th 2019) ------------------------------------ bugfix/update release **framework** * various minor enhancements, including: * speed up checking of OS dependencies (`#2703 `_) * add support for '``eb --show-system-info``' (`#2722 `_) * add support for '``%(arch)s``' template value in easyconfig files (x86-64, aarch64, ppc64le, ...) (`#2728 `_) * various bug fixes, including: * add timestamp to reprod dir while in tmp space (`#2705 `_) * avoid '``+``' in directory name for ``g++`` rpath wrapper (`#2710 `_) * pre-install vsc-install < 0.11.4 in bootstrap script to avoid requiring '``mock``' Python package (`#2717 `_) * fix check in ``--merge-pr`` whether PR is eligible for merging in to only consider the status of the last test report (`#2720 `_) * don't recreate build directory when '``buildininstalldir``' is enabled for iterative installations (`#2724 `_) * filter (CUDA) ``lib*/stubs`` paths in RPATH wrapper script (`#2725 `_) * other changes: * replace '``except IOError, err:``' pattern with '``except IOError as err:``' for compatibility with Python 3.x (`#2711 `_) * make all ``print`` statements compatible with Python 3 (`#2715 `_) * avoid use of ``sys.maxint`` in dependencies_for (`#2716 `_) **easyblocks** * minor enhancements, including: * update Ferret easyblock to handle Ferret 7.3 (`#1349 `_) * add support for defining ``$LDSHARED`` when installing Python packages if Python's value doesn't use toolchain compiler ($CC) (`#1455 `_) * update CP2K easyblock to add support for CP2K 6.1, and fix incorrect LibInt references (`#1545 `_) * make OpenFOAM easyblock handle debug build (`#1609 `_) * handle multiple installation keys for MATLAB (`#1610 `_) * run '``make check``' in parallel for GROMACS since it involves more compilation (`#1611 `_) * update OpenCV easyblock for recent versions (3.4.x >= 3.4.4 + 4.0.x) (`#1616 `_) * various bug fixes, including: * check current ``start_dir`` value before appending '``src``' subdirectory in MrBayes easyblock (`#1582 `_) * avoid that (system) Intel compilers are always considered when building SuiteSparse (`#1612 `_) * fix missing import statement in ROOT easyblock (`#1614 `_) * answer SELinux question with '``no``' in Mathematica easyblock (`#1617 `_) * disable "build isolation" feature in pip > 10.x in PythonPackage generic easyblock (`#1623 `_) * other changes * cleanup in Perl and PerlModule easyblocks (`#1603 `_) **easyconfigs** * added easyconfigs for new toolchains ``foss/2019a`` (`#7371 `_), ``intel/2019a`` (`#7372 `_) and ``iomkl/2019.01`` (`#7375 `_) * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html * added example easyconfig files for 43 new software packages: * Assimulo (`#6740 `_), C3D (`#7059 `_), CellMix (`#7422 `_), CESM-deps (`#6654 `_, `#6675 `_, `#6823 `_), DSA (`#7422 `_), DeMixT (`#7422 `_), deconf (`#7422 `_), DeconICA (`#7422 `_), double-conversion (`#7307 `_), dxpy (`#7079 `_), EPIC (`#7422 `_), expect (`#7387 `_), Flye (`#7430 `_), FMILibrary (`#6740 `_), FMRIprep (`#7059 `_), FUSE (`#7078 `_), GDCM (`#7310 `_), HDDM (`#7396 `_), ICA-AROMA (`#7059 `_), IntaRNA (`#7334 `_), imageio (`#6738 `_), KWIML (`#7308 `_), kWIP (`#7444 `_), MagresPython (`#7395 `_), medaka (`#7426 `_), MINC (`#7311 `_), MuSiC (`#7422 `_), netMHCIIpan (`#7377 `_), NIfTI (`#7311 `_), OPERA (`#7408 `_), psrecord (`#7331 `_), pyfits (`#7273 `_), PyFMI (`#6740 `_), PyGWAS (`#5852 `_), Pylint (`#6675 `_), QDD (`#7284 `_), RERconverge (`#7289 `_), samclip (`#7226 `_), SCIPhI (`#7419 `_), swarm (`#7453 `_), VXL (`#7309 `_), wrf-python (`#6736 `_), xCell (`#7422 `_) * added additional easyconfigs for various supported software packages, including: * Amber 18, Arrow 0.12.0, Biopython 1.73, Boost 1.69.0, CP2K 6.1, canu 1.8, Ferret 7.3, GATE 8.1.p01, GROMACS 2019, Geant4 10.5, HPL 2.3, libxsmm 1.10, matplotlib 3.0.2, NEURON 7.6.5, Octave 4.4.1, OpenBLAS 0.3.5, OpenCV 3.4.5 + 4.0.1, OpenFOAM v1812, PGI 18.10, PLUMED 2.5.0, ROOT 6.14.06, Theano 1.0.3, TopHat 2.1.2, Yade 2018.02b * minor enhancements, including: * add additional extensions to R 3.5.1 easyconfigs: * statnet (`#7370 `_), NMF, ComICS, dtangle, MCMCpack, shinythemes (`#7420 `_), csSAM (`#7423 `_), bridgedist (`#7477 `_) * add DeconRNASeq and GSVA extensions to R-bundle-Bioconductor 3.7 easyconfigs (`#7421 `_) * also install header files and CMake module for SeqAn 2.4.0 built with ``foss/2018b`` (`#7434 `_) * add download URL for ``intel/2018a`` components (`#7436 `_) * add missing checksums for protobuf easyconfigs using dummy toolchain (`#7492 `_) * various bug fixes, including: * fix source URL in Doxygen easyconfigs (`#7324 `_) * add fallback source URL for recent pigz versions (`#7346 `_) * promote FriBiDi to runtime dep of Pango rather than only build dep (`#7369 `_) * add ``--without-systemdsystemunitdir`` configure option to recent DBus easyconfigs (`#7373 `_) * fix issue of building M4 1.4.18 with glibc 2.28 (`#7384 `_) * fix broken source URLs in MariaDB easyconfigs (`#7413 `_) * bump up build dependency of flex 2.6.4 from Bison 3.0.4 to 3.0.5 (`#7414 `_) * disable building of OpenColorIO Python bindings since Python is not included as a dependency (`#7416 `_) * add missing build dependencies in old Harfbuzz/Pango easyconfigs (2016a generation) (`#7433 `_) * fix XML-LibXML linking with Intel compiler and GCCcore Perl (`#7440 `_) * prevent non-critical error from stopping Guile v1.8.8 build (`#7446 `_) * use ``%(arch)s`` template rather than hardcoding '``x86_64``' in XML-Parser easyconfigs (`#7450 `_) * use uniform configopts for Guile 1.8.8 (`#7452 `_) * fix configopts in PyQt5 easyconfig files to avoid installation of files in Python/Qt5 installation directories (`#7470 `_) * other changes: * fix homepage in easyconfigs for ``foss`` toolchains (`#7482 `_) and ``intel`` toolchains (`#7483 `_) .. _release_notes_eb380: EasyBuild v3.8.0 (December 18th 2018) ------------------------------------- feature release **framework** * various enhancements, including: * support use of version ranges in ``--filter-deps`` (`#2357 `_) * add support for ``--list-prs`` (`#2400 `_, `#2668 `_) * add support for ``--close-pr`` (`#2401 `_) * allow setting ``optarch`` compiler flags in the easyconfig via ``toolchainopts`` easyconfig parameter (`#2595 `_) * add option to skip pre-creation of install directory: ``--disable-pre-create-installdir`` (`#2629 `_, `#2637 `_) * flesh out setting up of configuration into dedicated '``set_up_configuration``' function (`#2638 `_) * clean error when '``eb``' is cancelled by user (`#2641 `_) * add support for using Slurm as backend for ``--job``, via ``--job-backend=Slurm`` (`#2642 `_, `#2666 `_) * save easyblocks along with easyconfig in '``reprod``' subdirectory of install directory (`#2653 `_) * add support for deprecating easyconfig files & toolchains (`#2656 `_) * changed ``EasyConfig.update`` to be able to specify not to allow duplicate values (`#2657 `_) * move adding of dependencies to prepare step instead of check readiness step (`#2674 `_) * add support for disabling mapping of (sub)toolchains when ``--try-toolchain`` is used, via ``--disable-map-toolchains`` (`#2682 `_) * add '``astro``' and '``quantum``' module classes (`#2693 `_) * various bug fixes, including: * make ``--from-pr`` always try to apply PR patch on top of PR target branch (`#2631 `_) * fix bug that could cause to silently overwrite an existing easyconfig when using ``--try-*`` (`#2635 `_) * don't pass down specific environment variables into submitted jobs (`#2643 `_) * update template constants for source URLs to use https (`#2648 `_) * fix lib64 fallback for '``lib``'/'``lib64``' dirs entry in ``sanity_check_paths`` (`#2649 `_) * change PGI F90 Fortran compiler to pgf90 (`#2650 `_) * use ``--set-upstream-to`` in ``install-EasyBuild-develop.sh`` script to deal with deprecated/no longer supported ``--set-upstream`` (`#2651 `_) * fix order of keys in '``toolchain``' value for dumped easyconfig file (name, version) + run style check on dumped easyconfigs in dump tests (`#2660 `_) * ensure checksums beside sources in dumped easyconfigs (`#2661 `_) * fix problems with easyconfig file saved in '``reprod``' directory by copying it before running any installation steps (`#2664 `_) * make print functions more robust w.r.t. arguments being passed to format the message to be printed (`#2670 `_) * use '``git am``' to apply patch for PRs in ``fetch_easyconfigs_from_pr`` (`#2680 `_) * correctly define ``$LIBFFT_MT`` for Intel MKL (`#2688 `_) * don't always require easyconfig files to resolve dependencies (`#2690 `_, `#2692 `_, `#2697 `_, `#2698 `_, `#2699 `_) * fixes for Travis CI config: * stop testing with Lmod 6.6.3, testing with Lmod 6.5.1 is sufficient (`#2627 `_) * Python 2.6 requires python-daemon 1.x as dep for GC3Pie (`#2673 `_) * stick to idna<2.8 with Python 2.6 in Travis + distable broken test for HgRepository (`#2678 `_) * other changes: * always skip symlinks in ``adjust_permissions`` (`#2644 `_) * flesh out '``avail_easyblocks``' function from support for ``--list-easyblocks`` (`#2663 `_) * deprecate the ``ictce`` toolchain (`#2667 `_) * deprecate ``goolf`` and ``goolfc`` toolchains (`#2676 `_) * deprecate ``intel`` toolchains older than ``intel/2016a`` (+ ``iccifort`` & ``iimpi`` subtoolchains) (`#2677 `_) * deprecate ancient ``gompi`` toolchain versions (`#2684 `_) * use '``tar xzf``' (gzip) rather than '``tar xZf``' (ancient ``compress``) to unpack ``*.tar.Z`` source files (`#2686 `_) * flesh out '``set_parallel``' method to it can be called separately (`#2687 `_) **easyblocks** * new generic easyblocks: * ``PythonBundle`` for installing a bundle of Python packages (`#1553 `_) * ``MesonNinja`` for installing using Meson & Ninja (`#1561 `_) * new software specific easyblock for ``RepeatMasker`` (`#1600 `_) * minor enhancements, including: * add ``-fno-delete-null-pointer-checks`` compiler flag for OpenFOAM versions older than v3.0 (`#1311 `_) * add support for building Tau with OTF included as dependency (`#1313 `_) * add support for Intel MPI version 2019 (`#1546 `_) * also populate the include dir for CP2K (`#1554 `_) * add custom easyconfig parameter in GCC easyblock to control use of gold linker: ``use_gold_linker`` (`#1555 `_) * replace '``-``' with '``_``' in default '``import``' check for Python packages (`#1560 `_) * update WRF and WPS to support version 4 (`#1563 `_) * adapt PSI easyblock for PSI4 > 1.2 (`#1568 `_) * update Siesta easyblock to 4.1-b4 and add custom test_step (`#1573 `_) * enhance Mothur easyblock to support use of Boost and HDF5 as dependencies (`#1576 `_) * enhance sanity check for icc & ifort: also check for ``compilers_and_libraries_*/linux`` subdirectory (`#1577 `_) * update Trinity easyblock for latest version 2.8 (`#1579 `_) * add version check in sanity check step of SCOTCH easyblock (+ code cleanup) (`#1580 `_) * add support in Clang easyblock to skip running of all tests (`#1584 `_) * update WRF easyblock to allow serial HDF5 + pick up on parallel netCDF (`#1592 `_) * avoid hardcoding '``PREFIX=``' in build/install options when using ``SCons`` easyblock (`#1594 `_) * enable TensorFlow to detect any MPI runtime (`#1597 `_) * enhance ``Bundle`` easyblock to allow installation of bundle components with additional easyblocks + build components in parallel (`#1598 `_) * enhance Trilinos easyblock to support building against MKL (`#1601 `_) * various bug fixes, including: * make FDTD_Solutions easyblock do the install by copying files instead of '``rpm rebuild``' (`#1307 `_) * re-add missing ``VT_(S)LIB_DIR`` env variable to itac module (`#1309 `_) * fix in QuantumESPRESSO easyblock: ifort compiler needs ``-assume byterecl`` (`#1556 `_) * extract targets from buildopts in Quantumespresso easyblock (`#1558 `_) * fixes for TensorFlow easyblock (`#1559 `_) * pass ``$PYTHONPATH`` while building TensorFlow * disable cross-compilation mode if optarch is set * fix sanity check for installing TensorFlow as extension * added a test to disable compiling FFTW with MPI if the toolchain does not support MPI (`#1562 `_) * fix permissions problem with CUDA nvvp tar files + correctly handle numactl symlink in LLVM subdir in PGI easyblock (`#1569 `_) * fix TensorFlow test tempdir problem (`#1572 `_) * tweak VMD easyblock so that ``configopts`` don't contain duplicate values (otherwise it fails to rebuild) (`#1575 `_) * fix running netcdf4-python tests to also support installation as extension (`#1578 `_) * added the openmp flags in the linker flags in MUMPS easyblock (`#1585 `_) * avoid hardcoding ``--with-rdma`` configure option in MVAPICH2 easyblock (`#1586 `_) * fix location of path-to-source argument in configure command of ``CMakeMake`` (`#1591 `_) * fix GROMACS use of MKL for non-Intel compilers (e.g. gomkl toolchain) (`#1596 `_) * other changes * inform Hound CI about Python 2 builtins (`#1604 `_) **easyconfigs** * added easyconfigs for new toolchains: ``intel/2018.04`` (`#7171 `_), ``intel/2019.00`` (`#7218 `_), ``intel/2019.01`` (`#7219 `_) * added example easyconfig files for 36 new software packages: * 4ti2 (`#7040 `_), ARPACK++ (`#6750 `_), CellRanger (`#7242 `_), CharLS (`#6762 `_) cscope (`#7057 `_), ctags (`#7057 `_), datamash (`#6693 `_), dcm2niix (`#6762 `_), DCMTK (`#6761 `_), deepdiff (`#7109 `_), Drake (`#7182 `_), fast5 (`#7250 `_), gap (`#7040 `_), Gerris (`#7211 `_), GPAW-setups (`#6984 `_), iCount (`#7080 `_), ipyparallel (`#6797 `_), Kratos (`#7149 `_), LCov (`#7160 `_), libvdwxc (`#6984 `_), libwebp (`#7065 `_), lrslib (`#7040 `_), MuPeXI (`#6991 `_), netMHCpan (`#6991 `_), Normaliz (`#7040 `_), OpenColorIO (`#7146 `_), OpenJPEG (`#7216 `_), PHLAT (`#7036 `_), poppler (`#7069 `_), RECON (`#7042 `_), RepeatMasker (`#7281 `_), TreeMix (`#7133 `_), unrar (`#7117 `_), utf8proc (`#7083 `_), VSEARCH (`#7153 `_), XMDS2 (`#7121 `_) * added additional easyconfigs for various supported software packages, including: * CheMPS2 1.8.8, Clang 6.0.1 + 7.0.0, dask 1.0.0, FFmpeg 4.1, GCC(core) 6.5.0 + 7.4.0, GPAW 1.4.0, HMMER 3.2.1, IPython 7.2.0, ITK 4.13.1, Keras 2.2.4, LLVM 7.0.0, Mothur 1.41.0, MultiQC 1.6, NAMD 2.13, OpenBLAS 0.3.4, OpenMPI 3.1.3 + 4.0.0, PSI4 1.2.1, Qt5 5.11.2, QuantumESPRESSO 6.3, Rust 1.30.1, Spark 2.4.0, Spyder 3.3.1, TensorFlow 1.11.0 + 1.12.0 * minor enhancements, including: * install misc tools for angsd (`#6995 `_) * add libXp component to X11 bundle for GCCcore 6.4.0 (`#7062 `_) * also install shared libraries for LZO (`#7073 `_) * add extensions to R 3.5.1 easyconfigs: ``gllvm`` (`#7123 `_), ``grpreg`` (`#7140 `_), ``gamlss`` + ``gamlss.tr`` (`#7263 `_) * install Tk private headers (`#7155 `_) * add ``File::Next`` extension to Perl 5.28.0 easyconfig (`#7276 `_) * various bug fixes, including: * fix installation of scikit-image 0.13.x by including missing required ``PyWavelets`` extension (`#7061 `_) * add missing dependencies to easyconfig for GC3Pie 2.5.0 (`#7066 `_) * stop setting ignored '``full_sanity_check``' easyconfig parameter in easyconfigs (`#7094 `_) * add missing checksums in X11/2016* easyconfigs (`#7095 `_) * add missing checksums in X11/2017* easyconfigs (`#7096 `_) * add missing ``cffi`` & ``pycparser`` extensions to recent Python easyconfigs (`#7105 `_, `#7118 `_) * fix homepage in QuantumESPRESSO easyconfigs (`#7114 `_) * use empty toolchain version in picard easyconfigs to ensure Java dependency is loaded during installation (`#7116 `_) * fix checksum for ``mgcv`` extension in R 3.5.* easyconfigs (`#7122 `_) * add missing 'patsy' extension in ARCH easyconfig + switch to using ``PythonBundle`` easyblock (`#7124 `_) * add missing (dummy) sklearn extension in NeuroKit easyconfig (`#7126 `_) * fix order of extensions in recent IPython easyconfigs to make '``pip check``' pass (`#7131 `_) * fix missing required Python packages in ASE 3.16.2 easyconfigs (`#7139 `_) * fix ``source_urls`` in CP2K easyconfigs (for official releases) (`#7240 `_) * update SCOTCH 6.0.5 easyconfigs in-place to 6.0.6 to fix wrong download URL (`#7159 `_) * add Autotools build dep in patchelf easyconfig (`#7175 `_) * STREAM fixes: use https + versioned source (`#7193 `_) * fix checksum in Molden easyconfig (`#7251 `_) * fix source URL for ADMIXTURE (`#7258 `_) * fix source URLs & versions + build procedure for SKESA (`#7275 `_) * fix checksum for TRF 4.09 (`#7278 `_) * add missing zlib dependency for NSS (`#7293 `_) * add required build deps for QtWebEngine in recent Qt5 easyconfigs (`#7300 `_) * fix ImageMagick source URLs: use ``launchpad.net`` for old versions, switch to GitHub for 7.0.8-* onwards (`#7301 `_) * other changes: * update ``Java/1.8`` wrapper to Java 1.8.0_192 (`#7097 `_) * don't enable ``optarch`` toolchain option in VCFtools easyconfigs, since it's enabled by default (`#7106 `_) * stop using lowopt in libxc 4.2.3 easyconfigs (`#7115 `_) * deprecate easyconfigs for ``ictce`` toolchains + ``intel`` toolchains older than ``intel/2016a`` (`#7231 `_) * deprecate easyconfigs for ``goolf(c)`` + corresponding ``gompi(c)`` subtoolchains (`#7243 `_) .. _release_notes_eb371: EasyBuild v3.7.1 (October 18th 2018) ------------------------------------ bugfix/update release **framework** - various enhancements, including: - generate ``.modulerc.lua`` when Lua syntax and Lmod >= 7.8 is used (`#2597 `_) - allow ``--force`` to use regex if ``--try-toolchain`` can not map intelligently (`#2605 `_) - add support for disabling modules tool version check (`#2610 `_) - add support to ``ModuleGenerator.modulerc`` method to also write ``.modulerc`` file (`#2611 `_) - check whether module file being wrapped exists in same directory as module wrapper when using Lmod 6.x (`#2611 `_) - various bug fixes, including: - stop relying on '``easy_install``' in bootstrap script, use '``python -m easy_install``' instead (`#2590 `_) - fix templating of values in ``list_software`` function (`#2591 `_) - fix composing of ``lib64`` fallback paths in sanity check (`#2602 `_) - determine ``file_info`` for all easyconfigs before any actual copying in ``copy_easyconfigs`` function (`#2604 `_) - also check for module wrappers in ``ModulesTool.exist`` method (`#2606 `_) - add trailing newline to module load message if it's not there yet (`#2613 `_) - retain all dependencies when determining dependency tree of a toolchain (`#2617 `_) - protect ``exts_lists`` from templating in ``dump`` method (`#2619 `_) - making CUDA capability detection more robust (`#2621 `_) - other changes: - lower required Lmod version to 6.5.1 (`#2593 `_) **easyblocks** - new software specific easyblocks for fastStructure (`#1529 `_) - minor enhancements, including: - support bypassing use of system type obtained with recent ``config.guess`` in ``ConfigureMake`` (`#1531 `_) - enhance generated module file for FreeSurfer (`#1543 `_) - add option in Qt easyblock to check for QtWebEngine component in sanity check (`#1544 `_) - also install CP2K as a library + code cleanup in CP2K easyblock (`#1547 `_) - various bug fixes, including: - fix checking for downloaded dependencies for stand-alone installations in ``PythonPackage`` generic easyblock (`#1530 `_) - also specify ``--host`` option to configure script based on config.guess result in ``ConfigureMake`` easyblock (`#1532 `_) - use short module name when creating module wrapper in ``ModuleRC`` generic easyblock (`#1535 `_) - use ``DOT_MODULERC`` constant in ``ModuleRC`` easyblock rather than hardcoding '``.modulerc``' (`#1533 `_) - use ``--no-deps`` when installing .whl in TensorFlow easyblock if extension are being installed, move test run to sanity check (`#1537 `_) - use ``os.getcwd()`` rather than ``self.startdir`` in TensorFlow easyblock to fix installation of TensorFlow as extension in a bundle (`#1540 `_) - add symlink to wrapped module file when creating ``.modulerc`` in temporary location (`#1539 `_) - properly handle Python dependency in Qscintilla easyblock (`#1499 `_) - other changes: - cleanup Tarball easyblock by using ``copy_dir`` function (`#1541 `_) **easyconfigs** - added easyconfigs for new toolchain ``foss/2018.08`` with GCC/8.2.0 (`#6992 `_) - added example easyconfig files for 26 new software packages: - ARCH (`#6939 `_), fbm (`#6948 `_), GenomeTester4 (`#6970 `_), GlobusConnectPersonal (`#6974 `_), MMseqs2 (`#6964 `_), NAG (`#5772 `_), NAGfor (`#5772 `_), NSPR (`#7005 `_), NSS (`#7005 `_), NeuroKit (`#6947 `_), novoalign (`#6944 `_), OptiType (`#6924 `_), OrthoFinder (`#6964 `_), pandas-datareader (`#6938 `_), pFUnit (`#6949 `_), PMIx (`#6930 `_), PSolver (`#6888 `_), PyDatastream (`#6951 `_), PyFR (`#6846 `_), Pyomo (`#6910 `_), Quandl (`#6950 `_), RTG-Tools (`#6862 `_), seq2HLA (`#6969 `_), suds (`#6951 `_), UCX (`#6931 `_), XMLSec (`#6929 `_) - added additional easyconfigs for various supported software packages, including: - binutils 2.31.1, dask 0.19.4, GCC(core) 8.2.0, OpenBLAS 0.3.3, OpenMPI 3.1.2, Pillow 5.3.0, PyCUDA 2018.1 - minor enhancements, including: - add clustree + plotly extensions (+ deps) for R 3.5.1 (`#6901 `_) - add tclsh symlink to recent Tcl easyconfigs (`#6915 `_) - update GROMACS 2016.3 with NVML patches (`#6936 `_) - use ``make=make`` in build options for ParMGridGen easyconfigs (`#6952 `_) - add ``Data::Dump`` as extension to Perl (dependency for GIMIC) (`#7004 `_) - various bug fixes, including: - inhibit ``-Werror`` in binutils 2.26 as new system GCC has case fallthrough warnings (`#5793 `_) - change fastStructure easyconfig to use custom easyblock (`#6893 `_) - fix toolchain for tbb dependency in ``Bowtie2-2.3.4.2-foss-2018b.eb`` (`#6927 `_) - fix uroot installation in R-3.5.1-foss-2018b (`#6934 `_) - add missing Python packages in TensorFlow 1.10.x easyconfigs (`#6940 `_) - add missing dep for Szip in 2017b builds of netCDF (`#6942 `_) - fix missing comment from ``OpenBabel-2.4.1-fix-link-path-tests.patch`` (`#6943 `_) - add patch to Python 3.6.1 - 3.6.3 that removes comment in comment (`#6946 `_) - add missing ``ulimit_unlimited=True`` (see issue `#6484 `_) in the newest Python builds (`#6959 `_) - solve '``version UUID_1.0 not found``' problem in LibUUID easyconfigs (`#6962 `_) - eliminate dependency on ancient problematic LibUUID library, replace with util-linux (`#6963 `_) - force building of ``ccmake`` for CMake 3.12.1 + fix deps (`#6967 `_) - fix broken installation for Python 3.6.2 & 3.6.3 with PyNaCl as dep for paramiko extension by explicitly including previous PyNaCl version as extension (`#6971 `_) - fix source URL for ADMIXTURE (no https) + add SHA256 checksum (`#6982 `_) - add missing NSS/DBus dependencies to Qt 5.10.1 easyconfigs built with foss toolchain to ensure that QtWebEngine component gets installed (`#7005 `_) - add '``openssl``' OS deps in Perl 5.28.0 easyconfig for ``Net::ssleay`` (`#7008 `_) - add missing checksum for ipaddress extension in Python easyconfigs (`#7021 `_ and `#7033 `_) - add missing extensions to Python 2.7.14 (`#7022 `_ and `#7023 `_), 3.6.2 (`#7025 `_), 3.6.3 (`#7027 `_) and 3.6.4 (`#7029 `_ and `#7030 `_) - add missing OS dependencies for git (`#7028 `_) - create default configuration for RTG-Tools (`#7032 `_) - also run checks on changed files when target branch for PR is something different than 'develop' (`#7034 `_) - other changes: - removed dead 'bzip.org' source URL for bzip2 source tarball (`#6983 `_) .. _release_notes_eb370: EasyBuild v3.7.0 (September 25th 2018) -------------------------------------- feature release **framework** - minimal Lmod version requirement bumped to 6.6.3 (`#2575 `_) - various enhancements, including: - add support to bootstrap script to force install specific EasyBuild version (`#2382 `_, `#2580 `_) - consider potential of multiple subtoolchains when resolving dependencies (`#2464 `_, `#2465 `_, `#2466 `_, `#2585 `_) - fall back to downloading using the ``requests`` Python package (if installed) when ``urllib2`` fails due to SSL error (`#2538 `_) - make ``--try-toolchain`` more aware of subtoolchains (`#2539 `_) - subtoolchain of original toolchains are now mapped to subtoolchains of target toolchain - add support for BLIS and goblf toolchain that uses BLIS for BLAS (`#2540 `_) - allow skipping of sanity check step via '``skipsteps``' easyconfig parameter (`#2549 `_) - add support for ``--check-contrib`` (`#2551 `_) - equivalent with ``--check-style``, but also verifies presence of SHA256 checksums (+ more checks in the future) - added support to 'download' sources from git (`#2555 `_) - see https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#downloading-from-a-git-repository - add '``parse``' hook to add support for applying site-specific customisations to the 'raw' easyconfig (`#2562 `_, `#2566 `_) - see https://easybuild.readthedocs.io/en/develop/Hooks.html - lift invalidating of module caches into helper method that can be used by easyblocks (`#2571 `_) - always dump a fully parsed easyconfig to the '``reprod``' subdir of the installation directory (`#2574 `_) - add '``modulerc``' method to ``ModuleGenerator`` class (`#2575 `_) - various bug fixes, including: - make GC3Pie stop build process if a dependency failed (`#2474 `_) - filter out patched files in test/ in ``fetch_easyconfigs_from_pr`` (`#2547 `_) - check GC3pie version using the ``pkg_resources`` API rather than using ``__version__`` (which was removed in GC3Pie 2.5.0) (`#2554 `_) - fix enforcing of checksums for extensions (`#2561 `_, `#2570 `_, `#2579 `_) - skip running of configuration checks while only a single configuration level is taken into account during ``--show-config`` (`#2567 `_) - fix error statements in modules tool version checks (`#2576 `_) - fix finding of software subdirectory for specified patch file in ``--new-pr``/``--update-pr`` (`#2577 `_) - take into account dependency 'wrappers' in check_conflicts (`#2583 `_) - stick to pycparser < 2.19 with Python 2.6 in Travis config (`#2584 `_) - other changes: - use ``namelower`` as default for '``github_account``' easyconfig parameter (`#2528 `_) - use ``.counts()`` rather than deprecated ``.stats()`` for GC3Pie (`#2573 `_) **easyblocks** - new generic easyblock: ``ModuleRC`` (`#1503 `_, `#1518 `_) - new software specific easyblocks for BWISE (`#1497 `_) and VEP (`#1512 `_) - minor enhancements, including: - update QuantumESPRESSO easyblock: stop building in installation dir, do not use external FoX dependency, support for recent versions (`#1312 `_) - updates to TensorFlow easyblock: - require cuDNN if CUDA support is enabled, enable mkl-dnn by default, fix problem with internal protobuf problem, add awareness for TensorRT & NCCL (`#1453 `_) - add support for IntelMPI (`#1507 `_) - update WIEN2k easyblock for version 18.1 (`#1460 `_) - add CUDA '``stubs``' subdirectory to $LIBRARY_PATH (`#1464 `_) - add support for building ScaLAPACK on top of BLIS (`#1467 `_) - handle X11 better and make '``static``' a build flag in Amber easyblock (`#1468 `_) - update Boost easyblock for Boost 1.67.0 (name change in Python 3.x library files) (`#1472 `_) - add CEI/bin to $PATH for ANSYS 19 & newer (`#1476 `_) - enhance SCons easyblock to enable building in parallel (`#1477 `_) - add awareness for CCOLAMD and CAMD in Trilinos easyblock (`#1480 `_) - add support to apply (binary) patches after main CUDA install (`#1481 `_, `#1483 `_) - add support for only building Python bindings (+ code cleanup) in Boost easyblock (`#1484 `_, `#1495 `_) - provide control over subdirectory in which R packages are installed (`#1485 `_) - added regex to fix ``$WM_PROJECT_VERSION`` correctly in OpenFOAM easyblock (`#1489 `_) - improve PGI siterc so it allows ``-pthread`` switch (`#1494 `_) - customise ``check_checksums method`` in Bundle easyblock to fix checking of checksums for components (`#1496 `_) - include a pkgconfig file '``hdf5.pc``' to HDF5 installations (`#1504 `_) - (download &) use an updated ``config.guess`` script in generic ConfigureMake easyblock (`#1506 `_, `#1522 `_, `#1523 `_, `#1524 `_) - make ``IntelBase`` generic easyblock aware of ``(pre)installopts`` (`#1509 `_) - update Siesta easyblock for v3.2 to 4.1-b3 (`#1510 `_) - take ``(pre)installopts`` into account in RPackage generic easyblock (`#1513 `_) - update DOLFIN easyblock for latest version (`#2018 `_.1) (`#1521 `_) - various bug fixes, including: - drop useless definition of ``$NLSPATH`` in ``IntelBase`` + fix ipp library paths (`#1442 `_) - fix order of arguments in log message in ``PythonPackage`` easyblock (`#1459 `_) - run ``ldconfig`` in post-install step of CUDA easyblock to create missing symlinks in 'stubs' subdirectory (`#1473 `_) - take into account that only name/version may be specified for some components in ``Bundle`` easyblock (`#1474 `_) - make SuperLU easyblock consider both ``lib`` and ``lib64`` subdirectories (`#1479 `_) - use short build dir for Trilinos to dance around "``Argument list too long``" problem + link with ``libmetis.a`` (`#1486 `_) - correct check for Red Hat 6 based OS in TensorFlow easyblock (`#1487 `_) - improve configuration choice in FSL easyblock (`#1498 `_) - don't check for ``mcc`` in MATLAB sanity check as it requires a specific toolbox license (`#1514 `_) - make sure Bazel doesn't write files in $HOME/.cache when building TensorFlow (`#1519 `_) - enable VSX on POWER for FFTW >= 3.3.7 (`#1520 `_) - add ``librt`` as dependency when linking Trilinos with SuiteSparse (`#1525 `_) - other changes: - switch to using CMake install procedure for Eigen 3.3.4 & newer (`#1482 `_) - bump Lmod version used in Travis config to 6.6.3 (now required by framework) (`#1505 `_) **easyconfigs** - added easyconfigs for new toolchains: ``fosscuda/2017b`` (`#6706 `_), ``intelcuda/#2017b`` (`#6709 `_), ``iomkl/2018b`` (`#6661 `_) - added example easyconfig files for 49 new software packages: - alleleCount (`#6676 `_), BCALM (`#6796 `_), BDBag (`#6672 `_), BFC (`#6647 `_), Bio-DB-HTS (`#6854 `_), bioawk (`#6865 `_), biomart-perl (`#6745 `_), BLIS (`#6614 `_), Boost.Python (`#6763 `_), BWISE (`#6802 `_), CapnProto (`#6542 `_), CaVEMan (`#6708 `_), CCL (`#5802 `_), cDNA_Cupcake (`#6787 `_), cget (`#6780 `_), coevol (`#6589 `_, `#6642 `_), Delly (`#6735 `_), earthengine-api (`#6556 `_), fineRADstructure (`#6586 `_), GIMIC (`#6575 `_), GitPython (`#6850 `_), HiC-Pro (`#5873 `_), Inelastica (`#6831 `_), JAXFrontCE (`#6837 `_), jq (`#6632 `_), KAT (`#6808 `_), KMC (`#6553 `_), Kraken2 (`#6569 `_), Lighter (`#6553 `_), Mash (`#6542 `_), MetaPhlAn2 (`#6600 `_), Minimac4 (`#6781 `_), mordecai (`#6670 `_), NCCL (`#5802 `_), NxTrim (`#6646 `_), parasail (`#6601 `_), PheWAS (`#6030 `_), Pilon (`#6553 `_), python-parasail (`#6601 `_), SearchGUI (`#6637 `_), shovill (`#6553 `_), SKESA (`#6553 `_), snakemake (`#6851 `_), strelka (`#6742 `_), SWIPE (`#6795 `_), ToFu (`#6322 `_), tqdm (`#6721 `_), TRUST (`#6601 `_), VEP (`#6854 `_) - added additional easyconfigs for various supported software packages, including: - Bazel 0.16.0, Boost 1.67.0 + 1.68.0, CUDA 10.0.1, DOLFIN (FEniCS) 2018.1, FSL 5.0.11, GC3Pie 2.5.0, GROMACS 2018.3, HTSlib + SAMtools 1.9, IPython 6.4.0, matplotlib 3.0.0, OpenCoarrays 2.2.0, OpenFOAM 6 & v1806, PyTorch 0.4.1, Python 3.6.6, R 3.5.1, TensorFlow 1.10.1, Trilinos 12.12.1, WIEN2k 18.1 - minor enhancements, including: - add test to enforce SHA256 checksums in touched files in pull requests to develop (`#5005 `_) - add various extensions to recent R easyconfigs (`#6590 `_, `#6686 `_, `#6858 `_) - add ``mpmath`` extension to Python 3.6.4 + 3.7.0 easyconfigs (`#6607 `_, `#6713 `_) - add Java 1.8 easyconfig that can be updated in-place to more recent JDK 1.8.x (`#6712 `_) - see also https://easybuild.readthedocs.io/en/latest/Wrapping_dependencies.html - add ``iso_c_binding`` support to arpack-ng 3.6.2 (`#6718 `_) - add ``XML::Parser``, ``XML::RegExp`` & ``XML::DOM`` extensions to Perl(`#6744 `_) - add ``tabulate`` extension to all Python > 3.6 easyconfigs (`#6809 `_) - enable MPI version of arpack-ng 3.5.0 (`#6840 `_) - add ``wish`` symlink to ``wish8.6`` in recent Tk easyconfigs (`#6870 `_) - add ``libXp`` and ``printproto`` to X11 bundle (`#6873 `_) - various bug fixes, including: - define '``_GNU_SOURCE``' to ensure that '``reallocarray``' is defined in flex 2.6.4 easyconfigs, fixes bootstrap crash (`#5792 `_, `#6766 `_) - added tabix dependency in VCFtools (`#6584 `_) - added zlib dependency to BWA (`#6591 `_), BEDTools (`#6592 `_), VCFtools (`#6653 `_) - add checksums to googletest easyconfigs (`#6611 `_) - fix source URL + add checksum to wkhtmltopdf-0.12.3-Linux-x86_64.eb (`#6628 `_, `#6641 `_) - don't use external FoX dependency in QuantumESPRESSO 6.2 (`#6638 `_) - update hwloc easyconfigs with libxml2 and libpciaccess dependencies (`#6639 `_) - fix gettext build dep for Mono-5.10.0.160 (`#6640 `_) - remove no longer existing config option ``--enable-mpi-thread-multiple`` in OpenMPI 3.x easyconfigs (`#6645 `_) - fix homepage in recent HDF5 easyconfigs (`#6687 `_) - add expat dependency to Mesa v18.1.1 (`#6706 `_) - add missing ``--with-trio-flavor=netcdf`` flag to ABINIT 8.x easyconfigs (`#6711 `_) - remove useless definition of $TORCH_CUDA_ARCH_LIST in PyTorch easyconfig that doesn't use CUDA (`#6719 `_) - fix building GCCcore 6.3.0 on recent OSs by backporting patches from 6.4.0 (`#6727 `_) - fix ``source_urls`` in bzip2 easyconfigs (`#6728 `_) - specify location of dependencies in configure options for libgd (to avoid system libraries being used instead) (`#6731 `_) - also install docs/man pages in recent git easyconfigs (versions 2.1x.y) (`#6751 `_) - add CMake build dep for Eigen 3.3.4 (`#6756 `_, `#6784 `_) - add expat dependency to Perl 5.26.0 (`#6758 `_) - add ncurses OS dependency to CMake for Debian distros (`#6783 `_) - fix checksums for pkgmaker, rngtools & RcppProgress extensions in R 3.4.3 easyconfigs (`#6815 `_) - add pkg-config build dependency to GTS (`#6819 `_) - do not check if hwloc-dump-hwdata utility was installed, since it's only built on x86 systems (`#6836 `_) - patch libxc 3.x and 4.0.x to compile on POWER (`#6868 `_) - consistently add patch for paycheck extension in Python 3.6/3.7 to fix UTF8 issue with README (`#6892 `_) - other changes: - bump Lmod version used in Travis config to 6.6.3 (now required by framework) (`#6834 `_) .. _release_notes_eb362: EasyBuild v3.6.2 (July 11th 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for including environment variable that is resolved at "module load time" in user module path (`#2395 `_) * ``{RUNTIME_ENV::EXAMPLE}`` is replaced by value of ``$EXAMPLE`` when module is loaded * also support generating Docker container recipes & image via ``--containerize`` (still experimental) (`#2479 `_) * add support for specifying source URLs directly in '``sources``' (`#2520 `_) * perform early 'raw' parse of provided easyconfig file to check for syntax error or faulty inputs (`#2523 `_) * add '``bitbucket_account``' easyconfig parameter and template, and let ``BITBUCKET*`` templates use it (`#2525 `_) * various bug fixes, including: * take into account ``--filter-deps`` when re-loading build dependencies in ``extensions_step`` (`#2516 `_) * fix for offline use of bootstrap script: ignore errors when determining source URLs if source tarballs are provided (`#2517 `_) * fix error message that is raised for incorrect type of value in ``sanity_check_paths`` (`#2524 `_) * other changes: * move flake8 config into ``setup.cfg`` + fix style issues in ``easybuild/tools/options.py`` (`#2511 `_) * make test that verifies that ``BuildOptions`` does not support updating a bit more flexible (`#2518 `_) **easyblocks** * new software-specific easyblock for OpenCV (`#1444 `_) * minor enhancements, including: * use ``$CPATH``/``$LD_LIBRARY_PATH`` for CMake's ``find_path``/``find_library`` functions in ``CMakeMake`` easyblock (`#1165 `_) * make cdft lib compilation optional for Intel MKL, by detecting MPI availability (`#1393 `_) * add ``use_glibcxx11_abi`` easyconfig parameter in Boost easyblock (`#1434 `_) * enable filtering of paths in ``$CPATH`` and ``$LIBRARY_PATH`` in TensorFlow easyblock (`#1436 `_) * add support for building GROMACS with ``--optarch=GENERIC`` (`#1440 `_) * check current stack limit and set it to '``unlimited``' if possible in Python easyblock (`#1441 `_) * trivial update for Q&A in SAS easyblock (`#1448 `_) * allow skipping tests when installing Perl extensions, by setting '``runtest``' to ``False`` (`#1451 `_) * add support for installing Intel products using serial numbers (`#1452 `_) * update version check to FFTW 3.3.8 for tests to pass on POWER (ppc64le) (`#1454 `_) * various bug fixes, including: * build MPFR in GCC stage 1 without LTO if (system) GCC used is too old (`#1435 `_) * make sure xmlpatterns always gets built with Qt (`#1437 `_) * fix symlink check in NWChem easyblock + use ``change_dir``/``remove_file``/``symlink`` functions (`#1438 `_) * other changes: * move flake8 configuration to ``setup.cfg`` and make HoundCI aware of it (`#1430 `_) **easyconfigs** * added easyconfigs for new toolchains: ``foss/2018b`` (`#6424 `_), ``fosscuda/2018b`` (`#6555 `_) and ``intel/2018b`` (`#6409 `_) * added example easyconfig files for 28 new software packages: * CUnit (`#6469 `_), eggnog-mapper (`#6513 `_), FANN (`#6468 `_), FTGL (`#6421 `_), FreeFem++ (`#5918 `_), fastStructure (`#6448 `_), fastq-tools (`#5396 `_), fullrmc (`#6422 `_), GDGraph (`#6529 `_), heaptrack (`#6450 `_), libgpuarray (`#5429 `_), lz4 (`#6449 `_), MAJIQ (`#5983 `_), makedepf90 (`#6504 `_), nanopolish (`#6464 `_), opencv_contrib (`#6441 `_), PRC (`#6477 `_), Pillow-SIMD (`#6152 `_), Pytorch (`#6152 `_), poretools (`#6467 `_), pystran (`#6395 `_), R-keras (`#6530 `_), Scoary (`#6521 `_), Scrappie (`#6469 `_), torchvision (`#6152 `_), WISExome (`#6524 `_), WannierTools (`#6539 `_), zstd (`#6449 `_, `#6452 `_) * added additional easyconfigs for various supported software packages, including: * GROMACS 2018.2, HDF5 1.10.2, IPython 6.3.1, Kraken 1.0, Mesa 18.1.1, netCDF 4.6.1, NWChem 6.8, OpenBLAS 0.3.1, OpenMPI 3.1.1, Perl 5.28.0, Python 2.7.15, R 3.5.0, X11 20180604 * minor enhancements, including: * add hint on file name differences between downloaded and expected in cuDNN easyconfig (`#6042 `_) * add '``gee``' extension to R 3.4.4 easyconfigs (`#6376 `_) * enable building of MPI libraries in VTK 8.1.0 easyconfigs (`#6460 `_, `#6429 `_) * minor changes, including: * rename '``Canu``' to '``canu``' for v1.7 (`#6389 `_) * update existing easyconfigs for OpenCV 3.4.1 to use new custom easyblock for OpenCV (`#6509 `_) * fix software name in ``Bsoft`` easyconfig (`#6557 `_) * various bug fixes, including: * fix SAMtools dependency for ChimPipe, required SAMtools < 1.0 (`#5930 `_) * skip installing of documentation in easyconfig for jemalloc 5.0.1 (`#6428 `_) * stop including GCCcore 6.4.0 as build dep for GCCcore 8.1.0 (`#6431 `_) * no longer needed with updated GCC easyblock * add patch for GCCcore 6.4.0 to fix compilation problems on glibc 2.26 systems (`#6432 `_, `#6495 `_) * fix checksums for ``pkgmaker``/``rngtools``/``RWeka``/``RcppProgress``/``mgcv`` extensions in R 3.4.4 easyconfigs (`#6446 `_, `#6502 `_) * added necessary compiler flag for Guile 1.8.8 (`#6457 `_) * build hwloc 1.11.10 with ``-fno-tree-vectorize`` to avoid segfaulting lstopo on Intel Skylake (`#6461 `_) * add patch for binutils 2.30 to fix assertion failure (`#6463 `_) * sync extensions in ``Python-3.6.4-iomkl-2018a.eb`` easyconfig with other Python 3.6.4 easyconfigs using 2018a toolchain (`#6471 `_) * enable checking/setting of unlimited stack limit in Python 3.6.x easyconfigs using an '``intel``' toolchain (`#6485 `_, `#6492 `_) * add missing ``libxml2`` dependency for HDF5 1.10.1 (`#6498 `_) * also copy eggnog-mapper scripts (`#6522 `_) * fix missing dependencies for Perl modules included as extensions for Perl 5.26.1 (`#6532 `_) and 5.28.0 (`#6533 `_) * fix location of include directory in libffi 3.2.1 easyconfigs (`#6565 `_) * other changes * also check for multiple dependency variants in easyconfigs using GCCcore 7.3.0 & newer (`#6444 `_) .. _release_notes_eb361: EasyBuild v3.6.1 (May 26th 2018) -------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for enabling fallback in sanity check to consider ``lib64`` equivalent for seemingly missing libraries (`#2477 `_) * add ``GITHUB_LOWER_SOURCE`` constant (`#2491 `_) * add '``exts_download_dep_fail``' as known easyconfig parameter (`#2493 `_) * add support for passing custom messages on failing sanity check for extensions (`#2494 `_) * add definition for ``fosscuda`` toolchain (`#2507 `_) * various bug fixes, including: * make ``--inject-checksums`` always re-order ``source_urls``/``sources``/``patches``/``checksums`` (`#2487 `_) * fix git remote url in ``CONTRIBUTING.md`` (`#2490 `_) * make ``flake8`` happy in ``easyblock.py`` (`#2492 `_) * handle missing permissions for adding labels in ``--new-pr`` (`#2497 `_) * restore tweaked ``$TMPDIR`` value after loading module (for sanity check) (`#2498 `_) * enhance ``get_module_path`` function to auto-detect generic vs software-specific easyblock class names (`#2502 `_) * don't blindly overwrite an existing easyconfig in ``tweak_one`` (`#2504 `_) * take account that ``PlaintextKeyring`` may be provided via ``keyrings.alt`` (`#2505 `_) * prepend location for temporary module file to ``$MODULEPATH`` with high priority + mark it as default in ``load_fake_module`` method (`#2506 `_) **easyblocks** * minor enhancements, including: * add support for detecting auto-downloaded dependencies in ``PythonPackage`` easyblock (`#1377 `_) * disabled by default, can be enabled using "``download_dep_fail = True``" in easyconfig file * add support to enable integration of pscom in psmpi easyblock (`#1397 `_) * set ``$CMAKE_*_PATH`` when ``CMake`` is loaded in ``PythonPackage`` easyblock (`#1398 `_) * update WIEN2k easyblock for v17 (`#1405 `_) * disable jemalloc support in TensorFlow on CentOS 6 & co (+ minor cleanups) (`#1412 `_) * update Maple easyblock to support recent versions (`#1414 `_) * enable ``nc-config`` usage for netCDF in ESMF >=7.1 (`#1419 `_) * enhance PETSc easyblock for version 3.9 (`#1421 `_) * check output of MATLAB installation command for invalid installation key error (`#1423 `_) * fix suffix for Boost Python library in Boost 1.67.0 & newer (`#1424 `_) * support adding specific paths to ``$PATH`` for generic Binary easyblock via '``prepend_to_path``' custom easyconfig parameter (`#1426 `_) * minor changes, including: * assume PGI Community edition is used when no license file is specified (`#1427 `_) * various bug fixes, including: * fix imkl sanity check overwriting base libs with interface libs (`#1392 `_) * install Chimera in a subdirectory to avoid its dependencies being added to the environment (`#1413 `_) * add conditional so "``--with-x``" is only added to configopts if left unspecified in R easyblock (`#1415 `_) * make ``configure`` and ``make`` look for FoX in ``$EBROOTFOX`` in QuantumESPRESSO easyblock (`#1420 `_) * fix path for ``$ICEM_ACN`` in ANSYS easyblock (`#1422 `_) * avoid hardcoding defaults in question patterns in Doris easyblock (`#1428 `_) **easyconfigs** * added easyconfigs for new toolchains ``fosscuda/2018a`` (`#6363 `_) and ``giolfc/2017b`` (`#5799 `_) * added example easyconfig files for 24 new software packages: * BAGEL (`#6332 `_), Bottleneck (`#6334 `_), cisTEM (`#6370 `_), cftime (`#6337 `_), dotNET-Core-Runtime (`#6345 `_), ecCodes (`#6235 `_), feh (`#6300 `_), Graphene (`#5043 `_), gffread (`#6306 `_), HOME (`#6227 `_), HiCExplorer (`#6342 `_), ICU (`#6371 `_), Imlib2 (`#6300 `_), KmerGenie (`#5929 `_), libgeotiff (`#6262 `_), NetPIPE (`#6062 `_), Pandoc (`#6247 `_), Pisces (`#6347 `_), Proteinortho (`#6333 `_), pyshp (`#6364 `_), SIMPLE (`#6019 `_), STIR (`#6349 `_), SimpleElastix (`#6114 `_), wxWidgets (`#6370 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.67.0, ESMF 7.1.0r, GATK 4.0.4.0, GCC 8.1.0, GROMACS 2018, OpenBLAS 0.3.0, PETSc 3.9.1, PGI 18.4, TensorFlow 1.8.0, WIEN2k 17.1 * minor enhancements, including: * add ``py_expression_eval`` extension to (recent) Python 2.7.14 & 3.6.4 easyconfigs (`#6285 `_) * add ``README`` for Java with information on downloading source tarball (`#6294 `_) * add several extensions to Perl 5.26.1 easyconfigs, incl ``Dist::Zilla`` & dependencies (`#6297 `_) * also include archive URLs for Bioconductor 3.6 (`#6311 `_) * add ``README.md`` file for installing icc/ifort (`#6317 `_) * various bug fixes, including: * consistently specify '``intel-mkl``' component in recent Intel MKL easyconfigs (`#6234 `_) * add ``pkg-config`` as build dependency to libdrm (`#6243 `_) * add ``pkg-config`` build dep to most recent libdrm easyconfigs (`#6244 `_) * fix checksum for foreign extension in R 3.4.3 and R 3.4.4 easyconfigs (`#6245 `_) * fix installation of Libint 2.4.2 by building with ``-std=c++11`` (`#6251 `_) * fix source spec for networkx 2.1 extension in scikit-image easyconfig (`#6254 `_) * avoid that Nipype downloads dependencies for included extensions (`#6261 `_, `#6263 `_) * consistently include patch for FLTK 1.3.4 (`#6265 `_) * fix Perl shebang in MCL v14.137 scripts (`#6269 `_) * add patch to build particular source file of matrixStats extension in R 3.4.4 easyconfig with ``-O1`` to work around ICE in Skylake systems (`#6278 `_) * add ``pkg-config`` build dependency to FFmpeg >= 3.3.1 (`#6291 `_) * change back checksum for libdap 3.19.1 (`#6305 `_) * add patch for Automake 1.15 to fix issue with recent Perl versions (`#6358 `_) * fix ``glog`` causing intel error in Intel compilers on Intel Skylake (`#6360 `_) * include ICU as dependency in recent R easyconfigs (v3.4.3 & v3.4.4) (`#6371 `_) * fix checksum for RSEM 1.3.0 after sneaky re-release (`#6379 `_) .. _release_notes_eb360: EasyBuild v3.6.0 (April 26th 2018) ---------------------------------- feature release **framework** * (experimental) support for generating Singularity container recipes & (optionally) images via '``sudo singularity``' (`#2332 `_, `#2480 `_, `#2481 `_, `#2482 `_, `#2483 `_) * see documentation at http://easybuild.readthedocs.io/en/latest/Containers.html * include ``-ftree-vectorize`` and ``-fno-math-errno`` in default compiler optimisation flags for GCC (`#2388 `_) * this significantly improves performance of generated binaries when building with a GCC-based toolchain * can be disabled if needed via the ``vectorize`` toolchain option * several enhancements/fixes to GitHub integration support: * loosen commit message requirements for ``--new-pr`` w.r.t. to patches as long as all easyconfigs are new (`#2438 `_) * automatically add '``new``' and/or '``update``' labels in ``--new-pr`` (`#2384 `_) * add ``force_in_dry_run=True`` to ``copy_file`` in ``copy_patch_files`` (`#2442 `_) * test for custom commit message when deleting a file instead of when adding a patch (`#2443 `_) * make ``diff_stat`` pattern also match output of older git versions in tests for ``--new``/``update-pr`` (`#2444 `_) * remove duplicates from ``--new-pr`` title (`#2478 `_) * add support for "``eb --fetch``" to only download sources (even without having a modules tool installed) (`#2457 `_) * add definitions for a bunch of new toolchains: * ``golf`` (`#2458 `_), ``gmkl`` (`#2460 `_), ``gomkl`` (`#2455 `_), ``pmkl`` (`#2460 `_) * toolchains including CUDA: ``gmklc``, ``gomklc``, ``iimklc``, ``iompic``, ``iomklc`` (`#2461 `_) * various minor enhancements, including: * avoid that '``--inject-checksums``' adds lines longer than 120 characters (`#2434 `_) * enable caching of ``$HOME/.cache/pip`` in Travis config (`#2435 `_) * replace raw strings with bytes literal as iterator sentinels in checksum calculation (`#2446 `_) * new command-line option '``--job-max-jobs``' to cap nr of submitted build jobs with GC3Pie (`#2378 `_) * add configuration for houndci + flake8 (`#2451 `_) * add ``Accept`` header when downloading file (`#2437 `_) * include running of '``eb --check-github``' in Travis config (`#2449 `_, `#2454 `_) * flesh out common code blocks in ``test/framework/options.py`` (`#2452 `_) * support '``depends_on``' load statements in generated modules via ``--module-depends-on`` and ``module_depends_on`` easyconfig parameter (`#2391 `_) * fix compatibility with Modules v4.1.x (`#2470 `_) * add support to ``run_cmd`` to enable streaming output (`#2476 `_) * various bug fixes, including: * determine whether included easyblocks are generic or not based on class they define (`#2432 `_) * make sure GitHub token is used in test for ``--preview-pr`` (`#2436 `_) * take into account that toolchain components may be hidden when determining toolchain composition (`#2440 `_) * stick to autopep8 1.3.4 when testing with Python 2.6 (`#2462 `_) * strip off ``.lua`` extension when backing up modules to ensure Lmod 6.x doesn't pick up on them (`#2463 `_) * check for ``modulecmd.tcl`` before modulecmd in bootstrap script to discriminate between Modules 4.1.x vs 3.2.10 (`#2468 `_) * fix ``derive_alt_pypi_url`` after PyPI switching to sha256 in package URLs + fix broken test for ``pypi_source_urls`` + fix bootstrap script (`#2471 `_) * make sure that both '``get_git_revision``' and '``this_is_easybuild``' return regular strings rather than Unicode strings (`#2472 `_) **easyblocks** * new software-specific easyblock for Nim (`#1402 `_) * minor enhancements, including: * enhance ``RPackage`` easyblock to support installing from unpacked sources (`#1383 `_) * add support to ``PythonPackage`` easyblock to install with '``pip install --editable``' (`#1384 `_) * add ``$EBROOTIFORT/include`` in ``$CPATH`` for ifort (`#1385 `_) * add houndci + flake8 configuration (`#1388 `_) * add additional location to ``$PATH`` for FLUENT installations (`#1389 `_) * make ``PythonPackage`` generic easyblock aware of '``unpack_options``' easyconfig parameter (`#1391 `_) * minor updates to ABAQUS easyblock to support latest version (`#1394 `_) * add support for extracting sources in ``Binary`` easyblock (`#1401 `_) * various bug fixes, including: * fix linking to FFTW for Doris: should be ``-lfftw3f`` (`#1387 `_) * fix for installing TensorFlow 1.6.0: use the absolute path for the C compiler when compiling with GPU support (`#1386 `_) * also take ``lib64`` into account for binutils libraries (`#1399 `_) * make sanity check in MPICH easyblock aware of libraries in ``lib64`` subdir (`#1403 `_) * take into account that ``self.debuggerpath`` may not be set in icc easyblock (`#1408 `_) * extend noqa in configure step of Qt easyblock (`#1409 `_) **easyconfig** * added easyconfigs for new toolchain golf/2018a (`#6080 `_) * added example easyconfig files for 39 new software packages: * ARAGORN (`#6138 `_, `#6219 `_), amask (`#6105 `_), BamBam (`#5490 `_), Bandage (`#6053 `_), bcgTree (`#6057 `_), biobambam2 (`#6040 `_), CODEX2 (`#5972 `_), coverage (`#5964 `_), DANPOS2 (`#5870 `_), EasyQC (`#6175 `_), elastix (`#6074 `_), FRANz (`#6035 `_), Filtlong (`#6050 `_), FriBidi (`#6181 `_), Gblocks (`#6057 `_), Grace (`#6036 `_), LMfit (`#6119 `_), libmaus2 (`#6040 `_), MathGL (`#6033 `_), MiGEC (`#6047 `_), MiXCR (`#6045 `_), Miniconda3 (`#6075 `_), Multiwfn (`#5403 `_), mosdepth (`#6169 `_), Nim (`#6167 `_), Porechop (`#6051 `_), propy (`#6091 `_), Roary (`#6056 `_), Rtree (`#6222 `_), SALib (`#6145 `_), SMRT-Link (`#6218 `_), SimpleITK (`#6172 `_), spectral.methods (`#6104 `_), supernova (`#6193 `_), TEToolkit (`#5912 `_), tbl2asn (`#6139 `_), udocker (`#5770 `_), vartools (`#6102 `_), XCfun (`#5975 `_) * added new easyconfigs for existing toolchains: * ``gmpich/2017.08`` (`#6143 `_), ``goolfc/2018a`` (`#6129 `_), ``intel/2018.02`` (`#6077 `_), ``iomkl/2018.02`` (`#6088 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.6.3, Anaconda2 5.1.0, Anaconda3 5.1.0, binutils 2.30, dask 0.17.2, FFmpeg 4.0, GCC(core) 7.3.0, GROMACS 2016.5, HTSlib 1.8, LLVM 6.0.0, Mesa 17.3.6, netCDF 4.6.0, Octave 4.2.2, OpenCV 3.4.1, PLUMED 2.4.1, PROJ 5.0.0, PostgreSQL 10.3, Qt5 5.10.1, R 3.4.4, SAMtools 1.8, Spack 0.11.2, TensorFlow 1.7.0, VTK 8.1.0 * minor enhancements, including: * add test to ensure there's only one variant for each dependency in dep graph of easyconfigs using particular toolchains (`#5970 `_, `#6023 `_) * add extensions required by CODEX2 v20180227 to Bioconductor w/ R 3.4.3 (`#5972 `_) * add config file for https://pre-commit.com/ (`#5785 `_) * add custom sanity check paths for GraphicsMagick consistently (`#5997 `_) * add custom sanity check paths to recent Ghostscript easyconfigs (`#5998 `_) * add svd, Rssa, JBTools, RUnit, DistributionUtils and gapfill extensions for R 3.4.3 (`#6099 `_) * add additional extensions to Bioconductor 3.6 bundle (`#6136 `_) * add xlrd extension to recent Python 2.x and 3.x easyconfigs (`#6162 `_) * minor changes, including: * use gettext 0.19.8.1 on top of libxml2 2.9.7 as dep for git built with ``foss/2018a`` (`#5993 `_) * bump hwloc dep for OpenMPI 2.1.2 that is part of ``iomkl/2018a`` to v1.11.8 (`#5994 `_) * use non-interactive plotting backend by default for matplotlib 2.1.2 (`#6024 `_) * don't use bare Perl as dependency for git with ``foss/2018a``, use variant with extensions (`#6058 `_) * various bug fixes, including: * fix ``moduleclass`` & add custom ``sanity_check_paths`` in gettext easyconfigs (`#5991 `_) * drop use of ``--disable-dlopen`` in (recent) OpenMPI easyconfigs due to negative performance impact (`#6060 `_) * add missing XZ dep in Python 3.6.4 easyconfigs built with ``*/2018a`` toolchain (`#6065 `_) * add 10 packages that were previously downloaded in Python 3.6.4 easyconfigs (`#6081 `_) * add patch for Tensorflow 1.6 & 1.7 to include missing -lrt link flag (needed in CentOS6) (`#6089 `_) * fix checksums for R extensions that were updated in place in easyconfigs for R versions 3.4.3 & 3.4.4 (`#6118 `_) * include pkg-config as build dep in recent R easyconfigs (required for at least nloptr) (`#6122 `_) * remove Intel-specific workaround for '``undefined symbol: __stack_chk_guard``' issue from Python 3.6.4 foss/2018a easyconfig (`#6130 `_) * add configopt ``--without-matlab``/``octave`` to all NLopt easyconfigs (`#6132 `_) * also consider ``lib64`` in ``sanity_check_paths`` for Bison 3.0.4 (`#6170 `_) * don't use libyaml built with dummy as dep for PyYAML (`#6208 `_) * add missing pkg-config build dep in recent GObject-Introspection, GLib & cairo easyconfigs (`#6216 `_) * don't include (ancient version of) ``Time::HiRes`` as Perl extension, since it's a core Perl module (`#6225 `_) * this fixes problems with the installation of BioPerl and proovread * add missing XML-LibXML dependency in recent BioPerl easyconfigs (`#6226 `_) * add ``--without-ada`` configure option in recent ncurses easyconfigs (`#6228 `_) * add patch for snaphu to fix segmentation fault due to use of short integer (`#6230 `_) .. _release_notes_eb353: EasyBuild v3.5.3 (March 7th 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#2425 `_) * print which hook is being executed in the command line output (`#2427 `_) * various bug fixes, including: * fix order in result of gen_list_easyblocks and gen_easyblocks_overview_rst (`#2421 `_) * fix target account for branch pushed when using ``--new-pr`` (`#2426 `_) **easyblocks** * minor enhancements, including: * make GROMACS easyblock select build type based on value for '``debug``' in '``toolchainopts``' (`#1374 `_) * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#1376 `_) * enhance Gurobi easyblock to support installing Python bindings (`#1378 `_) **easyconfigs** * added example easyconfig files for 2 new software packages: * CNVkit and hmmlearn (`#5954 `_) * added additional easyconfigs for various supported software packages, including: * matplotlib 2.1.2, TensorFlow 1.6.0 * minor enhancements, including: * re-enable testing against environment modules, bump Lmod to 7.7.16 (`#5944 `_) * add cghFLasso extension to R 3.4.3 easyconfigs (`#5953 `_) * add '``Math::CDF``' extension to recent Perl modules (`#5957 `_) * various bug fixes, including: * add missing ``--enable-ld-version-script`` configure option for LibTIFF 4.0.9 built with ``GCCcore/6.4.0`` (`#5945 `_) * hard disable UCX support in recent OpenMPI versions, to dance around bug in OpenMPI configure script (`#5949 `_) .. _release_notes_eb352: EasyBuild v3.5.2 (March 2nd 2018) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add functionality to skip devel module with naming scheme (`#2374 `_) * add pagination support in ``clean_gists.py`` (`#2379 `_) * allow basic compiler modulenames to be specified as keys in ``--optarch`` (`#2387 `_) * initial set of OHPC module meta data for EasyBuild (`#2392 `_) * allow different target account in ``post_comment_in_issue`` (`#2399 `_) * declare support for RPATH linking stable (`#2409 `_) * various bug fixes, including: * update bootstrap script to be compatible with Modules v4 (`#2390 `_) * avoid fatal error when determining glibc version on non-glibc Linux system (e.g. Alphine Linux) (`#2398 `_) * exclude location of RPATH wrappers from ``$PATH`` to avoid fork bomb (`#2410 `_) * fix target account for ``--update-pr`` in case it's different from GitHub account being used to push branch (`#2419 `_) **easyblocks** * new software-specific easyblocks for COMSOL (`#1317 `_), Stata (`#1241 `_) and TensorFlow (`#1287 `_, `#1361 `_) * enhance GCC easyblock to support building generically (via '``generic``' easyconfig parameter or ``--optarch=GENERIC``) (`#1336 `_) * minor enhancements, including: * make GROMACS easyblock aware of building for KNL via ``--optarch=MIC-AVX512`` (`#1360 `_) * unset ``$PERL_MM_OPT`` and ``$PERL_MB_OPT`` when installing Perl modules to avoid problems (`#1362 `_) * add custom '``use_pip_for_deps``' easyconfig parameter to ``PythonPackage`` easyblock (`#1366 `_) * add support for '``default_component_specs``' easyconfig parameter in ``Bundle`` easyblock (`#1369 `_) * various bug fixes, including: * fix logic in icc easyblock w.r.t. location of debugger libraries (libipt library for gdb) (`#1224 `_) * fix Tkinter easyblock to install Tkinter 3.x (`#1347 `_) * let impi modules also update ``$MANPATH`` (`#1354 `_) * enhance Octave extension filter to avoid false positives (`#1355 `_) * make CUDA easyblock aware of '``preinstallopts``' easyconfig parameter (`#1367 `_) * fix handling of per-component (checksums for) patches in ``Bundle`` easyblock (`#1369 `_) **easyconfigs** * added example easyconfig files for 24 new software packages: * AMPL-MP (`#5800 `_), AmberTools (`#5632 `_), bcolz (`#5864 `_), detonate (`#5709 `_), dropEst (`#5734 `_), EvidentialGene (`#5627 `_), faceswap (`#5825 `_), fineSTRUCTURE (`#5663 `_), Gradle (`#5828 `_), gbs2ploidy (`#5877 `_), HIPS (`#5725 `_), Ipopt (`#5800 `_), libMemcached (`#5804 `_), MEGAHIT (`#5748 `_), Mmg (`#5807 `_), methylpy (`#5874 `_), pstoedit (`#5884 `_), python-igraph (`#5905 `_), RNAcode (`#5854 `_), Seq-Gen (`#5695 `_), Stata (`#5102 `_), scikit-allel (`#5864 `_), TetGen (`#5681 `_), zarr (`#5864 `_) * added new easyconfigs for existing toolchains: giolf/2018a (`#5777 `_), goolfc/2017b (`#5768 `_), iomkl/2018a (`#5878 `_) * added additional easyconfigs for various supported software packages, including: * CP2K 5.1, IPython 6.2.1, OpenFOAM v1712, Perl 5.26.1, Python 3.6.4, TensorFlow 1.5.0, X11 20180131 * minor enhancements, including: * add ``feather`` and ``tidyverse`` as extensions for R 3.4.3 (`#5693 `_) * build recent PLUMED versions with all modules enabled (`#5696 `_) * add MAST/splatter/scDD to Bioconductor 3.6 bundle (`#5704 `_) * add ``dummies`` as extension for R 3.4.3 + ``monocle``/``scde``/``ROTS`` (+ deps) to Bioconductor 3.6 bundle (`#5724 `_) * include ``io`` and ``statistics`` extensions to Octave 4.2.1 easyconfigs (`#5798 `_) * switch to using TensorFlow as backend for recent versions of Keras (`#5821 `_) * various bug fixes, including: * using the correct binutils in jemalloc 5.0.1 easyconfig using ``GCCcore/6.4.0`` (`#5659 `_) * fix source URLs for MPC (`#5662 `_) * add Tkinter as dependency for ASE & matplotlib using Python 3.6.3 (`#5658 `_) * fix versions for updated extensions in Bioconductor 3.6 bundle (`#5704 `_, `#5724 `_, `#5880 `_) * fix missing M4 build dependency in nettle easyconfigs (`#5722 `_) * fix homepage for OpenFOAM 4.x & 5.x, should be ``openfoam.org`` (`#5422 `_, `#5780 `_) * add matplotlib, cairo & PyCairo dependencies for graph-tool 2.26 + enhance sanity check (`#5787 `_) * fix hardcoded version in scikit-image easyconfigs (`#5822 `_) * fix pkgconfig moduleclass, '``data``' doesn't make much sense (`#5817 `_) * add sanity check in recent matplotlib easyconfigs to ensure that Tkinter is available (`#5689 `_, `#5896 `_) * correct MPI path when building ABINIT with '``foss``' toolchain (`#5760 `_) * patch Hyperopt to make it work with networkx 2.0 (`#5642 `_) * add Tkinter sanity check to ASE easyconfigs (`#5691 `_, `#5909 `_) * include autotools as build dep in git easyconfigs (`#5718 `_) * fix sanity check paths for Debian OS in JasPer easyconfigs (`#5897 `_) * fix source_urls for recent versions of ABINIT (`#5908 `_) * add patch for recent GDAL easyconfigs using ``intel`` toolchain to fix icc get stuck on compiling ``ceos.c`` (`#5915 `_) * add explicit zlib dependency in Tkinter 2.x and 3.x (`#5797 `_, `#5926 `_) * fix source URLs & homepage in Singularity easyconfigs (`#5927 `_) * fix installation of TensorFlow 1.3 via binary wheel after introducing TensorFlow easyblock (`#5938 `_) .. _release_notes_eb351: EasyBuild v3.5.1 (January 16th 2018) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * add definition of ``giolfc`` toolchain (`#2359 `_) * add support for Environment Modules 4 (`#2365 `_) * various bug fixes, including: * install SQLAlchemy < 1.2.0 with Python 2.6 in Travis config (`#2367 `_) * make code in ``easybuild/tools/job/gc3pie.py`` forward-compatible with GC3Pie 2.5 (`#2373 `_) **easyblocks** * minor enhancements, including: * auto-detect default build target for Clang (`#1115 `_) * build GROMACS for target architecture based on ``--optarch`` (`#1163 `_) * ensure correct $PYTHONPATH for recent OpenBabel versions (`#1219 `_) * enhance Amber easyblock with support for OpenBLAS and better Intel MPI support (`#1305 `_) * also support only installing AmberTools through Amber easyblock (`#1305 `_) * also pick locations for CUPTI headers & libraries in CUDA easyblock (`#1306 `_) * update patching out of sanitizer tests for recent Clang versions (>=5.0) (`#1327 `_) * update known questions for Qt5 to support installing recent versions (`#1328 `_) * update BamTools easyblock for v2.5.0 (`#1332 `_, `#1337 `_) * disable ``libfox`` target if external module found in QuantumESPRESSO easyblock (`#1333 `_) * add support for linking Octave with multi-threaded BLAS/LAPACK library (`#1340 `_) * support ``install_target`` in PythonPackage + deprecate ``use_easy_install`` & ``use_setup_py_develop`` (`#1341 `_, `#1342 `_) * various bug fixes, including: * make RubyGem easyblock use ``$GEM_*`` environment variables except if as extension of Ruby itself (`#1247 `_) * move initialisation in ``SystemCompiler`` & ``SystemMPI`` easyblocks to the prepare step (`#1282 `_) * enable skipping sanitizer tests by default in Clang easyblock, they can't be relied on (`#1329 `_) * fix quotes when using ``$ORIGIN`` in ``RPATH`` locations for DOLFIN (`#1338 `_) * fix sanity check for shared libraries in Trilinos easyblock (`#1339 `_) **easyconfigs** * added easyconfigs for ``foss/2018a`` and ``intel/2018a`` common toolchains (`#5577 `_), (`#5578 `_) * added example easyconfig files for 26 new software packages: * BeautifulSoup (`#5601 `_), Calendrical (`#5588 `_), ChimPipe (`#5560 `_), crb-blast (`#5124 `_)), dammit (`#5125 `_), deepTools (`#5536 `_), FastQ_Screen (`#5404 `_), FoX (`#5496 `_), GffCompare (`#5581 `_), GlimmerHMM (`#5559 `_), LocARNA (`#5548 `_), MapSplice (`#5566 `_), MariaDB-connector-c (`#5557 `_), NextGenMap (`#5430 `_), nd2reader (`#5545 `_), PIMS (`#5545 `_), Pysolar (`#5585 `_), phono3py (`#5551 `_), preseq (`#5569 `_), proovread (`#5513 `_), QUAST (`#5610 `_), RNA-SeQC (`#5589 `_), RNAclust (`#5607 `_), Ragout (`#5608 `_), SOAPfuse (`#5417 `_), TransDecoder (`#5125 `_) * added additional easyconfigs for various supported software packages, including: * BLAST+ 2.7.1, BamTools 2.5.0, Boost 1.66.0, Clang 5.0.0, dask 0.16.0, FFmpeg 3.4.1, GROMACS 2016.4, HDF5 1.8.20, matplotlib 2.1.1, PLUMED 2.4.0, Pillow 5.0.0, Qt5 5.9.3, QuantumESPRESSO 6.2, Ruby 2.5.0, Rust 1.22.1 * minor enhancements, including: * include ``gomms`` in list of extensions for R 3.4.3 (`#5547 `_) * clean up BamTools easyconfigs to rely on updated easyblock + add SHA256 checksums (`#5575 `_) * add ``Time::HiRes`` to recent Perl versions (`#5616 `_) * add ``DNAcopy`` & ``dupRadar`` extensions to bundle for Bioconductor 3.6 (`#5587 `_, `#5618 `_) * switch to using ``install_target`` rather than now deprecated ``use_easy_install`` and ``use_setup_py_develop`` (`#5625 `_) * various bug fixes, including: * avoid auto-downloading of parcel in gdc-client 1.3.0 easyconfig (`#5523 `_) * fix permissions on ``make_raw_alos.pl`` script in ROI_PAC installation (`#5546 `_) * remove erroneous patch for Intel compiler support in Perl 5.26.0 easyconfig built with ``GCCcore/6.4.0`` (`#5561 `_) * include ``HWxtest`` as extension to fix issue with ``diveRsity`` in R 3.4.3 easyconfig file (`#5570 `_) * add pkg-config as build dependency for fontconfig, harfbuzz, gnuplot, pango (`#5580 `_) * fix versions of updated extensions in BioConductor bundle (`#5587 `_, `#5618 `_) * add missing libpng dependency in ROOT 6.10.08 easyconfigs (`#5595 `_) * fix option passed to configure in M4 (`#5606 `_) * rename SIBELia to Sibelia (`#5603 `_) * add patch for binutils 2.26 to fix compatibility with GCC 6.x (`#5611 `_) * fix for dependencies was set twice in OpenMPI 3.0.0 easyconfig (`#5619 `_) * fix download URL in comment of Kent tools easyconfigs (`#5633 `_) * add SHA256 checksums to various easyconfigs (`#5635 `_, `#5636 `_, `#5639 `_) * add ``rdma-core-devel`` to OS dependencies for OpenMPI 3.0.0 (`#5648 `_) .. _release_notes_eb350: EasyBuild v3.5.0 (December 15th 2017) ------------------------------------- feature release **framework** * add support for implementing pre- and post-step hooks (`#2343 `_) * documentation available at http://easybuild.readthedocs.io/en/latest/Hooks.html * various enhancements, including: * add support for foss-like toolchain with Spectrum MPI: ``gsolf`` (`#2329 `_) * add support for ``--preview-pr`` (`#2331 `_, `#2337 `_, `#2348 `_) * see also http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html#previewing-easyconfig-pull-requests-preview-pr * flesh out ``find_extension`` function, hoist dict with extract commands into a constant (`#2336 `_) * add support for using ``self.start_dir`` rather than using ``self.cfg['start_dir']`` (`#2339 `_) * add support for '``exts_default_options``' easyconfig parameter (`#2345 `_, `#2346 `_) * allow use of '``start_dir``' easyconfig parameter in extensions (`#2353 `_) * various bug fixes, including: * fix typo in '``giolf``' toolchain definition (`#2327 `_) * fix minor issues with ``--inject-checksums`` (`#2333 `_) * fix error message when '``gv``' Python package is not available (`#2340 `_) * install paramiko version < 2.4.0 for Python 2.6 in Travis config (`#2344 `_) * disable broken log rotation, avoid duplicate logging of output of executed commands under '``--debug``' (`#2347 `_) * also include $ORIGIN and absolute paths to '``lib``' and '``lib64``' subdirectories in RPATH locations (`#2358 `_) * fix repo references in ``install-EasyBuild-develop.sh`` script (`#2360 `_) **easyblocks** * new software-specific easyblock for Bazel (`#1286 `_) and Octave (`#1304 `_) * new generic easyblock for installing Octave packages as extensions (`#1304 `_, `#1318 `_) * minor enhancements, including: * remove ``foamExec`` & ``wdot`` from sanity checks, add ``blockMesh`` & ``checkMesh`` + enable logging for recent OpenFOAM versions (`#1205 `_, `#1272 `_) * add exceptions for FFTW/3.3.6 on POWER with GCC 5/6/7 (`#1274 `_) * add support for Spectrum MPI to the ``SystemMPI`` easyblock (`#1275 `_) * allow skipping of steps for ``Bundle`` components + fix issues with templates & formatting of error message (`#1278 `_) * update HPCG easyblock for v3.0 by changing configure syntax (`#1284 `_) * correctly configure for BLAS/LAPACK in R easyblock & check configure output (`#1292 `_, `#1300 `_) * make R easyblock set configure options for dependencies (`#1297 `_, `#1303 `_) * allow tuning of build command in ``PythonPackage`` via custom '``buildcmd``' easyconfig parameter (`#1299 `_) * set default Java encoding to ``UTF8`` when installing Trinity (`#1302 `_) * also define ``$CUDA_ROOT`` in generated module for CUDA (`#1234 `_) * make the ScaLAPACK easyblock capable of building in parallel (`#1288 `_, `#1321 `_, `#1324 `_) * various bug fixes, including: * avoid changing ``$CPATH``, ``$LD_LIBRARY_PATH`` an ``$LIBRARY_PATH`` in generated modules for Intel Advisor, Inspector, and VTune (`#1229 `_) * fix check for Intel MKL in PSI easyblock (`#1273 `_) * fix missing space in fftw easyblock (`#1277 `_) * fix use of FFTW on top of Intel MKL in CP2K easyblock (`#1281 `_) * fix wrong sanity check for Boost when using Python 3.x (`#1283 `_) * pick up per-component checksums in ``Bundle`` generic easyblock (`#1285 `_) * correctly pass down optimization flags in CP2K easyblock (`#1293 `_) **easyconfigs** * added example easyconfig files for 39 new software packages: * AmberMini (`#5476 `_), arrow (`#5416 `_), bat (`#5416 `_), CIRCexplorer (`#5356 `_), CIRCexplorer2 (`#5470 `_), CIRI (`#5358 `_), FALCON (`#5265 `_), FastaIndex (`#5465 `_), find_circ (`#5348 `_), future (`#5236 `_), GapCloser (`#5465 `_), glibc (`#5428 `_), GRNBoost (`#5373 `_), HDFView (`#5391 `_), Horovod (`#5239 `_), HPDBSCAN (`#5371 `_), Hyperopt (`#5455 `_), IntelClusterChecker (`#4970 `_), ITK (`#5434 `_), LAST (`#5465 `_), MDTraj (`#5317 `_), Meson (`#5228 `_), mkl-dnn (`#5319 `_, `#5362 `_), Ninja (`#5228 `_), OpenKIM-API (`#5479 `_), ParmEd (`#5476 `_), PCRaster (`#5386 `_), piSvM (`#5308 `_), piSvM-JSC (`#5316 `_), PTESFinder (`#5359 `_), pybedtools (`#5347 `_), pymbar (`#5476 `_), pyScaf (`#5465 `_), QIIME2 (`#5355 `_), QTLtools (`#5361 `_), Redundans (`#5465 `_), Rmath (`#5361 `_), sbt (`#5373 `_), SNAP (`#5465 `_) * added new easyconfigs for existing toolchains: ``intel/2017.09`` (`#5303 `_), ``intel/2018.00`` (`#5129 `_), ``intel/2018.01`` (`#5345 `_) * added additional easyconfigs for various supported software packages, including: * CGAL 4.11, CMake 3.10.0, Caffe 1.0, FFTW 3.3.7, GATE 8.0, gnuplot 5.2.2, HPCG 3.0, HTSlib 1.6, Keras 2.1.2, LLVM 5.0.0, Mesa 17.2.5, mpi4py 3.0.0, netCDF 4.5.0, OpenFOAM 5.0, ParaView 5.4.1, R 3.4.3, Ruby 2.4.2, Rust 1.21.0, SCons 3.0.1, Szip 2.1.1, Theano 1.0.0, VTK 8.0.1, X11 20171023 * minor enhancements, including: * add SHA256 checksums to Autoconf (`#5304 `_), Automake (`#5305 `_), libtool (`#5306 `_) and M4 (`#5307 `_) easyconfigs * avoid hardcoding extension versions in worker easyconfig, include '``perl``' as OS dep (`#5324 `_) * enable building ScaLAPACK in parallel with enhanced ScaLAPACK easyblock (`#5331 `_) * include ``RInside`` extension in R 3.4.0 easyconfig (`#5354 `_) * clean up configure options that are now handled by R easyblock (`#5478 `_, `#5485 `_) * update Octave easyconfigs to use Octave easyblock, add extensions for latest Octave versions (`#5484 `_, `#5503 `_, `#5507 `_) * add ``Log4perl`` extension to Perl 5.26.0 easyconfigs (`#5511 `_) * various bug fixes, including: * add missing extensions required by MultiQC & stick to networkx 1.11 (`#5240 `_) * disable ``optarch`` when using Intel compilers and enable tests in all libxc easyconfigs (`#5256 `_, `#5257 `_) * avoid downloads when installing matplotlib 2.1.0 w/ Python 2.7.14 (`#5267 `_) * fix ``$CPATH`` in recent libffi easyconfigs + enhance sanity check & add checksum (`#5271 `_) * use Github source URL, run ``autogen.sh`` + include Autotools build dep for numactl (`#5286 `_, `#5296 `_, `#5297 `_, `#5299 `_, `#5302 `_) * add hwloc to GROMACS dependencies (`#5295 `_) * fix ``source_urls`` (& ``sources`` spec) for GATE (`#5367 `_) * consistently add Autotools build dep in recent netCDF easyconfigs (`#5394 `_) * fix check in test suite for binutils build dep when ``GCCcore`` used as toolchain (`#5436 `_) * libdap 3.19.1 checksum changed (`#5473 `_) * disable new rfkill feature in easyconfig for util-linux 2.31 since it requires a recent kernel (`#5480 `_) * add missing PROJ dependency in recent GDAL easyconfigs (`#5481 `_) * fix name in TensorFlow easyconfigs (was 'TensorFlow') (`#5495 `_) * fix checksum for Szip 2.1.1 (`#5517 `_) * fix order of extensions for FSLeyes, add missing MarkupSafe (dep for Jinja2) (`#5520 `_) .. _release_notes_eb341: EasyBuild v3.4.1 (October 17th 2017) ------------------------------------ bugfix/update release **framework** * various enhancements, including: * improve trace output for executed commands + drop requirement for ``--experimental`` for ``--trace`` (`#2306 `_) * add ``giolf`` toolchain definition: GCC, IntelMPI, OpenBLAS, (Sca)LAPACK and FFTW (`#2310 `_) * add support for ``--force-download`` and ``--ignore-checksums`` (`#2313 `_, `#2314 `_) * flesh out ``pypi_source_urls`` from ``derive_alt_pypi_url`` (`#2319 `_) * various bug fixes, including: * also check for use of ``--rebuild`` next to ``--force`` to skip sanity check with ``--module-only`` (`#2307 `_) * ensure ``$TMPDIR`` is set to a short path for OpenMPI v2.x (`#2311 `_) * guard '``module load``' commands in generated modules under ``--recursive-unload`` to avoid load storms (`#2316 `_) * correctly deal with use of special characters in description & co (`#2320 `_) * fix incorrect ``FFT_INC_DIR`` for Intel MKL (`#2323 `_) **easyblocks** * add generic '``SystemMPI``' easyblock (`#1106 `_, `#1261 `_, `#1262 `_) * add software-specific easyblock for SAS (`#1263 `_) * minor enhancements, including: * run '``wcleanAll``' or '``wcleanPlatform -all``' before building OpenFOAM (`#780 `_, `#1258 `_) * enhance generic '``SystemCompiler``' easyblock (`#1106 `_) * clean up ``--trace`` output for Python & Python packages (`#1248 `_) * update Intel MPI easyblock to support 2018.* versions (`#1253 `_) * add support for Intel MPI and Intel MKL to ScaLAPACK easyblock (`#1255 `_) * enhance GCC easyblock to also put symlinks in place for ``cc``/``c++``/``f77``/``f95`` commands (`#1256 `_) * various bug fixes, including: * allow that '``gcc -print-multiarch``' fails in icc easyblock (`#1249 `_) * fix prefix subdirectory for older versions of icc (in particular 2011.3.174) (`#1250 `_) * use ``remove_file`` rather than ``os.remove`` in generic ``IntelBase`` easyblock to correctly deal with broken symlinks (`#1251 `_) * fix sanity check for MXNet easyblock + correctly detect unpacked source directory (`#1257 `_) * avoid building CP2K twice due to incorrect attempt at running '``make clean``' first (`#1266 `_) **easyconfigs** * added easyconfigs for new toolchain ``giolf/2017b`` (`#5140 `_) * added example easyconfig files for 13 new software packages: * ASAP3 (`#5200 `_), Albacore (`#5153 `_), CatMAP (`#5225 `_), DLCpar (`#5209 `_), FSLeyes (`#5192 `_), IQ-TREE (`#3695 `_), NEST (`#5515 `_), nanonet (`#5149 `_), OMA (`#5211 `_), , oxford_asl (`#5193 `_), QEMU (`#5220 `_), REMORA (`#5159 `_), SAS (`#5208 `_), supermagic (`#5187 `_) * added additional easyconfigs for various supported software packages, including: * Anaconda2/3 4.4.0, Blender 2.79, Boost 1.65.1, CMake 3.9.4, FFmpeg 3.3.4, GCC 5.5.0, h5py 2.7.1, Keras 2.0.8, matplotlib 2.1.0, mympingpong 0.8.0, OpenCV 3.3.0, OpenFOAM-Extend 4.0, OpenMPI 2.1.2 + 3.0.0, Pillow 4.3.0, Python 2.7.14 + 3.6.3, SAMtools 1.6, scikit-image 0.13.0, scikit-learn 0.19.0, Tensorflow 1.3.0, vsc-mympirun 4.0.2 * minor enhancements, including: * add ``xkeyboard-config`` component in X11 bundle (`#5066 `_) * clean up use of ``wcleanAll`` in OpenFOAM-Extend easyconfigs, now handled by OpenFOAM easyblock (`#5131 `_) * also install ``run_rcorrector.pl`` with Rcorrector (`#5135 `_) * add SHA256 checksum to PyCUDA easyconfig (`#5154 `_) * fix/improve description in HDF5 easyconfigs (`#5182 `_) * include heatmap3 extension for R 3.4.0 (`#5185 `_) * add ComplexHeatmap to Bioconductor 3.5 bundle + dep pkgs in R 3.4.0 easyconfig (`#5195 `_) * various bug fixes, including: * fix source URLs for AUGUSTUS 3.2.3 (`#5119 `_) * fix building Bison 2.5 on systems with recent glibc (`#5130 `_) * also consider ``rdma-core-devel`` as alternative to ``libibverbs-devel`` OS dependency (`#5132 `_) * consistently use empty toolchain version in icc & ifort easyconfigs to ensure that GCC(core) dep is loaded during installation (`#5133 `_, `#5134 `_) * add patches for Boost 1.64.0 to fix known issues (`#5148 `_) * remove PyCUDA easyconfig for ``intel/2017a``, doesn't work due to incompatibility between GCC 6.3.0 & CUDA 8 (`#5156 `_) * add missing Perl extensions in easyconfig for Worker 1.6.7 (`#5157 `_) * fix checksums for packages that download from ``github.com/x/y/archive`` (`#5162 `_) * add missing libpng dependency to g2lib-1.4.0 easyconfig using intel-2017a (`#5196 `_) * fix source_urls for Szip 2.1 & include SHA256 checksum (`#5206 `_) * remove unneeded ``--with-fft-incs`` configure option for ABINIT (`#5207 `_) * disable optarch for libjpeg-turbo 1.5.1 built with ``intel/2017a`` (`#5214 `_) * update ``$R_LIBS`` in plotly easyconfig (`#5215 `_) * include NLopt as a dependency in R easyconfigs that include ``nloptr`` as extension (`#5217 `_) .. _release_notes_eb340: EasyBuild v3.4.0 (September 10th 2017) -------------------------------------- feature release **framework** * various enhancements, including: * add support for backing up modules via ``--backup-modules`` (`#2134 `_) * enabled automatically with ``--module-only`` and ``--skip`` * see also http://easybuild.readthedocs.io/en/latest/Backup_modules.html * add support for ``--search-paths`` to extend list of locations considered by ``--search``/``-S`` (`#2255 `_) * include ``userInGroup`` check in Lua modules when installation is group-restricted (`#2274 `_) * add experimental support for '``eb --trace``' (`#2285 `_) * see also http://easybuild.readthedocs.io/en/latest/Tracing_progress.html * add support for '``eb --inject-checksums``' (`#2286 `_, `#2292 `_, `#2293 `_) * see also http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#adding-or-replacing-checksums-using-inject-checksums * add support for ``append_paths`` in module generator (`#2294 `_) * various bug fixes, including: * strip provided GitHub token of spaces in ``--install-github-token`` (`#2270 `_) * remove '``provides``' line from ``setup.py`` (`#2275 `_) * pass down stdin in '``import``' check for extensions during sanity check (`#2276 `_) * make sure location to 'eb' installed during stage 1 is included in ``$PATH`` during stage 2 of bootstrap procedure (`#2281 `_) * make resolve_path robust against ``None`` path being provided (`#2282 `_) * ensure clean error message on easyconfig file parse failure (`#2290 `_) * fix regex to avoid sucking up additional lines prior to module file path in ``modulefile_path`` (`#2291 `_) * fix error message when ``--use-ccache`` is used but ``ccache`` is not available in ``$PATH`` (`#2295 `_) **easyblocks** * minor enhancements, including: * update Siesta easyblock for versions 4.0.1 and 4.1-b3 (`#1218 `_) * updates GAMESS-US easyblock for version 20170420R1 + move ``ddikick.x`` when ``ddi_comm`` is set to '``sockets``' (`#1221 `_) * update MRtrix easyblock for 3.0 & beyond + use ``copy`` function (`#1230 `_) * update ROOT easyblock to support recent versions that require using CMake, add sanity check, clean up/enhance ``make_module*`` (`#1236 `_) * enhance icc easyblock to include multipath include dir in ``$CPATH`` (`#1237 `_, `#1242 `_) * various bug fixes, including: * use ``plumed-patch`` command rather than '``plumed patch``' in GROMACS easyblock (`#1212 `_) * remove '``provides``' line from ``setup.py`` (`#1217 `_) * fixed wrong use of ``build_type`` in ``self.cfg`` in WRF easyblock that resulted in an raised exception (`#1220 `_) * added a call to super ``post_install_step`` in CUDA easyblock (`#1226 `_) * fix ``$MCRROOT`` definition in generated module file under ``--module-only`` in MCR easyblock (`#1228 `_) * fix permissions for directories in SuiteSparse (`#1238 `_) * fix function signature for ``fetch_extension_sources`` in OCaml easyblock (`#1240 `_) **easyconfigs** * added easyconfigs for ``foss/2017b`` and ``intel/2017b`` common toolchains (`#4768 `_), (`#4618 `_) * added new easyconfigs for existing toolchains: * ``iomkl/2017b`` (`#5097 `_) * added example easyconfig files for 31 new software packages: * BAMM (`#4650 `_), BamM (`#4650 `_), bcl2fastq2 (`#4902 `_), CGNS (`#5078 `_), CLAPACK (`#5096 `_), CLISP (`#4926 `_, `#4986 `_), cadaver (`#4873 `_), destiny (`#5009 `_), GroopM (`#4650 `_), Lucene-Geo-Gazetteer (`#5064 `_), libffcall (`#4850 `_), libsigsegv (`#4840 `_), MERCKX (`#5056 `_), minimap2 (`#4991 `_), ncompress (`#4852 `_), OpenNLP (`#5059 `_, `#5061 `_), OpenRefine (`#5058 `_), PHAST (`#5096 `_), PYTHIA (`#5083 `_), ParallelIO (`#5071 `_), PnetCDF (`#5071 `_), plotly (`#5010 `_), QML (`#5101 `_), Quorum (`#5095 `_), Rcorrector (`#5095 `_), SCnorm (`#5008 `_), SOAPdenovo-Trans (`#5095 `_), Shannon (`#5095 `_), Tika (`#5063 `_), UNAFold (`#4997 `_), VERSE (`#4843 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1, MRtrix 3.0_RC2, Perl 5.26.0, ROOT 6.10.04, Spark 2.2.0 * minor enhancements, including: * add checksums to Perl 5.24.1 easyconfigs (`#4973 `_, `#4992 `_) * add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (`#5007 `_, `#5028 `_, `#5029 `_, `#5062 `_, `#5079 `_) * also define ``$INCLUDEPATH`` and ``$LIBRARY_PATH`` in Tesla-Deployment-Kit easyconfig (`#5018 `_) * add check to see whether binutils is included as build dep when GCCcore toolchain is used (`#5084 `_) * various bug fixes, including: * added Rmpi patch file for R built with intel toolchains incl. impi 5.x (`#4623 `_) * use single-line description in ``setup.py`` (`#4881 `_) * fix version and source for Seurat + add extensions required by Seurat in R 3.4.0 easyconfig (`#4889 `_) * add zlib as dependency to util-linux easyconfigs (`#4900 `_, `#4998 `_) * use ``modextrapaths`` instead of ``modextravars`` in OpenMM easyconfig (`#4903 `_) * update deprecated PLINK urls (`#4920 `_, `#5006 `_) * fix ``moduleclass`` for Cookiecutter (`#4947 `_) * fix order of OpenMPI dependency in ``iomkl/2016.09*`` easyconfigs, must come after icc/ifort (`#5024 `_) * fix typo in comment in util-linux easyconfigs & add SHA256 checksums (`#5052 `_) * remove superfluous ``$CPATH`` update in GLib 2.44.0 easyconfig (`#5053 `_) * update ncurses to not build a separate libtinfo but provide a soft link instead + force linking to ncurses in libreadline (`#5067 `_, `#5074 `_) * include Autotools as build dep for netCDF (`#5077 `_) * add missing binutils build dep for texinfo (`#5099 `_) .. _release_notes_eb331: EasyBuild v3.3.1 (July 12th 2017) --------------------------------- bugfix/update release **framework** * various enhancements, including: * add support for '``allow_prepend_abs_path``' easyconfig parameter (`#2254 `_) * support for ``--merge-pr`` (`#2266 `_) * various bug fixes, including: * resolve symlinks to location of '``eb``' in ``get_paths_for`` (`#2248 `_) * fall back to checking location relative to '``eb``' location in ``find_eb_script`` (`#2249 `_) * respect ``--suffix-modules-path`` value for user-specific module path extensions (`#2250 `_) * update EasyBuild bootstrap script to download ``distribute`` tarball from http://easybuilders.github.io/easybuild/files (`#2256 `_) * fix default target GitHub account/organisation for ``--new-pr`` & co + fix tests that got broken by migration to github.com/easybuilders (`#2258 `_) * fix checking for new easyconfigs in ``copy_easyconfigs``, pick up specified commit message as PR title if none was provided (`#2259 `_) * get rid of references to ``hpcugent`` after move to github.com/easybuilders (`#2261 `_) * automatically enable ``--ignore-osdeps`` under ``--new-pr`` and ``--update-pr`` (`#2262 `_) **easyblocks** * minor enhancements, including: * enhance HDF5 easyblock: define ``$HDF5_DIR`` & include ``-DMPICH_IGNORE_CXX_SEEK`` in ``$CXXFLAGS`` (`#1200 `_) * consistently pass down (named) arguments in ``prepare_step``, and check for it in the tests (`#1202 `_) * remove no longer supported ``VersionIndependentPythonPackage`` generic easyblock (`#1202 `_) * update ABAQUS easyblock for recent versions, incl. support for installing hotfixes (`#1203 `_) * get rid of references to '``hpcugent``' organisation after move to github.com/easybuilders (`#1206 `_) * make Boost easyblock fully aware of ``(pre)configopts``, ``(pre)buildopts`` and ``(pre)installopts`` (`#1207 `_) * drop check for '``ipython``' in sanity check of Anaconda easyblock, to also support Miniconda (`#1210 `_) **easyconfigs** * added example easyconfig files for 6 new software packages: * FastME (`#4811 `_), geopy (`#4821 `_), Miniconda2 (`#4841 `_), ngmlr (`#4818 `_), OpenCoarrays (`#4799 `_), Seurat (`#4832 `_) * added additional easyconfigs for various supported software packages, including: * ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, numpy 1.13.0, Tensorflow 1.2.0 * minor enhancements, including: * add ``SVG`` and ``Statistics::Basic`` to recent Perl versions (`#4796 `_) * remove ``buildopts`` from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (`#4779 `_) * include ``joblib`` as extension in recent Python easyconfigs (`#4805 `_) * changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (`#4807 `_) * get rid of references to '``hpcugent``' organisation after move to github.com/easybuilders (`#4815 `_, `#4837 `_) * add ``Rtsne`` as extension to R 3.4.0 (`#4831 `_) * various bug fixes, including: * use ``PYPI_SOURCE`` as source URL in Tensorflow easyconfigs (`#4786 `_) * fix ``homepage`` for skewer (`#4791 `_) * sync/fix ``source_urls`` & ``homepage`` in HDF5 easyconfigs (`#4800 `_) * fix ``ubsan`` error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 with system GCC 7.1 (`#4813 `_) .. _release_notes_eb330: EasyBuild v3.3.0 (June 26th 2017) --------------------------------- feature release **framework** * various enhancements, including: * clean up easyconfigs that are copied for inclusion in pull request (`#2197 `_, `#2227 `_) * use devel logging where relevant in ``easybuild.tools.toolchain`` (`#2198 `_) * check exit code for executed ``module`` commands (`#2200 `_) * also copy patches to installation directory & easyconfigs archive along with easyconfig file (`#2202 `_, `#2241 `_) * add support for SHA256 checksums (`#2215 `_) * also auto-detect whether provided checksum is MD5 or SHA256 based on length (if not checksum type is specified) * add support for ``--enforce-checksums``, to require availability of checksums for sources/patches * see http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#source-files-patches-and-checksums * add support for renaming sources on download (`#2223 `_) * also involves deprecating use of 2-tuple elements in list of sources, see http://easybuild.readthedocs.io/en/latest/Deprecated-functionality.html#depr-sources-2-element-tuple * add support for ``--detect-loaded-modules`` (`#2228 `_) * give extensions access to ``module_generator`` of parent (`#2229 `_) * pass down additional arguments to ``copy_dir`` down to ``shutil.copytree`` (`#2230 `_) * avoid reloading already loaded modules that extend ``$MODULEPATH`` (`#2232 `_) * various bug fixes, including: * make sure test account & accompanying token is used in tests for ``github.py`` (`#2220 `_, `#2224 `_) * only use MPD for old versions of Intel MPI (<4.1) in ``mpi_cmd_for`` (`#2221 `_) * escape dots in package filename to ensure correct match in ``derive_alt_pypi_url`` (`#2225 `_) * fix ``GNU_SOURCE`` template by adding missing ``/gnu/`` (`#2235 `_) * catch exception ``shutil.Error`` in ``copy_file`` (`#2239 `_) * report full error and traceback on unhandled exception in test report (`#2240 `_) * fix ``--set-default-module`` flag (`#2243 `_) **easyblocks** * added easyblocks for MXNet (`#1135 `_), Tkinter(`#1184 `_) * minor enhancements, including: * enhance sanity check for NCL (`#1169 `_, `#1179 `_) * enable building of shared FFTW libraries (`#1180 `_) * include update statements for ``$CPATH`` and ``$*LIBRARY_PATH`` in generated module in numpy easyblock (`#1183 `_) * stop using deprecated '``copytree``' function from ``easybuild.tools.filetools`` (`#1185 `_) * update SAMtools easyblock for v0.1.17 (`#1189 `_) * update MATLAB easyblock for 2016b & 2017a versions (adjust permissions and change dir) (`#1182 `_, `#1197 `_) * consider ``$EB_*_LICENSE_SERVER(_PORT)`` in MATLAB and ANSYS easyblocks (`#1195 `_) * add ``omp_num_threads`` custom parameter in CP2K easyblock to allow defining ``$OMP_NUM_THREADS`` during testing (`#1196 `_) * various bug fixes, including: * fix Siesta easyblock to enable and verify parallel build (`#1186 `_) * fix bug in alias definition in impi easyblock for ``mpigxx``, ``mpiicpc`` and ``mpiifort`` (`#1192 `_) **easyconfigs** * enable automatic style checks in easyconfig tests (`#2506 `_) * added example easyconfig files for 28 new software packages: * ada (`#4594 `_), Aspera-CLI (`#4635 `_), AUGUSTUS (`#4624 `_), ada (`#4594 `_), Bio-SamTools (`#4637 `_), Bpipe (`#4590 `_), BUSCO (`#4624 `_), CNVnator (`#4649 `_), davix (`#4755 `_), EricScript (`#4594 `_), FUNWAVE-TVD (`#4743 `_), gmpy2 (`#4609 `_), gSOAP (`#4755 `_), libsndfile (`#4628 `_), lpsolve (`#4264 `_), LUMPY (`#4682 `_), MaSuRCA (`#4706 `_), modred (`#4729 `_), MXNet (`#4765 `_), NRGLjubljana (`#4651 `_), OrfM (`#4703 `_), Perl4-CoreLibs (`#4670 `_), prodigal (`#4468 `_), pydlpoly (`#4756 `_), SeqAn (`#4603 `_), sharutils (`#4745 `_), Spyder (`#4627 `_), Tkinter (`#4620 `_), VariantMetaCaller (`#4632 `_) * added new easyconfigs for existing toolchains: * ``gimkl/2017a`` (`#4646 `_) * added additional easyconfigs for various supported software packages, including: * ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1 * minor enhancements, including: * use '``git diff --name-only``' and ``$TRAVIS_COMMIT_RANGE`` in Travis config to get list of changed files (`#4606 `_, `#4619 `_) * add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ libsndfile as dep) (`#4628 `_, `#4680 `_, `#4747 `_) * also copy ``README`` for GapFiller (`#4631 `_) * enable inclusion of version symbol by using ``--enable-ld-version-script`` configure option for LibTIFF (`#4639 `_) * add SHA256 checksums for libpciaccess to discriminate from old tarballs that required running ``autogen.sh`` (`#4688 `_) * fix ``NE_GLOBAL_DIR`` path for ne by also specifying ``PREFIX`` in ``buildopts`` (`#4698 `_) * more (trivial) style fixes (`#4761 `_) * avoid use of ``import`` in ANSYS & MATLAB easyconfigs (`#4762 `_) * set ``$OMP_NUM_THREADS`` during CP2K test step via dedicated easyconfig parameter (`#4763 `_) * avoid use of '``import``' in BFAST easyconfigs, just strip of '``a``' from version (`#4764 `_) * add the docopt module to all Python 2017a easyconfigs (`#4770 `_) * stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (`#4774 `_) * various bug fixes, including: * fix typo in statsmodels source url (``/sources/`` -> ``/source/``) (`#4612 `_) * add location to ``DotLib.pm`` to ``$PERL5LIB`` for SSPACE_Basic (`#4638 `_) * add missing ``/gnu/`` in ftpmirror.gnu.org ``source_urls``, or use ``GNU_SOURCE`` where possible (`#4653 `_) * consistently use ``--with-harfbuzz=no`` configure option in freetype easyconfigs (`#4668 `_) * use ``--with-x=yes`` in R easyconfigs that include X11 as a dependency (`#4701 `_) * remove '``4.0``' in tbb description (`#4707 `_) * add lib sanity check paths for Debian compatibility in nettle (`#4722 `_) * fix source URLs for HDF5 (`#4749 `_) .. _release_notes_eb321: EasyBuild v3.2.1 (May 12th 2017) -------------------------------- bugfix/update release **framework** * various enhancements, including: * make hardcoded max ratio for failures in ``adjust_permissions`` configurable (`#2213 `_) * allow ``https://`` on direct download in sources (`#2214 `_) * various bug fixes, including: * bump version bootstrap script to sync with latest update (`#2208 `_) * fix crash during module generation when '``%``' character is used in description (`#2209 `_) **easyblocks** * added easyblock for Siesta (`#1105 `_) * minor enhancements, including: * enhance GROMACS easyblock to build with PLUMED support (`#1121 `_) * enhance NAMD easyblock: add OpenMP support, update for recent NAMD versions (2.12), fix compatibility with Tcl versions other than 8.5 (`#1173 `_) **easyconfigs** * added example easyconfig files for 12 new software packages: * AdapterRemoval (`#4509 `_), blasr_libcpp (`#4566 `_), canu (`#4473 `_), enchant (`#4567 `_), hunspell (`#4567 `_), memkind (`#4544 `_), NLTK (`#4565 `_), pbbam (`#4566 `_), pbdagcon (`#4566 `_), pyenchant (`#4567 `_), Siesta (`#4562 `_), xarray (`#4556 `_) * added new easyconfigs for existing toolchains: * goolfc 2017.01 (`#4577 `_) * added additional easyconfigs for various supported software packages, including: * HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0 * minor enhancements, including: * update source URLs in libpciaccess easyconfigs (`#3960 `_) * enable use of double precision floating point in METIS 5.1.0 ``foss/2016a`` easyconfig (`#4555 `_) .. _release_notes_eb320: EasyBuild v3.2.0 (May 5th 2017) ------------------------------- feature release **framework** * various enhancements, including: * add support for marking installed module file as new default version using ``--set-default-module`` (`#2110 `_) * additional easyconfig parameters for documentation: ``docpaths``, ``examples``, ``site_contacts``, ``upstream_contacts``, ``usage`` (`#2113 `_) * add support for ``--allow-use-as-root-and-accept-consequences`` (`#2123 `_) * enable extraction of patches from compressed files before applying them (`#2128 `_) * alphabetically sort functions and methods in ``module_generator`` module (`#2132 `_) * introduce function ``ensure_iterable_license_specs`` (`#2157 `_) * bump Travis config to use Lmod 7.4 (`#2176 `_) * implement ``copy_dir`` function in ``filetools`` (`#2177 `_) * clarify error message when no software-specific easyblock was found (`#2178 `_) * make ``log.deprecated`` more verbose by also printing deprecation warnings to stderr (`#2179 `_) * add ``copy`` function to ``filetools`` for easy copying of lists of files/directories (`#2180 `_) * add support for ``--verify-easyconfig-filenames`` (`#2185 `_) * add support for ``--package-tool-options`` (`#2187 `_) * take into account inline trailing comments in ``fetch_parameters_from_easyconfig`` (`#2192 `_) * add support for customising easyconfig parameters on a per-extension basis (`#2194 `_) * perform sanity check after stage 2 of EasyBuild bootstrap script, module file should be in place (`#2199 `_) * change order in which module commands are checked, consider Lmod first (`#2201 `_) * various bug fixes, including: * fix use of compiler-specific ``--optarch`` value in combination with ``--job`` (`#2183 `_) * call ``run_all_steps`` in regtest mode rather than running steps individually (`#2203 `_) **easyblocks** * added easyblocks for Doris (`#1154 `_, `#1161 `_), VMD (`#1148 `_) and WRF-Fire (`#1153 `_, `#1159 `_) * minor enhancements, including: * update ``IntelBase``, PGI and TotalView easyblocks to allow list of license files/servers via '``license_file``' easyconfig parameter (`#1129 `_) * update Bowtie2 easyblock to set correct build options, copy more files, extend sanity check (`#1146 `_) * added the option to build Boost with multi-threading support (`#1147 `_) * allow libpng as OS dependency for WPS (`#1150 `_) * extend Boost ``TIME_UTC`` patch to Boost versions <= 1.49.0 (`#1152 `_) * enhance Python sanity check to check for Tkinter support if Tk is included as a dependency (`#1156 `_, `#1158 `_) * add support to install Python extensions without unpacking (`#1166 `_) * enhance TBB easyblock to also support building open source versions (`#1168 `_) * various bug fixes, including: * update FFTW easyblock: ``--enable-avx-128-fma`` depends on the ``fma4`` CPU feature (AMD), not ``fma`` (`#1142 `_) * fix problems when ``usempi`` not defined in toolchain in NAMD easyblock (`#1162 `_) **easyconfigs** * added example easyconfig files for 34 new software packages: * ACTC (`#4386 `_), atomate (`#4484 `_), BreakDancer (`#4455 `_), bx-python (`#4486 `_), ClusterShell (`#4432 `_), custodian (`#4484 `_), DFTB+ (`#4398 `_), Doris (`#4404 `_), ED2 (`#4402 `_), FireWorks (`#4484 `_), GETORB (`#4414 `_), GapFiller (`#4462 `_), IPy (`#4450 `_), imbalanced-learn (`#4373 `_), ipyrad (`#4507 `_), libiconv (`#4499 `_), MultiQC (`#3564 `_), NLopt (`#1750 `_), Node-RED (`#4542 `_), PyCUDA (`#4523 `_), pymatgen-db (`#4484 `_), QuTiP (`#4371 `_), ROI_PAC (`#4414 `_), Rascaf (`#4459 `_), RepastHPC (`#4395 `_), rootpy (`#4242 `_), SSPACE_Basic (`#4461 `_), Sambamba (`#4442 `_), Spack (`#4431 `_), SpiceyPy (`#4406 `_), StaMPS (`#4454 `_), samblaster (`#4435 `_), VMD (`#4391 `_), WRF-Fire (`#4403 `_) * added additional easyconfigs for various supported software packages, including: * BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5 * various enhancements, including: * sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (`#4380 `_) * use ``pl2`` source tarball for FFTW 3.3.6 which already includes patch for ``F03`` interface (`#4529 `_) * various bug fixes, including: * add missing XZ dep in easyconfig for libunwind 1.1 w/ ``GCC/4.9.2``, sync ``sanity_check_paths`` across libunwind easyconfigs (`#4369 `_) * use '``use_fma4``' rather than deprecated '``use_fma``' easyconfig parameter in FFTW easyconfigs using ``intel`` toolchain (`#4384 `_) * fix ``pkgconfig`` patch for Qhull (`#4451 `_) * also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for ``foss/2016b`` (`#4467 `_) * add dependency NLopt for R extension ``nloptr`` (`#4481 `_) * fix issue with ``configparser`` and ``backports`` namespace blocking inclusion of ``nbconvert`` with IPython (`#4504 `_) * change source_urls of pycrypto to encrypted ``https://pypi.python.org/...`` (`#4505 `_) * fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (`#4531 `_) * also build IMB-IO in IMB 4.1 easyconfig using ``foss/2016a`` (`#4539 `_) .. _release_notes_eb312: EasyBuild v3.1.2 (March 20th 2017) ---------------------------------- bugfix/update release **framework** * fix broken packaging support by fixing ``run_cmd`` bug with ``shell=False`` (`#2153 `_) * minor enhancements, including: * implement ``change_dir`` function in ``filetools`` module (`#2155 `_) * use ``checker_state`` in trailing whitespace style check + add dedicated test (`#2160 `_, `#2169 `_) * consider both ``pycodestyle`` and ``pep8`` Python modules in style checks (`#2161 `_) * make bootstrap script aware various modules-related ``$EASYBUILD_*`` environment variables (`#2170 `_) * various bug fixes, including: * interpret statements that extend ``$MODULEPATH`` in ``modpath_extensions_for`` method (`#2104 `_) * also fixes inclusion of superfluous load statements in modules installed in user HMNS module tree (cfr. `#2172 `_) * take into account that ``$PATH`` or ``$PYTHONPATH`` may be empty when running tests (`#2149 `_) * handle duplicates in ``--include-*`` (`#2151 `_) * exclude dependencies of dependencies that extend ``$MODULEPATH`` (`#2152 `_) * add ``ld.bfd`` to RPATH wrappers (`#2156 `_) * fix ``test_vsc_location``, ``vsc.__file__`` may not be available when ``vsc`` is installed as a namespace package (`#2159 `_) * fix reported problems with scripts & docs tests (`#2164 `_) * fix ``--try-software-version`` using non-greedy matching + lookahead assertion, add test for ``tweak_one`` (`#2166 `_) * avoid creating empty modulefile directories when using ``modaltsoftname`` (`#2168 `_) * fix ``fftw_libs`` for MKL without interface libraries (`#2171 `_) **easyblocks** * add easyblock for QScintilla (`#1127 `_) * minor enhancements, including: * auto-disable quad precision on POWER and ARM in FFTW (`#1102 `_, `#1138 `_) * allow "download install" for PETSc (`#1114 `_) * modify Trinity sanity check for versions 2.3 and above (`#1133 `_) * make unpacking Python extensions optional (`#1134 `_) * update SAMtools easyblock for version 1.4 (`#1139 `_) * various bug fixes, including: * reduce number of environment variables in ``icc`` and ``ifort`` modules (`#1126 `_, `#1143 `_) * also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (`#1128 `_) * rename member variable to avoid conflict with member of base class in PGI (`#1137 `_) * don't set ``$FPATH`` environment variable in multiple easyblocks (`#1140 `_) **easyconfigs** * add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (`#4334 `_) * note that this warrants rebuilding FFTW that is a part of ``foss/2017a`` * added example easyconfig files for 14 new software packages: * DBG2OLC (`#4281 `_), disambiguate (`#4125 `_), fqtrim (`#4280 `_), GFOLD (`#4293 `_), Kaiju (`#4349 `_), LSMS (`#4335 `_), L_RNA_scaffolder (`#4282 `_), PileOMeth (`#4289 `_), psycopg2 (`#4319 `_), QGIS (`#4307 `_, `#4332 `_), QJson (`#4305 `_), QScintilla (`#4306 `_, `#4313 `_), sketchmap (`#4360 `_), snaphu (`#4362 `_) * added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4 * various enhancements, including: * fix style in several easyconfigs (`#4267 `_-`#4271 `_, `#4274 `_, `#4275 `_, `#4277 `_, `#4279 `_, `#4286 `_-`#4288 `_, `#4318 `_) * various bug fixes, including: * correctly set ``$PYTHONPATH`` in ROOT easyconfigs (`#4239 `_, `#4331 `_) * correct libjpeg turbo references in GDAL (`#4276 `_) * make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (`#4278 `_) * fix issues with miRDeep2 installation (`#4291 `_, `#4301 `_, `#4316 `_) * also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (`#4315 `_) * fix PostgreSQL homepage + minor style fixes (`#4318 `_) * detect use of '``$root``', which is not compatible with module files in Lua syntax (`#4330 `_) * fix ``homepage``/``source_urls`` for ViennaRNA (`#4338 `_) * pass down ``$FFLAGS`` via ``FLAGS_OPT`` in SWASH easyconfigs (`#4341 `_) * remove ``include/GL/wglext.h`` from Mesa sanity check (`#4354 `_) * rename ``S.A.G.E.`` to ``SAGE``, can't have directories with trailing dot in Windows (`#4368 `_) .. _release_notes_eb311: EasyBuild v3.1.1 (March 7th 2017) --------------------------------- bugfix/update release **framework** * minor enhancements, including: * print more useful error message when no compiler-specific ``optarch`` flag is defined (`#1950 `_) * add ``ec`` parameter to ``expand_toolchain_load()`` (`#2103 `_) * clarify unstable/closed PR warning message (`#2129 `_) * various bug fixes, including: * ensure that ``$EBEXTSLIST*`` is also included in generated module under ``--module-only`` (`#2112 `_) * fix formatting issues in generated documentation for ``--list-software`` and ``--avail-easyconfig-licenses`` (`#2121 `_) * fix problem with backticks in description breaking '``fpm``' packaging command (`#2124 `_) * replace ``--enable-new-dtags`` with ``--disable-new-dtags`` instead of removing it in RPATH wrapper script (`#2131 `_) * only perform ``is_short_modname_for`` sanity check in ``det_short_module_name`` if ``modaltsoftname`` is available (`#2138 `_) * fix logic in ``make_module_dep`` w.r.t. excluding loads for toolchain & toolchain components (`#2140 `_) * skip ``test_check_style`` if ``pep8`` is not available (`#2142 `_) **easyblocks** * minor enhancements, including: * change the sanity check for MCR 2016b since the directory structure has changed (`#1096 `_) * update NWChem easyblock for version 6.6.x and to handle different versions of OpenMPI for older versions (`#1104 `_) * allow per-component ``source_urls`` with templating in ``Bundle`` easyblock (`#1108 `_) * add slib to ``$LD_LIBRARY_PATH`` for itac (`#1112 `_) * consider both ``lib`` and ``lib64`` in CGAL sanity check (`#1113 `_) * add support for installing Intel tools that do not require license at installation time (`#1117 `_) * required for Intel MPI and Intel MKL version 2017.2.174 * remove ``prefix_opt`` as custom easyconfig parameter for Qt easyblock (`#1120 `_) * various bug fixes, including: * use '``-prefix ``' rather than '``--prefix=``' for ``configure`` in Qt (`#1109 `_) * fix indentation problem in PETSc easyblock (`#1111 `_) **easyconfigs** * added example easyconfig files for 16 new software packages: * Caffe (`#3667 `_), DIAMOND (`#4107 `_), fmt (`#4131 `_), googletest (`#4132 `_), igraph (`#4172 `_), MEGA (`#4202 `_), meRanTK (`#4175 `_), meshio (`#4178 `_), miRDeep2 (`#4229 `_, `#4255 `_), OOMPA (`#4211 `_), PBSuite (`#4224 `_, `#4230 `_), randfold (`#4217 `_), skewer (`#4246 `_), Smoldyn (`#4110 `_), SpiecEasi (`#4215 `_), stress (`#4180 `_) * added additional easyconfigs for various supported software packages, including: * binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a * added new easyconfigs for existing toolchains: * ``iomkl/2017a`` (`#4216 `_), ``intel/2017.02`` (`#4248 `_) * various enhancements, including: * fix style in several easyconfigs (`#4174 `_, `#4176 `_, `#4190 `_, `#4233 `_) * add sanity check command to Yade easyconfig to make sure that '``import yade``' works, include bzip2 as dep (`#4193 `_) * add ``PDF::API2`` extension to Perl 5.24.0 easyconfigs + sync ``exts_list`` (`#4221 `_) * various bug fixes, including: * add Bison and gettext as build deps for X11 (`#4111 `_) * clean up dependencies in libdrm (`#4113 `_) * make sure Ghostscript picks up external libraries (`#4118 `_) * fix ippicv source download and library install for OpenCV v3.1.0 (`#4126 `_) * fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (`#4134 `_, `#4135 `_) * get rid of backticks in gettext descriptions, causes problems when packaging with FPM (`#4146 `_) * remove duplicate sources specification in OpenMPI (`#4150 `_) * fix definition of ``buildopts``/``installopts`` in Cantera easyconfig (`#4133 `_, `#4164 `_, `#4177 `_) * use ``http://`` rather than ``ftp://`` source URLs in CFITSIO easyconfigs (`#4167 `_) * add patch for XZ 5.2.2 to include ``5.1.2alpha`` symbols required by '``rpm``' command on CentOS 7.x (`#4179 `_) * add patch for Boost v1.61-1.63 to fix problem with ``make_array``/``array_wrapper`` in Boost serialization library (`#4192 `_) * set ``CMAKE_PREFIX_PATH`` to ncurses install directory in CMake easyconfigs (`#4196 `_) * switch to ``lowopt=True`` for libxc v2.2.* and v3.* (`#4199 `_) * remove custom ``sanity_check_paths``, since it's identical to that used by the R easyblock (`#4200 `_) * fix ``version`` (& ``homepage``) in ea-utils easyconfigs (`#4205 `_) * remove ``--with-threads`` configure option in OpenMPI-2.* (`#4213 `_) * fix check for Szip library in configure script for netCDF 4.1.3 (`#4226 `_) * fix ``source_urls`` in several easyconfigs, including: * bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (`#4227 `_) .. _release_notes_eb310: EasyBuild v3.1.0 (February 3rd 2017) ------------------------------------ feature release **framework** * various enhancements, including: * ARM: GCC optimal/generic architecture compiler flags (`#1974 `_) * add support for ``--check-style`` to check style in easyconfig files (`#1618 `_, `#2038 `_) * add ``HOME`` and ``USER`` from env to available cfg file constants (`#2063 `_) * ``--optarch`` can now be specified on a toolchain basis (`#2071 `_) * implement ``get_cpu_features`` function in systemtools (`#2074 `_, `#2078 `_) * support use of ``linalg`` without MPI, add ``iimkl`` toolchain definition (`#2082 `_) * spoof HTTP request header with empty agent (`#2083 `_) * exclude dependencies of dependencies that extend $MODULEPATH in make_module_dep (`#2091 `_) * various bug fixes, including: * make ``fetch_github_token`` more robust against ``RuntimeError`` from ``keyring`` (`#2070 `_) * POWER: Fix ``--optarch=GENERIC`` for GCC (`#2073 `_) * fix docstring in toolchain class (`#2075 `_) * skip test cases involving ``.yeb`` if ``PyYAML`` is not installed, silence test in options subsuite (`#2081 `_) * fix traceback with '``eb --check-github``' if ``GitPython`` is not installed (`#2085 `_) * fix regex for determining list of patched files in GitHub diff (`#2088 `_) * modify robot so that it only appends dependencies of tweaked easyconfigs (`#2090 `_) * escape metacharacters in paths passed to ``re.compile`` in ``dry_run_set_dirs`` (`#2098 `_) * fix broken error message in ``get_toolchain_hierarchy`` + dedicated test case (`#2099 `_) **easyblocks** * new easyblock for FFTW (`#1083 `_) * various enhancements, including: * update sanity check for flex 2.6.3, no more ``libfl_pic.a`` library (`#1077 `_) * cleanup build before proceeding with full Boost (`#1080 `_) * update CP2K easyblock: copy data dir, support version 4.1, support ELPA, fix psmp build with foss toolchain (`#996 `_, `#1020 `_, `#1043 `_, `#1084 `_) * add sanity check support for OpenSSL 1.1 (`#1087 `_) * support the latest changes in Inspector 2017 (`#1047 `_) * update NEURON easyblock to support the lack of ``hoc_ed`` in 7.4 (`#987 `_) * add support for WPS 3.8 (`#1079 `_) * also consider ``setuptools`` in ``EasyBuildMeta`` easyblock (`#1093 `_) * various bug fixes, including: * (correctly) define ``$ROSETTA3_DB`` in Rosetta easyblock (`#1092 `_) **easyconfigs** * added easyconfigs for ``foss/2017a`` and ``intel/2017a`` common toolchains (`#3968 `_, `#3969 `_) * added example easyconfig files for 16 new software packages: * ack (`#3983 `_), cclib (`#4065 `_), ConnectomeWorkbench (`#3411 `_), GroIMP (`#3994 `_), hyperspy (`#3991 `_), I-TASSER (`#1216 `_), ImageJ (`#4023 `_, `#4062 `_), libconfig (`#4051 `_), libspatialindex (`#4002 `_), mahotas (`#3990 `_), Minia (`#3949 `_), muParser (`#4007 `_), NetLogo (`#3941 `_), QIIME (`#3868 `_), QwtPolar (`#4019 `_), Tensorflow (`#4084 `_, `#4095 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11 * various enhancements, including: * update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (`#3985 `_) * add FME extensions (+ deps) in R 3.3.1 easyconfigs (`#4063 `_) * various bug fixes, including: * add libxml2 dependency on HDF5 (`#3759 `_) * remove unnecessary dependency in libmatheval (`#3988 `_) * fix permissions on SWASH binaries (`#4003 `_) * add conda-forge channel to perl-app-cpanminus (`#4012 `_) * add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (`#4032 `_) * modloadmsg style fixes in multiple easyconfigs (`#4035 `_) * include X11 as dep for Molden (`#4082 `_) * remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (`#4083 `_) * fix source URLs for several easyconfigs, including: * arpack-ng 3.1.3 + 3.1.5 (`#4050 `_), ChIP-Seq 1.5-1 (`#4050 `_), Ghostscript 9.10, 9.14 + 9.16 (`#4050 `_), Git 1.7.12, 1.8.2 + 1.8.3.1 (`#4050 `_), HBase 1.0.2 (`#4043 `_), libevent 2.0.22 (`#4037 `_), libsodium 1.0.3 (`#4046 `_), lynx 2.8.7 (`#4050 `_), Maven 3.2.2 and 3.3.3 (`#4039 `_), MEME 4.8.0 (`#4050 `_), PCC 20131024 (`#4044 `_), S-Lang 2.3.0 (`#4045 `_), Spark 1.3.0 (`#4041 `_), splitRef 0.0.2 (`#4040 `_) .. _release_notes_eb302: EasyBuild v3.0.2 (December 22nd 2016) ------------------------------------- bugfix release **framework** * various bug fixes, including: * also skip dependencies of dependencies marked as external module in get_toolchain_hierarchy (`#2042 `_) * disable verbose setvar in modules.py (`#2044 `_) * force copying of easyconfigs in --new-pr/--update-pr, even when combined with -x (`#2045 `_) * fix verification of filename for easyconfigs used to resolve deps (`#2051 `_) * skip RPATH sanity check when toolchain did not use RPATH wrappers (`#2052 `_) * check whether file-like paths are readable before reading them in systemtools module (`#2065 `_) * various small enhancements, including: * add 'rpath' toolchain option to selectively disable use of RPATH wrappers (`#2047 `_) **easyblocks** * various enhancements, including: * enhance DL_POLY_Classic easyblock to support building with Plumed support (REVIEW) (`#829 `_) * make the Allinea easyblock search for the templates in the easyconfig paths (`#1025 `_) * make FortranPythonPackage aware of (pre)buildopts (`#1065 `_) * update sanity check for Mono to support recent versions (`#1069 `_) * fix Eigen sanity check for latest version 3.3.1 (`#1074 `_) * various bug fixes, including: * skip RPATH sanity check for binary installations (`#1056 `_) * pass CXXFLAGS and LDFLAGS to Boost bjam (`#1064 `_) * make pip ignore already installed versions of the package being installed (`#1066 `_) * don't pass empty string as custom installopts for numpy in test_step (`#1067 `_) * make the Rosetta EasyBlock work in --module-only mode (`#1073 `_) **easyconfigs** * added example easyconfig files for 13 new software packages: * CryptoMiniSat (`#3952 `_), MATSim (`#3902 `_), Molcas (`#2084 `_), ne (`#3376 `_), psmc (`#3910 `_), PyCogent (`#3897 `_), PyNAST (`#3897 `_), RASPA2 (`#3903 `_, `#3946 `_), SimPEG (`#3876 `_), SolexaQA++ (`#3892 `_), taco (`#3882 `_), UCLUST (`#3896 `_), USPEX (`#3767 `_) * added additional easyconfigs for various supported software packages, including: * Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02 * various enhancements, including: * trivial style fixes (`#3878 `_, `#3893 `_, `#3895 `_) * various bug fixes, including: * add X11 develop libs to ncview easyconfig (`#3881 `_) * fix source_urls in pkg-config easyconfigs (`#3907 `_) * install numpy/scipy as .egg to ensure shadowing of numpy/scipy in parent Python installation (`#3921 `_) * fix broken source URL + homepage for Infernal (`#3928 `_) * fix test that verifies dumped easyconfig, take into account that dumped dependencies may include hardcoded dependency (`#3932 `_) * include libGLU as dependency in freeglut easyconfigs with recent Mesa (`#3936 `_) * add patch for FreeSurfer to fix issue with MATLAB 2013 (`#3954 `_) .. _release_notes_eb301: EasyBuild v3.0.1 (November 30th 2016) ------------------------------------- bugfix release **framework** * important changes * always use Intel-specific MPI compiler wrappers (``mpiicc``, ``mpiicpc``, ``mpiifort``) for toolchains using both Intel compilers and Intel MPI (`#2005 `_) * various small enhancements, including: * use ``setvar`` in ``modules.py`` to define environment variables (`#2011 `_) * include output of ``sanity_check_commands`` in the build log (`#2020 `_) * various bug fixes, including: * fix testing of bootstrap script in Travis config (`#2003 `_) * use correct module syntax in bootstrap script if Lmod is not used (i.e. Tcl) (`#2007 `_) * fix packaging issue with non-Python scripts in easybuild/scripts (`#2015 `_) * fixes issue where RPATH wrapper template script (``rpath_wrapper_template.sh.in``) was not included in the v3.0.0 release * make tests more robust against running headless (`#2016 `_) * avoid rewrapping already wrapped compiler/linker command with RPATH wrapper script (`#2022 `_) * fix ``log.error`` traceback due to '``raise EasyBuildError``' involving a '``%s``' in error message (`#2024 `_) * make sure '``modules_tool``' attribute is also defined for extensions (`#2026 `_) * only dump easyconfig with modified deps due to ``--minimal-toolchains`` to 'reprod' subdir of install dir (`#2028 `_) * avoid appending '``-h'`` to sanity check commands specified as a string (`#2030 `_) * fix bug in ``list_software_rst``: always include version suffix regardless of value (`#2032 `_) **easyblocks** * various enhancements, including: * update SAMtools easyblock for recent versions (`#1048 `_) * various bugfixes, including: * fix QuantumESPRESSO easyblock to handle gipaw correctly (`#1041 `_) * always specify name of serial Fortran compiler to ALADIN, it already knows to use MPI wrapper commands (`#1050 `_) **easyconfigs** * added example easyconfig files for 7 new software packages: * Cookiecutter (`#3827 `_), ETE (`#3857 `_), findhap (`#3860 `_), graphviz (Python bindings, `#3826 `_), LoFreq (`#3856 `_), PhyloBayes-MPI (`#3859 `_), XGBoost (`#3849 `_) * added additional easyconfigs for various supported software packages * various enhancements, including: * add ``ipywidgets`` and ``widgetsnbextension`` extensions to IPython 5.1.0 easyconfigs (`#3818 `_, `#3823 `_) * run dadi test suite as a sanity check command (`#3858 `_) * various bug fixes, including: * fix incorrect descriptions for ifort (`#3817 `_) * fix ``modulename`` for Jinja2 and Pygments (`#3823 `_) * fix download URL in BLAST 2.2.26 easyconfig (`#3861 `_) .. _release_notes_eb300: EasyBuild v3.0.0 (November 16th 2016) ------------------------------------- feature release **framework** * backward-incompatible changes: * make robot always consider subtoolchains, even without ``--minimal-toolchains`` (but in reverse order) (`#1973 `_) * clean up behaviour that was deprecated for EasyBuild v3.0 (`#1978 `_) * change *default* config to use ``Lmod``/``Lua`` for modules tool/syntax, ``GC3Pie`` as job backend (`#1985 `_) * the minimal required version of Lmod was bumped to 5.8 (`#1985 `_) * major new features: * (experimental) support for RPATH linking via ``--rpath`` (`#1942 `_) * see http://easybuild.readthedocs.org/en/latest/RPATH-support.html * add support for ``--consider-archived-easyconfigs`` (`#1972 `_) * see http://easybuild.readthedocs.org/en/latest/Archived-easyconfigs.html * stabilize ``--new-pr`` and ``--update-pr`` (`#1979 `_) * see http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html * various other small enhancements, including: * add support for '``devel``' log level (`#1815 `_) * make ``remove_file`` aware of ``--extended-dry-run`` + add dedicated unit test (`#1932 `_) * add support for filtering out setting/updating particular environment variables from generated modules (`#1943 `_) * see ``--filter-env-vars`` * clean up output of EasyBuild bootstrap script & add version (`#1944 `_) * improved ARM platform/CPU detection (`#1953 `_) * use '``0``' as letter dir for funky software names that don't start with a letter, e.g., ``3to2`` (`#1954 `_) * make bootstrap script aware of ``vsc-install`` for offline installation (`#1955 `_) * add support for ``blas_family()`` and ``lapack_family()`` methods in ``Toolchain`` instances (`#1961 `_) * make ``copy_file`` dry-run aware (`#1963 `_) * reorganise test easyconfigs to match structure in easyconfigs repo (`#1970 `_) * add a toolchain compiler option for enforcing IEEE-754 conformance (`#1975 `_) * support for ``intelcuda`` compiler toolchain (`#1976 `_) * check that each glob pattern matches at least one file ``expand_glob_paths`` (important for ``--include-*``) (`#1980 `_) * enhance bootstrap to auto-skip stage 0 in case a suitable setuptools is already available (`#1946 `_, `#1984 `_) * simplify ``GC3Pie`` version check (`#1987 `_) * include suggestion on how to change configuration w.r.t. modules tool/syntax (`#1989 `_) * various bug fixes, including: * fix test for ``find_easybuild_easyconfig`` (`#1931 `_) * remove existing module file under ``--force``/``--rebuild`` (`#1933 `_) * fix combining ``--search`` and ``--try-*`` (`#1937 `_) * fix appending to existing ``buildstats`` in ``FileRepository.add_easyconfig`` (`#1948 `_) * fix handling of iterate easyconfig parameters, restore them during cleanup (`#1949 `_) * fix filtering loads for (hidden) build deps from generated module (`#1959 `_) * handle multi-flag compiler options on all types of options (`#1966 `_) * fix ``--list-software`` by making ``letter_dir_for`` function aware of '``*``' wildcard name (`#1969 `_) * skip dependencies of toolchain marked as external modules when determining module hierarchy (`#1977 `_) * bump page limit in ``fetch_latest_commit_sha``, spit out more meaningful error if too many branches were encountered (`#1981 `_) * fix CUDA-related issues in ``HierarchicalMNS`` (`#1986 `_) **easyblocks** * backwards incompatible changes: * remove deprecated GenomeAnalysisTK/GATK easyblock (`#1001 `_) * remove deprecated '``get_netcdf_module_set_cmds``' function from netCDF easyblock (`#1015 `_) * remove deprecated '``get_blas_lib``' function from LAPACK easyblock (`#1016 `_) * remove ``QLogicMPI`` easyblock (`#1023 `_) * new easyblock for installing Anaconda (`#950 `_) * add generic easyblock for Conda installations (`#950 `_) * various enhancements, including: * enable use of ``GCCcore`` as toolchain for Clang, fail if no GCC prefix is found (`#1002 `_) * also build Boost MPI library in parallel (`#1005 `_, `#1038 `_) * enhance g2clib easyblock to allow to install 1.6.0 or higher (`#1006 `_) * update QuantumESPRESSO easyblock to support packaging changes in 6.0 (`#1007 `_) * add support to ``Scons`` generic easyblock to provide argument to specify installation prefix (`#1008 `_) * update ``IntelBase`` and imkl easyblocks to handle the 2017 versions of compilers/imkl (`#1012 `_) * leverage ``toolchain.linalg`` functionality in ScaLAPACK easyblock, use ``copy_file`` (`#1014 `_) * allow netCDF-C++4 to be used with ESMF (`#1019 `_) * update Advisor easyblock to support latest versions (`#1021 `_) * update CBLAS easyblock to build with ``foss`` toolchain (`#1024 `_) * update Gurobi easyblock to use ``copy_file`` (`#1028 `_) * add support for giving ``/lib`` preference over ``/lib64`` & co in GCC installation (`#1030 `_, `#1035 `_) * enable installation of ``libiberty`` by default for binutils (`#1030 `_) * avoid CMake fiddling with the RPATHs injected by EasyBuild via ``--rpath`` in CMakeMake and METIS easyblocks (`#1031 `_, `#1034 `_) * simplify scipy sanity check to make it more robust w.r.t. version updates (`#1037 `_) * various bug fixes, including: * make sure '``None``' doesn't appear in modules generated with ``--module-only`` (`#998 `_) * fix ATLAS easyblock for non-x86 systems (`#1003 `_) * fix '``usempi``' and '``with_mpi``' usage to allow for a serial build of Amber 16 (`#1013 `_) * add both ``lib/python2.7/site-packages/{,wx-3.0-gtk2}`` to ``$PYTHONPATH`` for wxPython (`#1018 `_) * only hard inject RPATH for ``/usr/lib*`` directories when building binutils with ``dummy`` toolchain (`#1026 `_) * make HDF5 easyblock handle ``--filter-deps`` correctly (`#1027 `_) * update Travis config w.r.t. changes framework config defaults and required Lmod version (`#1029 `_) * be more patient when running Mathematica Q&A installer (`#1036 `_) **easyconfigs** * backwards incompatible changes: * archive easyconfigs using old inactive toolchains * see `#3725 `_, `#3728 `_, `#3729 `_, `#3730 `_, `#3731 `_, `#3732 `_, `#3733 `_, `#3735 `_, `#3736 `_, `#3737 `_, `#3738 `_ * only taken into account by EasyBuild if ``--consider-archived-easyconfigs`` is enabled * no easyconfigs available outside of archive for QLogicMPI + 15 toolchains: * ``ClangGCC``, ``cgmpich``, ``cgmpolf``, ``cgmvapich2``, ``cgmvolf``, ``cgompi``, ``cgoolf``, ``gmacml``, ``goalf``, ``gpsmpi``, ``gpsolf``, ``iiqmpi``, ``intel-para``, ``ipsmpi``, ``iqacml`` * fix name in PyTables easyconfigs (was 'pyTables') (`#3785 `_) * added example easyconfig files for 32 new software packages: * 3to2 (`#3655 `_), Anaconda2 (`#3337 `_), Anaconda3 (`#3337 `_), ART (`#3724 `_), atools (`#3631 `_), awscli (`#3645 `_), behave (`#3751 `_), Blosc (`#3785 `_), bokeh (`#3790 `_), Cantera (`#3655 `_), Cargo (`#3764 `_), dadi v1.7.0, distributed (`#3786 `_), ea-utils (`#3634 `_), Elk (`#3644 `_), FGSL (`#3638 `_), gencore_variant_detection (`#3337 `_), help2man (`#3768 `_), lbzip2 (`#3791 `_), Log-Log4perl (`#3574 `_), Minimac2 (`#3783 `_), mypy (`#3694 `_), OBITools (`#3573 `_), perl-app-cpanminus (`#3337 `_), PGDSpider (`#3625 `_), prokka (`#3755 `_), Reads2snp (`#3609 `_), spglib-python (`#3620 `_), SUNDIALS (`#3654 `_, `#3655 `_), SelEstim (`#3626 `_), XMLStarlet (`#3797 `_), x265 (`#3090 `_) * added easyconfigs for new '``intelcuda``' toolchain (`#3750 `_) * added new easyconfigs for existing toolchains: * ``goolfc/2016.08`` (`#3796 `_), ``goolfc/2016.10`` (`#3666 `_, `#3775 `_), ``intel/2017.00`` (`#3543 `_), ``intel/2017.01`` (`#3757 `_), ``iomkl/2016.09-GCC-4.9.3-2.25`` (`#3680 `_), ``iomkl/2016.09-GCC-5.4.0-2.26`` (`#3772 `_) * added additional easyconfigs for various supported software packages, including: * Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3, OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1 * various other enhancements, including: * STREAM builds using ~56GiB and ~111GiB (`#3670 `_) * various bug fixes, including: * fix source spec in VASP easyconfig, ensure static linking with Intel MKL (`#3381 `_) * fix source URL in GCCcore 6.2.0 easyconfig (`#3608 `_) * correct STAMP dependency in i-cisTarget, must be 1.3 (`#3613 `_) * consistently specify to use ``-fgnu89-inline`` flag in M4 1.4.17 easyconfigs (`#3623 `_) * fix source URLs for Cython (`#3636 `_) * add Bison as build dep and M4 as runtime dep for flex 2.6.0 (`#3656 `_) * enable parallel building of flex 2.6.0 (`#3630 `_) * add zlib and bzip2 dependencies to X11 bundle (`#3662 `_) * use '``letter_dir_for``' function rather than just grabbing 1st letter of software name in easyconfigs tests (`#3664 `_) * add patch to fix typo in GRIT 2.0.5 (`#3675 `_) * fix typo in patch for WRF 3.8.0 (`#3702 `_) * use ``$CC``, ``$CXX`` rather than ``$I_MPI_CC``, ``$I_MPI_CXX`` in patch for OpenFOAM 4.0 (`#3703 `_) * patch FLTK to fix '``undefined symbol``' issue when building Octave (`#3704 `_) * include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (`#3723 `_) * update Travis config w.r.t. changes framework config defaults and required Lmod version (`#3773 `_) * don't limit parallellism to 4 in recent GCC easyconfigs (`#3776 `_, `#3777 `_, `#3778 `_) * include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (`#3782 `_) * consistently apply patch for ncurses 6.0 (`#3792 `_) * eliminate dependency on ``mpi-mic-rt`` in ifort (`#3793 `_) * include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (`#3794 `_) * make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (`#3795 `_) * include original download URL for ISL source tarball in GCC easyconfigs (`#3798 `_) * disable installing ``libiberty`` for binutils built with intel toolchain (`#3802 `_) .. _release_notes_eb290: EasyBuild v2.9.0 (September 23rd 2016) -------------------------------------- feature release **framework** * note: vsc-base 2.5.4 or more recent is now required * various small enhancements, including: * change option ``--color`` choices to auto/always/never (`#1701 `_, `#1898 `_, `#1911 `_) * add support for '``hidden``' easyconfig parameter (`#1837 `_) * add support for using ``ccache`` and ``f90cache`` compiler caching tools (`#1844 `_, `#1912 `_) * see ``--use-ccache`` and ``--use-f90cache`` * update Cray metadata for 16.06 CrayPE release (`#1851 `_) * also include patch files in ``--new-pr`` and ``--update-pr`` (`#1852 `_) * handle deleted files in ``--new-pr`` (`#1853 `_) * add support for ``--install-latest-eb-release`` (`#1861 `_) * add support for hiding toolchains, see ``--hide-toolchains`` and '``hidden``' key in '``toolchain``' spec (`#1871 `_) * add template for GitHub source URL (`#1872 `_) * add support for combining ``--new-pr``/``--update-pr`` and ``--robot`` (`#1881 `_) * add support for ``--list-software`` and ``--list-installed-software`` (`#1883 `_, `#1910 `_, `#1917 `_) * print message on which extension is being installed, incl. progress counter (`#1886 `_, `#1914 `_) * add support for ``--github-org`` to specify GitHub organisation rather than GitHub user (`#1894 `_) * add support for running Lmod in debug mode (`#1895 `_) * avoid needless use of deepcopy, speed up support for templating in easyconfigs (`#1897 `_) * convert ``all_dependencies`` to a property in ``EasyConfig`` class (`#1909 `_) * add support for ``--mpi-cmd-template`` (`#1918 `_) * add support for ``--disable-mpi-tests`` (`#1920 `_) * various bug fixes, including: * merge with develop when using ``--from-pr`` (`#1838 `_, `#1867 `_) * ensure ``--new-pr`` doesn't open empty pull requests (`#1846 `_) * better error handling for outdated ``GitPython`` module in ``--check-github`` (`#1847 `_) * fix formatting for generated easyblocks documentation (`#1860 `_) * make sure the robot ignores filtered dependencies when creating toolchain cache (`#1862 `_) * honor ``--filter-deps`` under ``--minimal-toolchains`` (`#1863 `_) * correct format for '``param``' and '``author``' tags in docstrings (`#1866 `_) * ignore failing bootstrap test in Travis config file (`#1870 `_) * make sure all output of executed command is included in generated temporary log file (`#1873 `_, `#1874 `_) * ensure ``--show_hidden`` is used in the correct location for '``avail``' with Lmod (`#1875 `_) * make sure ``self.path`` is passed down in copy method of ``EasyConfig`` object (`#1884 `_) * take into account possible multi-line modloadmsg in ``ModuleGeneratorLua`` (`#1885 `_) * fix extracting ``.bz2`` source files (`#1889 `_) * don't resolve path to Lmod command (`#1892 `_) * fix skipping of stage 0 in bootstrap script (`#1893 `_) * fix function signature of ``log.deprecated`` compared to ``fancylogger.deprecated`` (`#1896 `_, `#1899 `_) * apply patch to Tcl/C environment modules tool for Tcl 8.6 support in Travis config (`#1901 `_) * fix combining ``--extended-dry-run`` with ``--from-pr`` (`#1902 `_) * also template dict keys (`#1904 `_) * don't pass '``--try-*``' command-line options to EB instance running within job script (`#1908 `_) * add workaround for incorrectly passing command line arguments with ``--job`` (`#1915 `_) * fix issues with ``--module-only`` (`#1919 `_, `#1924 `_, `#1925 `_) * correctly deal with specified start_dir * do not remove installation directory when build-in-installdir is enabled * make sure '``which``' function returns path to a file (`#1921 `_) * fix ``:param:``, ``:return:`` tags in docstrings & add test for it (`#1923 `_) **easyblocks** * new easyblocks for 6 software packages that require customized support: * cppcheck (`#983 `_), HEALPix (`#982 `_), IMOD (`#847 `_), IronPython (`#321 `_), Mono (`#321 `_), MyMediaLite (`#321 `_) * various enhancements, including: * extend OpenFoam-Extend sanity check for decomp libraries (`#784 `_) * enhance Java easyblock to support installing Java 6.x (`#940 `_) * make QuantumESPRESSO easyblock aware of multithreaded FFT (`#954 `_) * extend PSI easyblock to use PCMSolver and CheMPS2 (`#967 `_) * make Boost easyblock add definition for ``$BOOST_ROOT`` to generated module file (`#976 `_) * add support to Bundle easyblock to install list of components (`#980 `_) * enhance & clean up libxml2 easyblock to also enable installing without Python bindings (`#984 `_) * update Libint easyblock for Libint 2.1.x (`#985 `_) * update sanity check for OpenFOAM to support OpenFOAM 4.x (`#986 `_) * make easyblocks that run MPI tests aware of '``mpi_tests``' build option (`#993 `_) * various bug fixes, including: * fix compatibility of OpenFOAM easyblock with ``--module-only`` (`#784 `_) * fix testing of ``--module-only`` compatibility for OpenFOAM and IMOD easyblocks (`#784 `_) * add '``include/libxml2``' to ``$CPATH`` in libxml2 easyblock (`#981 `_) * fix compatibility of IntelBase generic easyblock with ``--module-only`` (`#994 `_) * make sure correct config script is used for Tcl/Tk deps of R (`#995 `_) **easyconfigs** * added example easyconfig files for 88 new software packages: * ADMIXTURE (`#3359 `_), angsd (`#3593 `_), ASHS (`#3429 `_), AutoDock (`#3465 `_), AutoGrid (`#3466 `_), BayeScan (`#2748 `_, `#3356 `_), BayPass (`#3451 `_), Bazel (`#3379 `_), Blender (`#3553 `_, `#3558 `_), bwakit (`#3567 `_), BXH_XCEDE_TOOLS (`#3410 `_), CastXML (`#3403 `_), CHASE (`#3304 `_), configparser (`#3368 `_, `#3424 `_), configurable-http-proxy (`#3380 `_), cppcheck (`#3508 `_), CRPropa (`#779 `_), DicomBrowser (`#3432 `_), DMTCP (`#3422 `_), entrypoints (`#3368 `_, `#3424 `_), f90cache (`#3570 `_), fastPHASE (`#3343 `_), fastQValidator (`#3192 `_), FFindex (`#1135 `_), FragGeneScan (`#1198 `_), gdc-client (`#3399 `_), gflags (`#3417 `_), glog (`#3417 `_), GRIT (`#3561 `_), H5hut (`#3431 `_), HAPGEN2 (`#3344 `_), HEALPix (`#779 `_), IMOD (`#1187 `_, `#3347 `_), IronPython (`#607 `_), jhbuild (`#3476 `_), jupyterhub (`#3380 `_), Keras (`#3581 `_), khmer (`#1158 `_), LeadIT (`#3345 `_, `#3599 `_), LevelDB (`#3417 `_), libbitmask (`#3481 `_), libcpuset (`#3481 `_), LMDB (`#3417 `_), log4cplus (`#1136 `_), MACH (`#3346 `_), Mako (`#3460 `_), Maq (`#3428 `_), MetaGeneAnnotator (`#3307 `_), Metal (`#3324 `_), Mono (`#607 `_), MyMediaLite (`#607 `_), nco (`#2575 `_), nose-parameterized (`#3579 `_), OpenEXR (`#3553 `_), OpenImageIO (`#3553 `_), path.py (`#3368 `_, `#3424 `_), PCRE2 (`#3325 `_), pftoolsV3 (`#3317 `_), PHASE (`#3385 `_), PLAST (`#3288 `_), PLINKSEQ (`#3402 `_), POV-Ray (`#3551 `_), ProbABEL (`#3108 `_), prompt-toolkit (`#3368 `_, `#3424 `_), protobuf-python (`#3563 `_), PSORTb (`#3317 `_), py (`#3403 `_, `#3482 `_), pygccxml (`#3403 `_, `#3482 `_), pyGIMLi (`#3403 `_, `#3482 `_), pyplusplus (`#3403 `_, `#3482 `_), PyQt5 (`#3533 `_), Pyro4 (`#3527 `_), pytest (`#3403 `_, `#3482 `_), QCA (`#3595 `_), RDMC (`#1137 `_), S.A.G.E. (`#3427 `_), SDL2 (`#3551 `_), SHORE (`#3531 `_), SimVascular (`#3555 `_), SortMeRNA (`#3326 `_), SUMACLUST (`#3316 `_), SUMATRA (`#3316 `_), Text-CSV (`#3323 `_), Triangle (`#3403 `_), VEGAS (`#3457 `_), VirSorter (`#3307 `_), wcwidth (`#3368 `_, `#3424 `_), X11 (`#3340 `_) * added new easyconfigs for existing toolchains: * CrayGNU + CrayIntel 2016.06 (`#3377 `_) * foss 2016.07 (`#3517 `_) + 2016.09 (`#3523 `_) * iomkl 2016.07 (`#3458 `_) * pomkl 2016.09 (`#3516 `_) * added additional easyconfigs for various supported software packages, including: * FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0, OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0, Yade 2016.06a * various enhancements, including: * adjust PSI4 easyconfigs for updated easyblock (`#3312 `_) * clean up libxml2 easyconfigs according to updated libxml2 easyblock (`#3479 `_, `#3509 `_) * significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (`#3520 `_) * include sanity checks for all MATIO config files (`#3528 `_) * remove ``--with-tcl-config``/``--with-tk-config`` from R easyconfig, already done in R easyblock (`#3580 `_) * various bug fixes, including: * disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (`#3178 `_) * add SQLite as dep to GDAL 2.1.0 easyconfigs (`#3342 `_) * add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (`#3342 `_) * add bzip2 as a dependency of freetype (`#3464 `_) * specify correct MPI target in FDS easyconfigs (`#3488 `_) * add tcsh as OS dep in NAMD easyconfigs (`#3491 `_) * statically link ncurses/libreadline in Lua easyconfig with '``dummy``' toolchain (`#3545 `_) * add M4 as dep for flex 2.6.x (`#3542 `_, `#3550 `_) * add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (`#3548 `_) * make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (`#3556 `_) * add missing patches for extensions in Python 3.x easyconfigs (`#3557 `_) * add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (`#3568 `_) * enable running of tests for HPCG (`#3578 `_) * fix ``buildopts`` in tabix easyconfigs (`#3584 `_) .. _release_notes_eb282: EasyBuild v2.8.2 (July 13th 2016) --------------------------------- bugfix release **framework** * various small enhancements, including: * add support for rst output for ``--list-*`` and ``--avail-*`` (`#1339 `_) * add support for '``eb --check-conflicts``' (`#1747 `_, `#1807 `_, `#1833 `_) * ensure nice error message when non-existing path is passed to ``apply_regex_substitutions`` (`#1788 `_) * add check for module output, empty stdout is a sign of trouble with Lmod (`#1793 `_) * add multi-threaded FFT to toolchain (`#1802 `_) * avoid special characters like '[', ']' in path to temporary directory (`#1808 `_) * add support for ``--zip-logs`` (`#1820 `_) * add support for ``--extra-modules`` (`#1821 `_) * add type conversion for 'checksums' and 'patches' parameter in .yeb easyconfigs (`#1826 `_, `#1840 `_) * add support for filtering tests by name (`#1828 `_) * add support for ``--avail-toolchain-opts`` (`#1830 `_, `#1839 `_) * use absolute path for robot and easyconfig files (`#1834 `_) * add backup URL for tarballs hosted on SourceForge in ``install_eb_dep.sh`` script (`#1843 `_) * various bug fixes, including: * fix installation of Lua in ``install_eb_dep.sh`` script (`#1789 `_) * fix OpenMP flag for Cray compiler wrappers (`#1794 `_) * only reset ``$MODULEPATH`` before loading a module if environment was reset (`#1795 `_) * include vsc-install as dependency in ``setup.py`` (`#1805 `_) * cache ``$PATH`` & ``$PYTHONPATH`` in test setUp, restore them in tests where '``eb``' is used (`#1806 `_) * don't reset ``$MODULEPATH`` in stage 2 of bootstrap script, support forced installation during stage 2 (`#1810 `_) * fix issue with templates defined by deps being required while still parsing deps (`#1812 `_) * skip unneeded unuse/use commands on tail of ``$MODULEPATH`` in ``check_module_path`` (`#1813 `_) * fix auto-convert for all ``*dependencies`` params in ``.yeb`` easyconfigs, ensure version is a string (`#1818 `_) * fix ``keyring`` version in Travis config (`#1819 `_) * fix dumping of ``.yeb`` easyconfig files in easyconfigs archive (`#1822 `_) * fix format of supported easyconfig templates in help output (`#1825 `_) * stick to ``pydot`` 1.1.0 for Python 2.6 in Travis config (`#1827 `_) **easyblocks** * new easyblocks for 5 software packages that require customized support: * Amber (`#958 `_), Extrae (`#955 `_), Gurobi (`#962 `_), Paraver (`#956 `_), Tau (`#887 `_) * various enhancements, including: * add support for building & installing old GROMACS versions (`#569 `_, `#960 `_) * add support for building Boost with Cray toolchain (`#849 `_) * libxsmm support for CP2K (`#942 `_) * pick up specified components for imkl (`#943 `_) * add support for building GROMACS with double precision (`#946 `_, `#960 `_) * add support for building GROMACS with CUDA support and using dynamic libraries using ``Cray`` toolchains (`#951 `_, `#960 `_) * also install vsc-install in ``EasyBuildMeta`` easyblock, if tarball is provided (`#957 `_) * enhance PSI easyblock to support PSI4 1.0 (`#965 `_) * various bug fixes, including: * also install scripts with MRtrix 0.3.14 (`#941 `_) * enhance Qt easyblock to support Qt3 (`#944 `_) * create '``release``' symlink in MRtrix install dir (`#947 `_) * fix ``make_installdir`` in Inspector & VTune easyblocks (`#952 `_) * make ``Binary`` and ``MakeCp`` easyblocks aware of '``keepsymlinks``' (`#959 `_) * correctly define ``$G4*`` environment variables in Geant4 easyblock (`#961 `_, `#970 `_) * prepend tmp install path to ``$PYTHONPATH`` in numpy test step, move to build dir when removing '``numpy``' subdir (`#963 `_) * correct full path to ALADIN config file & patch it to use right Fortran compiler flags (`#964 `_) * ensure correct compiler command/flags are used for SAMtools (`#966 `_) **easyconfigs** * added example easyconfig files for 54 new software packages: * Amber (`#3200 `_), Bullet (`#3175 `_), CONTRAlign (`#690 `_), Cluster-Buster (`#3191 `_), damageproto (`#3222 `_, `#3308 `_), DCA++ (`#3219 `_), EIGENSOFT (`#3147 `_, `#3163 `_), Extrae (`#507 `_), fdstools (`#3237 `_), ffnet (`#3273 `_), GP2C (`#3257 `_), Gurobi (`#3239 `_), gc (`#3202 `_, `#3261 `_), gputools (`#546 `_), IMa2p (`#3300 `_), IOzone (`#3253 `_), i-cisTarget (`#3191 `_, `#3194 `_), icmake (`#3243 `_), io_lib (`#3255 `_), Kent_tools (`#3191 `_), libcmaes (`#3256 `_), libpsortb (`#3259 `_), libxsmm (`#3099 `_), MEGACC (`#3263 `_), MM-align (`#1428 `_), MOSAIK (`#880 `_), MView (`#1345 `_), MySQL-python (`#3172 `_, `#3189 `_), magma (`#3219 `_), mrFAST (`#862 `_), mrsFAST (`#862 `_), mysqlclient (`#3172 `_, `#3232 `_), NTL (`#3183 `_), PARI-GP (`#3257 `_), Paraver (`#508 `_), psutil (`#3171 `_, `#3231 `_), PSI4 (`#3293 `_), Qwt (`#3157 `_), RMBlast (`#3142 `_), STAMP (`#3191 `_), Seqmagick (`#3264 `_), splitRef (`#946 `_), TAU (`#509 `_), TRF (`#3141 `_), TVB (`#3053 `_, `#3247 `_, `#3251 `_), TVB-deps (`#3053 `_, `#3247 `_, `#3251 `_), tvb-data (`#3053 `_, `#3247 `_, `#3251 `_), tvb-framework (`#3053 `_, `#3247 `_, `#3251 `_), tvb-library (`#3053 `_, `#3247 `_, `#3251 `_), VampirTrace (`#509 `_), Voro++ (`#3174 `_), wheel (`#3235 `_), wxPropertyGrid (`#508 `_), xonsh (`#3159 `_) * added easyconfigs for update of common toolchains: ``foss/2016b`` (`#3271 `_), ``intel/2016b`` (`#3270 `_) * added new easyconfigs for existing toolchains: ``CrayGNU/2016.03`` & ``CrayGNU/2016.04`` (`#3291 `_), ``foss/2016.06`` (`#3184 `_), ``intel/2016.03-GCC-5.4`` (`#3185 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2, Python 2.7.12, Python 3.5.2, Qt 3.3.8, R 3.3.1 * various enhancements, including: * use ``check_conflicts`` function in easyconfigs tests (`#2981 `_) * also include vsc-install in list of sources for recent EasyBuild easyconfigs, to support offline installation (`#3203 `_) * enable building of ``libmysqld.*`` in MariaDB easyconfigs (`#3230 `_) * add ALDEx2, phyloseq to bundles for Bioconductor 3.2 (`#3211 `_, `#3241 `_) * add biom, geepack, lubridate, pim to list of R 3.2.3 extensions (`#3186 `_, `#3211 `_, `#3275 `_) * various bug fixes, including: * add patch for Boost 1.60.0 to fix bug resulting in ``TypeError`` (`#3162 `_) * add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU (`#3176 `_) * fix location of ``libelf.h``, only (also) installed as ``include/libelf.h`` is there's no ``/usr/include/libelf.h`` (`#3201 `_) * fix software name for Guile & GnuTLS (was 'guile' & 'gnutls') (`#3207 `_) * added missing space in Geant4 configopts to specify ``-DGEANT4_INSTALL_DATA`` (`#3209 `_) * fix Cython download URL in Python 2.7.11 easyconfigs (`#3212 `_) * add missing build deps for X stack in easyconfigs using ``foss/2016a`` or ``intel/2016a`` (`#3222 `_, `#3308 `_) * fix overruling of exts_list in Perl 5.22.2 easyconfig (`#3224 `_) * add missing dependency on GMP in R 3.2.3 easyconfigs (`#3226 `_) * don't hard specify toolchain for binutils build dep in likwid easyconfig, since it matches parent toolchain (`#3240 `_) * fix ``homepage`` & ``source_urls`` in HMMER easyconfigs (`#3246 `_) * stick to ``pydot`` 1.1.0 for Python 2.6 in Travis config (`#3282 `_) * add ``python-dev(el)`` to OS deps in GC3Pie easyconfigs (`#3310 `_) .. _release_notes_eb281: EasyBuild v2.8.1 (May 30th 2016) -------------------------------- bugfix release **framework** * various bug fixes, including: * fix error message on missing module command in bootstrap script (`#1772 `_) * expand '``~``' in paths specified to ``--include-*`` (`#1774 `_) * break after deleting cache entry to avoid attempt to delete cache entry again (`#1776 `_) * avoid changing ``$MODULEPATH`` when prepending with symlink of path already at head of ``$MODULEPATH`` (`#1777 `_) * filter out duplicates in ``find_flexlm_license`` (`#1779 `_) * stick with GitPython < 2.0 with Py2.6 in Travis configuration (`#1781 `_) * don't use ``LooseVersion`` to define ``version_major``/``version_minor`` (`#1783 `_) **easyblocks** * various enhancements, including: * update MRtrix easyblock for version 0.3.14 (`#932 `_) * update Inspector easyblock for recent versions (`#934 `_) * update VTune easyblock for recent versions (`#935 `_) * add debug message to IntelBase easyblock w.r.t. switching to 'exist_lic' (`#936 `_) **easyconfigs** * added example easyconfig files for 13 new software packages: * drFAST (`#906 `_), git-lfs (`#2478 `_), grabix (`#3127 `_), JWM (`#3007 `_), libcroco (`#3007 `_), librsvg (`#3007 `_), MaCH (`#3136 `_), mayavi (`#3106 `_), OpenMM (`#2762 `_), Pysam (`#3080 `_), SeqPrep (`#3097 `_), vt (`#3128 `_), wkhtmltopdf (`#3098 `_) * added new easyconfigs for existing toolchains: ``intel/2016.03-GCC-4.9`` (`#3088 `_) * added additional easyconfigs for various supported software packages, including: * Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 update 3 * various bug fixes, including: * apply libreadline patch to fix bug triggering segmentation fault (`#3086 `_) .. _release_notes_eb280: EasyBuild v2.8.0 (May 18th 2016) -------------------------------- feature + bugfix release **framework** * significant speedup improvements of EasyBuild itself, thanks to: * stop creating ``ModulesTool`` instances over and over again (`#1735 `_) * cache result of '``module avail``' calls (`#1742 `_) * add support for using PGI as toolchain compiler (`#1342 `_, `#1664 `_, `#1759 `_, `#1761 `_, `#1764 `_) * incl. new toolchain definitions ``pompi`` and ``pomkl`` (`#1724 `_) * add test configuration for Travis (`#1733 `_, `#1737 `_, `#1743 `_, `#1767 `_) * various other enhancements, including: * add ``get_total_memory()`` function in ``systemtools`` module (`#1623 `_) * ignore ``__init__.py`` files in ``--include-*`` (`#1704 `_) * use ``-fopenmp`` rather than ``-openmp`` for Intel compilers, since ``-openmp`` is deprecated (`#1718 `_) * add modules to metadata for Cray modules (`#1721 `_) * make sure user write permissions are set after failed removal attempt of installation directory (`#1722 `_) * escape special characters in software name in ``find_related_easyconfigs`` (`#1726 `_) * add support for ``CrayPGI`` compiler toolchain (`#1729 `_) * ensure read permission to all installed files for everybody (unless other options specify otherwise) (`#1731 `_) * also consider ``$LMOD_CMD`` in bootstrap script (`#1736 `_) * translate PyPI download URL to alternate URL with a hash (`#1749 `_) * make ``get_software_libdir`` compatible with ``-x`` (`#1750 `_) * set ``$LMOD_REDIRECT`` to '``no``' when initialising Lmod (`#1755 `_) * add test for broken modules tool setup affecting '``module use``' (`#1758 `_) * various bug fixes, including: * isolate '``options``' tests from easyblocks other than the ones included in the tests (`#1699 `_) * don't run '``module purge``' in tests, since EasyBuild may be made available through a module (`#1702 `_) * avoid rehandling ``--include-*`` options over and over again during ``--show-config`` (`#1705 `_) * remove useless ``test_cwd`` (`#1706 `_) * fix bootstrap script: make sure setuptools installed in stage0 is still available at end of stage1 (`#1727 `_) * forcibly create target branch in ``--update-pr`` (`#1728 `_) * remove check whether '``easybuild``' is being imported from dir that contains ``easybuild/__init__.py`` (`#1730 `_) * (re)install vsc-base during stage1 using ``--always-copy`` in bootstrap script, if needed (`#1732 `_) * use ``os.path.realpath`` in ``test_wrong_modulepath`` to avoid symlinked path breaking the test (`#1740 `_) * unset ``$PYTHONPATH`` in before tested bootstrapped EasyBuild module (`#1743 `_) * take into account that paths in modulepath may be symlinks in ``test_module_caches`` (`#1745 `_) * change to install dir rather than buildpath in sanity check of extension, latter may not exist (`#1746 `_, `#1748 `_) * only load modules using short module names (`#1754 `_) * (re)load modules for build deps in extensions_step (`#1762 `_) * fix ``modpath_extensions_for method``: take into account modules in Lua syntax (`#1766 `_) * fix broken link to VSC website in license headers (`#1768 `_) **easyblocks** * add test configuration for Travis (`#895 `_, `#897 `_, `#900 `_, `#926 `_) * new easyblocks for 4 software packages that require customized support: * binutils (`#907 `_), libQGLViewer (`#890 `_), SuperLU (`#860 `_), wxPython (`#883 `_) * various other enhancements, including: * update SuiteSparse easyblock for version >= 4.5 (`#863 `_) * enhance imkl easyblock to install on top of PGI (`#866 `_, `#916 `_) * enable runtime logging of install cmd in ``IntelBase`` (`#874 `_) * enhance Qt easyblock to support installing with ``dummy`` toolchain (`#881 `_) * delete libnuma symbolic links in PGI installation directory (`#888 `_) * enhance PDT easyblock to support installing with ``dummy`` toolchain (`#894 `_) * add support for building Clang with OpenMP support (`#898 `_) * update Score-P easyblock for additional compilers, MPI libraries & dependencies (`#889 `_) * drop deprecated '``testrb``' from sanity check in Ruby easyblock (`#901 `_) * enhance WRF easyblock to support versions >= 3.7 (`#902 `_) * update QuantumESPRESSO easyblock for version 5.3.0 (`#904 `_) * add support in PythonPackage easyblock to use '``setup.py develop``' (`#905 `_) * update Qt easyblock for Qt 5.6.0 (`#908 `_) * extend bzip2 easyblock to also build dynamic libraries (`#910 `_) * make threading an explicit option rather than relying on MPI library in SCOTCH easyblock (`#914 `_) * update PGI easyblock to install siterc file so PGI picks up ``$LIBRARY_PATH`` (`#919 `_) * enhance sanity check paths for compiler commands in PGI easyblock (`#919 `_) * also filter out ``-ldl`` from $LIBBLAS & co for Intel MKL in numpy easyblock (`#920 `_) * define ``$MIC_LD_LIBRARY_PATH`` for impi (`#925 `_) * various bug fixes, including: * don't hardcode Python version in ``test_make_module_pythonpackage`` (`#876 `_) * make PythonPackage easyblock compatible with ``--module-only`` (`#884 `_, `#906 `_) * remove check whether '``easybuild``' is being imported from dir that contains ``easybuild/__init__.py`` (`#891 `_) * fix passing compiler configure option in PDT easyblock (`#894 `_) * fix bug in Score-P easyblock w.r.t. ``--with-libbfd`` (`#889 `_) * fix extension filter for Ruby (`#901 `_) * fix ``ACTIVATION_TYPES`` list in IntelBase + minor style change (`#913 `_) * correctly define ``$MIC_LD_LIBRARY_PATH`` in imkl 11.3.x and newer (`#915 `_) * fix broken link to VSC website in license headers (`#927 `_) **easyconfigs** * added example easyconfig files for 69 new software packages: * ALPS (`#2888 `_), annovar (`#3010 `_), BayeScEnv (`#2765 `_), BayesAss (`#2870 `_), BerkeleyGW (`#2925 `_), Blitz++ (`#2784 `_, `#3004 `_), bam-readcount (`#2850 `_), Commet (`#2938 `_), CrossTalkZ (`#2939 `_), cuDNN (`#2882 `_), DBus (`#2855 `_), DFT-D3 (`#2107 `_), DIAL (`#3056 `_), dask (`#2885 `_), dbus-glib (`#2855 `_), FFLAS-FFPACK (`#2793 `_), FLAC (`#2824 `_), FLANN (`#3015 `_, `#3029 `_), FLEUR (`#3043 `_), GConf (`#2855 `_), GROMOS++ (`#1297 `_), GST-plugins-base (`#2855 `_), GStreamer (`#2855 `_), GTOOL (`#2805 `_), Givaro (`#2793 `_), gdist (`#2935 `_), gromosXX (`#1297 `_), HISAT2 (`#2809 `_), i-PI (`#2940 `_), Kraken (`#3037 `_, `#3041 `_), LAME (`#2823 `_), LASTZ (`#3002 `_), LinBox (`#2793 `_), Loki (`#2839 `_), libQGLViewer (`#2923 `_, `#3008 `_), libXxf86vm (`#2855 `_), MDSplus (`#2787 `_, `#2838 `_, `#3027 `_), MRIcron (`#2831 `_), Mawk (`#2732 `_), minieigen (`#2839 `_), mpmath (`#3058 `_), NBO (`#3047 `_, 3048), NGS (`#2803 `_), NGS-Python (`#2810 `_), ncbi-vdb (`#2808 `_), OptiX (`#2795 `_), PCL (`#3024 `_), PEAR (`#2731 `_), PLplot (`#2990 `_), Postgres-XL (`#2891 `_), PyGTS (`#2969 `_), RSeQC (`#2788 `_), Rust (`#2920 `_, `#2943 `_), rainbow (`#2730 `_), SHAPEIT (`#2806 `_), SIONlib (`#2908 `_), Saxon-HE (`#2773 `_), Singularity (`#2901 `_), SoX (`#2825 `_), Subread (`#2790 `_), SuperLU (`#2665 `_), travis (`#2953 `_), VASP (`#2950 `_), Wannier90 (`#2906 `_, `#3042 `_), wget (`#3041 `_), wxPython (`#2855 `_), xf86vidmodeproto (`#2855 `_), Yade (`#2839 `_), Yambo (`#2932 `_) * add test configuration for Travis (`#2942 `_, `#2944 `_, `#2954 `_, `#3061 `_) * added easyconfigs for new PGI-based toolchains * ``pomkl/2016.03`` (`#2899 `_, `#2900 `_, `#3046 `_), ``pomkl/2016.04`` (`#3044 `_), ``CrayPGI/2016.04`` (`#2927 `_) * added new easyconfigs for existing toolchains: * ``foss/2016.04`` (`#3013 `_), ``intel/2016.02-GCC-5.3`` (`#2523 `_), ``intel/2016.03-GCC-5.3`` (`#3009 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181, LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8 * various other enhancements, including: * enhance ORCA easyconfig for compatibility with SLURM (`#1819 `_) * enable ``-fPIC`` in GraphicsMagick easyconfig, required by Octave (`#2764 `_) * clean up binutils easyconfigs to use binutils easyblock (`#3006 `_) * add ``include/GraphicsMagick`` to ``$CPATH`` in GraphicsMagick easyconfigs (`#3034 `_) * update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (`#3050 `_) * various bug fixes, including: * fix Perl extensions download urls (`#2738 `_) * add Autoconf as build dep for ``GCCcore`` (`#2772 `_) * fix versions of extensions in Bioconductor 3.2 bundles (`#2769 `_) * fix (build) deps for ``intel/2016a`` easyconfigs of cairo, libXext, libXrender (`#2785 `_, `#2874 `_) * use '``env``' wherever preconfig/build/installopts is used to set environmental variables (`#2807 `_, `#2811 `_, `#2812 `_) * add zlib as explicit dep in Tk easyconfigs (`#2815 `_) * consistently specify to use ``-fgnu89-inline`` flag in M4 1.4.17 easyconfigs (`#2774 `_, `#2779 `_, `#2816 `_) * fix homepage and description in Pygments easyconfigs (`#2822 `_) * include pkg-config as build dependencies for libXau, libXdmcp, libxcb (`#2827 `_) * consistently use ``XORG_*_SOURCE`` constants (`#2829 `_, `#2830 `_, `#2848 `_) * update source URLs in ScientificPython easyconfig files (`#2847 `_) * add checksums in SuiteSparse easyconfigs (`#2849 `_) * fix build deps for GObject-Introspection (`#2852 `_) * correctly specify Perl location in git easyconfig (`#2866 `_) * fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (`#2880 `_) * fix Perl dependency in worker easyconfigs, it requires non-standard Perl modules (`#2884 `_) * add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (`#2887 `_) * fix download URL for packmol (`#2902 `_) * drop ``usempi`` toolchain in numexpr easyconfigs, not needed (`#2937 `_) * fix use of ``resolve_dependencies`` in tests according to changes in framework (`#2952 `_) * add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (`#2967 `_) * add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (`#2971 `_) * add xproto build dependency for makedepend v1.0.5 (`#2982 `_) * disable parallel build for Doxygen (`#2986 `_) * fix source URLs for ``FreezeThaw`` and ``Tie::Function`` extensions for Perl v5.22.1 (`#2988 `_) * add ``sed`` command in worker easyconfig files to fix module_path in conf/worker.conf (`#2997 `_, `#3000 `_) * drop toolchainopts from Eigen easyconfigs, since it is headers-only (`#3025 `_) * clean up dummy bzip2 easyconfig, define buildopts rather than defining ``$CC`` and ``$CFLAGS`` via ``os.environ`` (`#3036 `_) * use ``%(pyshortver)s`` template rather than hardcoding 2.7 in VTK easyconfigs (`#3052 `_) * correct install location of OpenCV Python bindings (`#3054 `_) * include XZ as dependency for libunwind (`#3055 `_) * add patch to fix broken OpenSSL tests due to expired certificates (`#3057 `_) * fix broken link to VSC website in license headers (`#3062 `_) .. _release_notes_eb270: EasyBuild v2.7.0 (March 20th 2016) ---------------------------------- feature + bugfix release **framework** * stabilize Cray support * enable '``dynamic``' toolchain option by default for ``Cray*`` toolchains (`#1581 `_) * remove FFTW from the Cray toolchains definition (`#1585 `_) * add external modules metadata for Cray systems (`#1638 `_) * fix independency of Cray toolchains w.r.t. toolchain build environment (`#1641 `_, `#1647 `_) * remove requirement to use ``--experimental`` for Cray toolchains (`#1663 `_) * enable Python optimization mode in '``eb``' (`#1357 `_) * improved GitHub integration * improve error handling on git commands + better logging for ``--new-pr``/``--update-pr`` (`#1590 `_) * use ``git`` rather than ``https`` in ``--new-pr``/``--update-pr`` (`#1602 `_) * add ``-u`` as shorthand for ``--upload-test-report`` (`#1605 `_) * fix ``--from-pr`` for PRs that include renamed/deleted files (`#1615 `_) * add support for ``--install-github-token`` and ``--check-github`` (`#1616 `_) * fix ``fetch_easyconfigs_from_pr`` w.r.t. duplicate files in PRs (`#1628 `_) * various other enhancements, including: * add support for ``--search-filename`` and ``--terse`` (`#1577 `_) * support complete bash completion (`#1580 `_) * add support for ``%(*ver)s`` and ``%(*shortver)s`` templates (`#1595 `_, `#1604 `_) * incl. ``%(javaver)s``, ``%(javashortver)s``, ``%(perlver)s``, ``%(perlshortver)s``, ``%(pyver)s``, ``%(pyshortver)s``, ``%(rver)s``, ``%(rshortver)s`` * define ``HOME`` constant that can be used in easyconfig files (`#1607 `_) * implement support for generating '``swap``' statements in module files (`#1609 `_) * add support for ``--show-config`` (`#1611 `_, `#1620 `_) * simplified support for ``--minimal-toolchains`` (`#1614 `_, `#1619 `_, `#1622 `_, `#1625 `_, `#1646 `_) * add support for ``--dump-env-script`` (`#1624 `_) * enhance ModulesTool.exist to also recognize partial module names (`#1630 `_) * improve error message for toolchain definition errors (`#1631 `_) * make default is_short_modname_for check less strict to support versionless external modules as deps (`#1632 `_) * mention hostname in comment made by ``--upload-test-report`` (`#1635 `_) * support providing additional relative path for prefix in external module metadata (`#1637 `_) * add ``ThematicModuleNamingScheme`` (`#1645 `_) * enhance logging format: remove logger name, mention location instead (`#1649 `_, `#1654 `_) * update kernel versions for SLES12 (`#1659 `_) * raise ``EasyBuildError`` rather than ``ImportError`` in ``only_if_module_is_available`` decorator (`#1662 `_) * various bug fixes, including: * fix Lmod spider output in generated modules (`#1583 `_) * correctly define '``easybuild``' namespaces (`#1593 `_, `#1666 `_, `#1680 `_) * this change requires that the ``setuptools`` Python package is available (at runtime) * using custom easyblocks by adding them in the Python search path (``$PYTHONPATH``) may require adjustments, i.e. also using ``pkg_resources.declare_namespace`` in the ``__init__.py`` files; *we highly recommend to use* ``--include-easyblocks`` *instead*, see http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html * note: this has the side-effect of not being able anymore to reliably use '``eb``' in the parent directory of the easybuild-framework repository (`#1667 `_) * fix template for ``savannah.gnu.org`` source URL (`#1601 `_) * stop running '``module purge``', only restore environment (`#1608 `_) * fix license headers: Hercules foundation is now FWO (`#1629 `_) * avoid that ``fancylogger`` tries to import ``mpi4py`` to determine MPI rank (`#1648 `_) * fix error in tests when '``file``' backend is not available in Python keyring (`#1650 `_) * update develop install script (`#1651 `_) * handle allowed system deps during ``prepare_step`` rather than during parsing of easyconfig (`#1652 `_) * add function to find FlexLM licenses: ``find_flexlm_license`` (`#1633 `_, `#1653 `_) * fix availability check for external modules with partial module name (`#1634 `_, `#1643 `_) * fix bootstrap script to ensure ``setuptools`` is also installed (`#1655 `_) * fix issue in bootstrap script with ``vsc-base`` being picked up from the OS (`#1656 `_) * fix bootstrap script for environment where '``python``' is Python 3.x (`#1660 `_) * remove ``--experimental`` for tests related to ``--package`` (`#1665 `_) * ensure path to setuptools is included in ``$PYTHONPATH`` being used to test scripts (`#1671 `_) * sanitize environment before initializing easyblocks (`#1676 `_) * remove ``reload`` statements in ``include.py``, since they are not required and break ``--include-toolchains`` (`#1679 `_) **easyblocks** * new easyblocks for 6 software packages that require customized support: * ADF (`#826 `_), MPICH (`#844 `_, `#852 `_, `#868 `_), mutil (`#859 `_), pplacer (`#835 `_), psmpi (`#852 `_), SNPhylo (`#865 `_) * various other enhancements, including: * implement support for '``use_pip``' in PythonPackage easyblock (`#719 `_, `#831 `_) * add support in CUDA easyblock to install wrappers for host compilers (`#758 `_) * update sanity check for picard version 1.124 and above (`#796 `_) * use '``module swap``' for all components in ``CrayToolchain`` (`#823 `_) * update PSI4 easyblock to cope with changed name of PSI4 data dir (`#824 `_) * use ``find_flexlm_license`` function and avoid defining ``$CPATH`` in PGI easyblock (`#837 `_) * use ``find_flexlm_license`` function in ``IntelBase`` generic easyblock (`#839 `_) * add unit test to check module file generated by ``PythonPackage`` easyblock (`#841 `_) * rework MVAPICH2 easyblock on top of new MPICH easyblock (`#844 `_) * add CUDA support in CP2K easyblock (`#850 `_) * also define ``$LD`` in ``buildopts`` for GATE (`#855 `_) * use ``find_flexlm_license`` function in TotalView easyblock (`#839 `_) * enhance ``MakeCp`` easyblock to also support renaming of files while copying them (`#859 `_) * hunt for usable '``python``' command in ``PythonPackage`` easyblock when system Python is used (`#861 `_) * add sanity check in ``easybuild/__init__.py`` w.r.t. current working dir (`#869 `_) * change suffix of original file to ``.easybuild`` when using ``fileinput`` in impi easyblock (`#870 `_) * various bug fixes, including: * make sure Python unicode settings match that of the system Python (`#817 `_) * remove FFTW related statements in HPL easyblock, since HPL doesn't require FFTW at all (`#822 `_) * use ``pkg_resources.declare_namespace`` rather than ``pkgutil.extend_path`` to declare '``easybuild``' namespaces (`#827 `_) * fix license headers: Hercules foundation is now FWO (`#836 `_) * fix check for non-empty lib dirs in ``PythonPackage`` easyblock (`#840 `_) * consider all Python lib dirs in sanity check for libxml2 (`#842 `_) * correctly handle deprecated configure options (``--with-hwloc``/``--enable-mpe``) in MVAPICH2 easyblock (`#853 `_) * use correct configure option for checkpoint/restart in MVAPICH2 easyblock (`#854 `_) * ensure list of Python lib dirs always has a '``lib/...``' entry (`#858 `_) * check whether ``rpm``/``rpmrebuild`` commands are available using '``which``', rather than checking for OS deps (`#864 `_) * fix ``test_step`` in UFC easyblock (`#872 `_) **easyconfigs** * added example easyconfig files for 63 new software packages: * ATSAS (`#616 `_, `#2587 `_), astropy (`#2724 `_, `#2727 `_), attr (`#2706 `_), BamUtil (`#2654 `_), BBMap (`#2322 `_), BH (`#2508 `_), CheMPS2 (`#2445 `_), CosmoloPy (`#2723 `_, `#2727 `_), csvkit (`#2639 `_), Firefox (`#2648 `_), FreeXL (`#2422 `_), GL2PS (`#2667 `_), Glade (`#2631 `_), htop (`#2538 `_), IGV (`#2019 `_), IGVTools (`#2019 `_), ImageMagick (`#2438 `_), jModelTest (`#2529 `_), KEALib (`#2420 `_), libcerf (`#2656 `_), libgcrypt (`#2201 `_), libglade (`#2631 `_), libgpg-error (`#2201 `_), libspatialite (`#2431 `_), LittleCMS (`#2438 `_), MAST (`#2542 `_), MLC (`#2577 `_), MPJ-Express (`#2529 `_), mutil (`#2201 `_), neon (`#758 `_), NextClip (`#2544 `_), npstat (`#2686 `_, `#2703 `_), Octopus (`#2643 `_), QuickFF (`#2721 `_), p4vasp (`#2328 `_), PCMSolver (`#2445 `_), PFFT (`#2643 `_), PHYLIP (`#2694 `_), pkgconfig (`#2475 `_, `#2476 `_), Platypus (`#2618 `_), pplacer (`#1056 `_), PRINSEQ (`#2437 `_, `#2444 `_, `#2585 `_), PyFFmpeg (`#2501 `_, `#2519 `_), PyGObject (`#2443 `_), PyGTK (`#2443 `_), PyOpenGL (`#2628 `_), pyringe (`#2533 `_), qrupdate (`#2675 `_), rgeos (`#2635 `_), rpmrebuild (`#2402 `_), shift (`#2201 `_), SNAPE-pooled (`#2688 `_), SNPhylo (`#2701 `_), sratoolkit (`#2715 `_), STAR-Fusion (`#2463 `_), statsmodels (`#2719 `_), StringTie (`#2527 `_), synchronicity (`#2508 `_), testpath (`#2461 `_), USEARCH (`#2537 `_), VarScan (`#2464 `_), vsc-install (`#2165 `_), Whoosh (`#2725 `_), xprop (`#2645 `_) * added new easyconfigs for existing toolchains: * ``intel/2016.02-GCC-4.9`` (`#2620 `_), ``gmpolf/2016a`` & ``gmvolf/2016a`` (`#2589 `_) * stable Cray-specific easyconfigs * delete deprecated Cray toolchains and easyconfig files (`#2400 `_) * don't hardcode ``PrgEnv`` version, remove ``craype`` and ``fftw`` components in Cray toolchains (`#2554 `_) * remove ``-XC`` versionsuffix for stable definitions for ``Cray*`` toolchains (`#2714 `_) * support for various software packages with ``CrayGNU`` and ``CrayIntel`` toolchains: CP2K, GROMACS, WRF * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1, R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1 * various other enhancements, including: * copy ``contrib`` dir in Velvet easyconfigs so scripts are also available (`#2456 `_) * redefine matplotlib 1.5.1 easyconfig as a bundle, also include ``cycler`` extension (dep for matplotlib) (`#2470 `_) * add bitstring extension to Python 2.7.11 easyconfigs (`#2471 `_) * enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (`#2473 `_) * add custom sanity check for libjpeg-turbo (`#2480 `_) * add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (`#2495 `_, `#2729 `_, `#2733 `_) * add source URL in RAxML 7.2.6 easyconfigs (`#2536 `_) * update MPICH easyconfigs to use new MPICH easyblock (`#2589 `_) * free libX11 & co from unneeded Python dependency/versionsuffix (`#2549 `_, `#2563 `_, `#2605 `_, `#2664 `_) * add '``--enable-utf --enable-unicode-properties``' configure options in PCRE easyconfigs (`#2561 `_) * required for latest R versions * add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (`#2553 `_, `#2578 `_) * add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (`#2547 `_, `#2556 `_) * update psmpi easyconfig files to use the new psmpi easyblock (`#2619 `_) * add easyconfig for Python 2.7.11 on top of X11-enabled Tk (`#2614 `_, `#2621 `_) * add virtualenv as extension in Python 2.7.11 easyconfigs (`#2660 `_) * various bug fixes, including: * fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (`#2468 `_) * don't hardcode ``CC``/``CXX`` in OpenMPI easyconfigs (`#2472 `_) * remove Google Code source URL for mpi4py (`#2474 `_) * rename ffmpeg to FFmpeg (`#2425 `_, `#2481 `_) * use available easyblock for flex (`#2486 `_) * fix determining list of easyconfigs in unit test suite, don't assume locations are correct (`#2530 `_) * fix specifying DB dependency in DB_File easyconfigs (`#2539 `_) * remove hard-coded ``-xSSE4.2`` for numpy/scipy with Intel compilers (`#2546 `_) * fix license headers: Hercules foundation is now FWO (`#2550 `_) * add ``--with-zlib`` configure argument in libxml easyconfigs (`#2555 `_) * don't hardcode ``optarch=True`` in xextproto/xtrans easyconfigs (`#2601 `_) * change toolchain version to '' in easyconfigs that use ``dummy`` toolchain and include dependencies (`#2612 `_) * GLib doesn't require libxml2 with Python bindings (`#2632 `_) * add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '``--``' in build path (`#2634 `_) * add missing 'pkgconfig' dependency for h5py (`#2476 `_, `#2650 `_) * correct software name in FastQC easyconfigs (was 'fastqc'), use '``dummy``' toolchain for all FastQC version (`#2657 `_, `#2666 `_) * add missing libxml2 dependencies in GLib easyconfigs (`#2658 `_) * fix Xerces-C++ download location (`#2668 `_) * enable ``XML::Bare`` extension in all Perl easyconfigs (`#2672 `_) * update dead link for SuiteSparse (`#2679 `_) * remove custom ``exts_filter`` in easyconfigs used ``PythonPackage`` easyblock (`#2683 `_, `#2685 `_) * add M4 as build dep for binutils & flex (`#2681 `_) * add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (`#2704 `_) * fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (`#2707 `_) * style cleanup in various easyconfigs (`#2378 `_, `#2387 `_, `#2395 `_, `#2396 `_, `#2488 `_-`#2493 `_, `#2496 `_-`#2500 `_, `#2502 `_-`#2504 `_, `#2602 `_) * working towards automated style review of pull requests .. _release_notes_eb260: EasyBuild v2.6.0 (January 26th 2016) ------------------------------------ feature + bugfix release **framework** * add (experimental) support for opening/updating (easyconfigs) pull requests (``--new-pr``, ``--update-pr``) (`#1528 `_) * sanitize environment before each installation by undefining ``$PYTHON*`` (`#1569 `_, `#1572 `_) * various other enhancements, including: * allow user-local modules with hierarchical naming schemes (``--subdir-user-modules``) (`#1472 `_) * enhance ``--extended-dry-run`` output to include paths for requirements in ``make_module_req`` (`#1520 `_) * rewrite read_file to use '``with``' (`#1534 `_) * add support for ``eb --last-log`` (`#1541 `_) * support using fixed install dir scheme (``--fixed-installdir-naming-scheme``) (`#1546 `_) * add edge attributes for build dependencies in ``--dep-graph`` output (`#1548 `_) * check whether dependencies marked as external module are hidden (`#1552 `_) * implement support for ``--modules-header`` (`#1558 `_) * add support to specify '``else``' body for conditional statements in modules (`#1559 `_) * add extra test for ``--include-easyblocks`` for generic easyblocks (`#1562 `_) * allow user to define the default compiler optimization level (``--default-opt-level``) (`#1565 `_) * make ``toolchain.get_variable`` more robust w.r.t. dummy toolchain (`#1566 `_) * various bug fixes, including: * fix missing '``yaml``' module check in tests (`#1525 `_) * fix 'develop' install script (`#1529 `_) * correctly quote FPM option values in packagin support (`#1530 `_) * correctly handle '``.``' in software name w.r.t. ``$EB*`` environment variables (`#1538 `_) * exclude logs and test reports from packages (`#1544 `_) * also pass down ``--job-cores`` for ``pbs_python`` job backend (`#1547 `_) * skip dependencies marked as external modules when packaging (`#1550 `_) * fix syntax for ``set_alias`` statement in Lua syntax (`#1554 `_) * handle the case of all 'offline' nodes correctly for ``--job`` (`#1560 `_) * fix ``test_modules_tool_stateless`` unit test for stateless ModulesTool with Lmod as modules tool (`#1570 `_) **easyblocks** * add generic easyblock for Cray toolchains (`#766 `_) * new easyblocks for 2 software packages that require customized support: * EggLib (`#811 `_), PGI (`#658 `_) * various other enhancements, including: * update BamTools easyblock for versions 2.3.x and newer: some shared libraries are now static) (`#785 `_) * don't hardcode ``.so``, use ``get_shared_lib_ext`` instead (`#789 `_, `#790 `_, `#791 `_, `#793 `_, `#794 `_, `#803 `_, `#815 `_) * enhance CPLEX easyblock by adding more subdirs to ``$PATH``, define ``$LD_LIBRARY`` and ``$CPLEXDIR`` (`#797 `_) * make sanity check for netcdf4-python work with both egg and non-egg installs (`#799 `_) * update sanity check in PETSc/SLEPc easyblocks for v3.6.x (`#800 `_) * update Trinity easyblock for 2.x versions (`#802 `_) * update DOLFIN easyblock for v1.6.0 (`#804 `_) * check for ``libkokkoscore.a`` rather than ``libkokkos.a`` for Trilinos 12.x (`#805 `_) * add an option to skip the sanitizer tests of Clang (`#806 `_) * update Molpro easyblock to support binary installs and 2015 version (`#807 `_) * make ``ConfigureMake`` more robust w.r.t. custom easyconfig parameters (`#810 `_) * various bug fixes, including: * add back support for Eigen 2.x in Eigen easyblock (`#798 `_) * fix for vsc-base being picked up from OS in EasyBuildMeta easyblock (`#813 `_) * remove ``setuptools.pth`` if it includes absolute paths after installing EasyBuild (`#813 `_) **easyconfigs** * add easyconfigs for ``foss/2016a`` and ``intel/2016`` common toolchains (`#2310 `_, `#2311 `_, `#2339 `_, `#2363 `_) * incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains * added example easyconfig files for 21 new software packages: * BLASR (`#922 `_), BioKanga (`#2247 `_), BoltzTraP (`#2365 `_), basemap (`#2221 `_), CppUnit (`#2271 `_), EggLib (`#2335 `_), FLASH (`#2281 `_), GLM (`#2288 `_), hub (`#2249 `_), MACS2 (`#1983 `_), MotEvo (`#843 `_), numba (`#2243 `_), PGI (`#1833 `_, `#2367 `_), PLY (`#2305 `_), PaStiX (`#2319 `_, `#2326 `_), patchelf (`#2327 `_), pip (`#2284 `_), RSEM (`#2316 `_), RcppArmadillo (`#2289 `_), SCDE (`#2289 `_), slepc4py (`#2318 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0, LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2, Trinity 2.1.1, VTK 6.3.0 * various other enhancements, including: * added new ``Cray*`` toolchain versions with pinned dependency versions (`#2222 `_) * don't hardcode ``.so``, use ``SHLIB_EXT`` constant instead (`#2245 `_) * add custom sanity check in GEOS easyconfigs (`#2285 `_) * various bug fixes, including: * add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (`#2096 `_) * remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (`#2323 `_) * various style fixes, including: * get rid of tabs (`#2302 `_) * remove trailing whitespace (`#2341 `_) .. _release_notes_eb250: EasyBuild v2.5.0 (December 17th 2015) ------------------------------------- feature + bugfix release **framework** * add support for IBM XL compilers on Power7 and PowerPC (BlueGene) (`#1470 `_) * add support for generic compilation using ``--optarch=GENERIC`` (`#1471 `_) * see also :ref:`controlling_compiler_optimization_flags` * update experimental support for ``.yeb`` easyconfigs (`#1515 `_) * support clean way to specify toolchain + dependencies in ``.yeb`` easyconfigs * various other enhancements, including: * add support for '``whatis``' easyconfig parameter (`#1271 `_) * add support for SLES 12 and kernel 3.12.x (`#1412 `_) * add GCCcore toolchain definition (`#1451 `_) * use '``diff --git``' lines to determine patched files in pull request with ``--from-pr`` (`#1460 `_) * add proper option parser to bootstrap script (`#1468 `_) * add ``get_gcc_version()`` function in systemtools module (`#1496 `_) * don't load fake module in sanity_check_step during a dry run (`#1499 `_) * allow string values to be passed in ``make_module_req`` by hoisting them into a list (`#1502 `_) * add support for listing build dependencies as hidden dependencies (`#1503 `_) * also consider ``lib32/pkgconfig`` and ``lib64/pkgconfig`` for ``$PKG_CONFIG_PATH`` (`#1505 `_) * add support to ``make_module_dep`` to specify module to unload before loading a dependency module (`#1506 `_) * add support to ``make_module_extra`` to specify alternative root/version for ``$EBROOT``/``$EBVERSION`` (`#1508 `_) * packaging support is no longer considered experimental (`#1510 `_) * various bug fixes, including: * also consider ``lib64`` in sanity check performed during EasyBuild bootstrap (`#1464 `_) * also add description/homepage to packages created with FPM (`#1469 `_) * fix develop setup script to install EasyBuild-develop module in subdirectory (`#1480 `_) * don't create a whole set of temporary '``minimal-easyconfigs``' subdirs with ``--minimal-toolchains`` (`#1484 `_) * only keep polling if exit code is ``None`` in ``run_cmd_qa``, to correctly deal with negative exit codes (`#1486 `_) * fix bootstrap script for missing sys_platform by using newer distribute 0.6.49 in stage 0 (`#1490 `_) * make sure that extra custom easyconfig parameters are known for extensions (`#1498 `_) * add missing import for ``EasyBuildError`` in ``easybuild/toolchains/linalg/libsci.py`` (`#1512 `_) * isolate tests from possible system-wide configuration files (`#1513 `_) * only use ``glob`` in ``make_module_req`` on non-empty strings (`#1519 `_) * this fixes the problem where ``$CUDA_HOME`` and ``$CUDA_PATH`` are not defined in module files for CUDA **easyblocks** * update easyblocks for Intel tools to support 2016 versions (`#691 `_, `#745 `_, `#756 `_, `#777 `_) * IntelBase easyblock has been enhanced to support specifying which components to install * new easyblocks for 3 software packages that require customized support: * Intel Advisor (`#767 `_), DIRAC (`#778 `_), MRtrix (`#772 `_) * various other enhancements, including: * update numpy and SuiteSparse easyblock to use scikit-umfpack (`#718 `_) * add an option to allow removal of the ``-Dusethreads`` flag in Perl easyblock (`#724 `_) * update Doxygen easyblock for 1.10.x (CMake) (`#734 `_) * update sanity check in Qt easyblock for Qt 5.x (`#740 `_) * add support for multilib build of GCC on PowerPC (`#741 `_) * add support to OpenFOAM and SCOTCH easyblocks to support 64-bit integers, via 'i8' toolchain option (`#744 `_) * fix sanity check to support numpy 1.10 (dropped _dotblas.so) (`#757 `_, `#761 `_, `#762 `_) * update IPP easyblock for v9.x (`#759 `_) * cleaner output for PythonPackage under dry run, make numpy easyblock dry-run aware (`#760 `_, `#671 `_) * add support for using netCDF-Fortran as dependency in ALADIN easyblock (`#764 `_) * add support for tbb 4.4.x in tbb easyblock (`#769 `_) * add support for specifying altroot/altversion in Bundle easyblock (`#773 `_) * update OpenFOAM easyblock for OpenFOAM-Extend 3.2 + use apply_regex_substitutions (`#770 `_) * various bug fixes, including: * fix module path extension of system compiler in HMNS setup (`#742 `_) * only restore ``$PYTHONPATH`` if it was defined in EasyBuildMeta easyblock (`#743 `_) * make sure ``$PYTHONPATH`` is defined correctly in module file for Python packages created with ``--module-only`` (`#748 `_) * fix WRF easyblock to produce correct module under ``--module-only --force`` (`#746 `_, `#752 `_) * don't hardcode '``openPBS``' in GATE easyblock, use value for ``default_platform`` easyconfig parameter (`#753 `_) * avoid adding lib subdirs to ``$*LIBRARY_PATH`` if no libraries are there in ``PythonPackage`` easyblock (`#755 `_) * fix installing Python bindings for libxml2 to correct installation prefix (`#765 `_) **easyconfigs** * add GCCcore easyconfig that can be used as base for all compilers (without getting in the way) (`#2214 `_) * along with easyconfig for ``GCC/4.9.3-2.25``: bundle of GCCcore 4.9.3 and binutils 2.25 * intended to replace the GNU toolchain * added example easyconfig files for 39 new software packages: * DIRAC (`#2212 `_), GeoIP (`#2172 `_, `#2185 `_), GeoIP-C (`#2172 `_, `#2185 `_), graph-tool (`#1591 `_), gtkglext (`#2217 `_), Intel Advisor (`#2210 `_), InterProScan (`#2225 `_, `#2227 `_, `#2234 `_), intltool (`#2136 `_), kallisto (`#2173 `_), LibUUID (`#1930 `_), LuaJIT (`#2153 `_), libXcursor (`#2136 `_), libXrandr (`#2136 `_), libXtst (`#2143 `_), libdap (`#1930 `_), libtasn1 (`#2208 `_), libxkbcommon (`#2136 `_), MRtrix (`#2217 `_, `#2218 `_), MultiNest (`#2166 `_, `#2168 `_), Nipype (`#2150 `_), PPfold (`#2183 `_, `#2187 `_), p11-kit (`#2208 `_), pangox-compat (`#2217 `_), Qt5 (`#2136 `_), randrproto (`#2136 `_), rhdf5 (`#2175 `_), Stampy (`#2180 `_, `#2182 `_), scikit-umfpack (`#2061 `_), scp (Python pkg) (`#2196 `_), sleuth (`#2175 `_), traits (`#2150 `_), vincent (`#2169 `_, `#2185 `_), XKeyboardConfig (`#2136 `_), xcb-util (`#2136 `_), xcb-util-image (`#2136 `_), xcb-util-keysyms (`#2136 `_), xcb-util-renderutil (`#2136 `_), xcb-util-wm (`#2136 `_), zlibbioc (`#2175 `_) * added new easyconfigs for existing toolchains: ``intel/2015.08`` (`#2194 `_), ``intel/2016.00`` (`#2209 `_), ``intel/2016.01`` (`#2219 `_), ``iomkl/2015.03`` (`#2155 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0, OpenFOAM 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11 * various other enhancements, including: * add tidyr to R 3.2.1 easyconfigs (`#2174 `_) * enable C++ support in MIGRATE-N (`#2178 `_) * also installed shared libraries for AMD and UMFPACK in SuiteSparse (`#2061 `_) * fix software name for ParaView (was: Paraview) (`#2132 `_) * enable building of shared libraries for binutils (`#2133 `_) * harden binutils built with dummy toolchain by linking to system libraries via ``RPATH`` (`#2228 `_) * enhance easyconfig unit tests to check that each easyconfig file is in the right subdirectory (`#2232 `_) * various bug fixes, including: * fix ALADIN patch file to not use relative paths, and adjust list of ALADIN sources accordingly ((`#2207 `_), (`#2213 `_)) * rename patch files for OpenFOAM to be in line with other patches (`#2226 `_) * fix typo in bzip2 source URLs (`#2204 `_) * force linking of ncurses in libreadline (`#2206 `_) * enable ``-fPIC`` in all zlib 1.2.8 easyconfigs (`#2220 `_) * move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right location (`#2232 `_) * restrict parallel build in OpenFOAM-Extend easyconfigs via '``maxparallel``', not '``parallel``' (`#2233 `_) .. _release_notes_eb240: EasyBuild v2.4.0 (November 10th 2015) ------------------------------------- feature + bugfix release **framework** * add support for ``--extended-dry-run``/``-x`` (`#1388 `_, `#1450 `_, `#1453 `_, `#1455 `_) * detailed documentation is available at :ref:`extended_dry_run` * fix checking of sanity check paths w.r.t. discriminating between files and directories (`#1436 `_) * this impacts several easyconfig files where ``sanity_check_paths`` was not 100% correct * make '``eb``' script aware of Python v3.x, fall back to using ``python2`` if required (`#1411 `_) * add experimental support for parsing .yeb easyconfig files in YAML syntax (`#1447 `_, `#1448 `_, `#1449 `_) * see also :ref:`easyconfig_yeb_format` * add experimental support for resolving dependencies with minimal toolchains (`#1306 `_) * see also :ref:`minimal_toolchains` * various other enhancements, including: * refactor ``extract_cmd`` function to get rid of if/elif/else spaghetti blob (`#1382 `_) * add support for ``--review-pr`` (`#1383 `_) * add ``apply_regex_substitutions`` function to perform runtime patching from easyblocks (`#1388 `_, `#1458 `_) * add support for specifying alternate name to be part of generated module name (`#1389 `_) * via '``modaltsoftname``' easyconfig parameter * support overriding # used cores via ``--parallel`` (`#1393 `_) * also define ``$FC`` and ``$FCFLAGS`` in build environment (`#1394 `_) * add support extracting for ``.tar.Z`` files (`#1396 `_) * include easybuild/scripts in installation (`#1397 `_) * ignore hidden directories in find_base_dir (`#1413 `_, `#1415 `_) * add ``only_if_module_is_available`` decorator function to guard functionality that uses optional dependencies (`#1416 `_) * give easyblocks the possibility to choose ``maxhits`` for ``run_cmd_qa`` (`#1417 `_) * use class name (string) rather than License instances as values for software license constants (`#1418 `_) * support controlling recursive unloading of dependencies via '``recursive_module_unload``' easyconfig parameter (`#1425 `_) * implement basic support for type checking of easyconfig parameters (`#1427 `_) * support auto-converting to expected value type for easyconfig parameters (enabled by default) (`#1428 `_, `#1437 `_) * add support for ``--rebuild`` command line option, alternative for ``--force`` which doesn't imply ``--ignore-osdeps`` (`#1435 `_) * add support for Mercurial easyconfig repository (`#979 `_, `#1446 `_) * add dedicated class for psmpi toolchain MPI component, and use it in gpsmpi and ipsmpi toolchains (`#1454 `_) * various bug fixes, including: * fix extracting of comments from an easyconfig file that includes 'tail' comments (`#1381 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#1403 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * allow ``get_cpu_speed`` to return ``None`` if CPU freq could not be determined (`#1421 `_) * relax ``sanity_check_paths`` in EasyBuild bootstrap script to deal with possible zipped .egg (`#1422 `_) * use empty list as default value for src/patches in Extension class (`#1434 `_) * skip symlinked files in ``adjust_permissions`` function (`#1439 `_) * fix HierarchicalMNS to always use full version number (`#1440 `_) **easyblocks** * 3 new generic easyblocks: OCamlPackage (`#467 `_), SCons (`#689 `_, `#700 `_), Waf (`#722 `_) * new easyblocks for 2 software packages that require customized support: * OCaml (`#467 `_), Samcef (`#678 `_) * various other enhancements, including: * add support for installing OpenFOAM with external METIS, CGAL and Paraview (`#497 `_) * update netCDF easyblock updated for netCDF v4.3.3.1 (`#674 `_) * update Rosetta easyblock for recent Rosetta versions (`#677 `_) * make unpacked source dir detection in easyblock for VSC-tools a little bit more flexible (`#679 `_) * add support for building with Plumed support enabled in CP2K easyblock (`#681 `_) * update Go easyblock for Go v1.5 (`#683 `_) * use ``apply_regex_substitutions`` function in WRF easyblock (`#685 `_) * update MUMPS easyblock for 5.x (`#686 `_) * implement runtime patching of ``$WM_*`` and compiler variables for OpenFOAM (`#688 `_) * specify sequential compiler to use in compiler command that gets injected in OpenFOAM easyblock (`#692 `_) * make ``PythonPackage`` and WRF easyblocks dry-run aware (`#696 `_) * see also :ref:`extended_dry_run_guidelines_easyblocks` * add support in ``PythonPackage`` for installing with ``easy_install`` + installing zipped eggs (`#698 `_, `#711 `_, `#715 `_) * update Bowtie easyblock for recent Bowtie versions (`#707 `_) * update CUDA easyblock for CUDA 7.x(`#708 `_) * also consider ``config/make.sys.in`` for want in QuantumESRESSO easyblock (`#714 `_) * define ``$NWCHEM_LONG_PATH`` if needed in NWChem easyblock (`#720 `_) * remove custom post-install step in PDT easyblock (`#723 `_) * no longer needed now that ``adjust_permissions`` functions ignores symlinks * use ``$LIBS`` in HPL easyblock (`#727 `_, `#736 `_) * various bug fixes, including: * also define ``$MCRROOT`` for MCR in module (`#687 `_) * add missing '``super``' call in ``configure_step`` of easyblock for python-meep (`#694 `_) * only prepend existing non-empty paths to ``$PYTHONPATH`` in ``PythonPackage`` easyblock (`#697 `_) * fix extra_options definition in ``CMakePythonPackage`` easyblock (`#698 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#702 `_, `#703 `_, `#704 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * consider both ``lib`` and ``lib64`` in sanity check paths for flex (`#705 `_) * also copy signature file and don't copy CMake files in Eigen easyblock (`#709 `_) * fix directory names in ``make_module_req_guess`` of ANSYS easyblock (`#713 `_) * fix imports for ``set_tmpdir`` in easyblock unit tests after function was moved in EasyBuild framework (`#726 `_) * use ``--with-tcltk*`` configure options for Python to point to ensure Tcl/Tk deps are picked up (`#729 `_) * fix order of subdirs for QuantumESPRESSO binaries (`#730 `_) * correctly handle having both ``$FC``/``$FCFLAGS`` and ``$F90``/``$F90FLAGS`` defined when building MVAPICH2 (`#732 `_) * fix OpenSSL sanity check paths: lib/engines is a directory (`#731 `_, `#733 `_) * fix sanity check paths for netcdf-python (`#735 `_) **easyconfigs** * added example easyconfig files for 45 new software packages: * animation (`#2007 `_), ANSYS CFD (`#1969 `_), ANTLR (`#1191 `_, `#1980 `_), APR (`#1970 `_), APR-util (`#1970 `_), Aspera Connect (`#2005 `_), ChIP-Seq (`#2119 `_), deap (`#2082 `_), DISCOVARdenovo (`#1932 `_), FastQC (`#1984 `_), fontsproto (`#1618 `_, `#2038 `_), GraphicsMagick (`#2007 `_), HBase (`#1990 `_), ISIS (`#1972 `_), libedit (`#293 `_), libfontenc (`#1618 `_, `#2038 `_), libGLU (`#1627 `_), libXdamage (`#1618 `_, `#2038 `_), libXfont (`#1618 `_, `#2038 `_), LLVM (`#1620 `_, `#1989 `_, `#2031 `_), MIGRATE-N (`#1944 `_), MIRA (`#1938 `_), mympingpong (`#2049 `_), MySQLdb (`#2011 `_), NCO (`#1191 `_, `#1980 `_), NIPY (`#2064 `_), Nilearn (`#2064 `_), NiBabel (`#2064 `_), PBZIP2 (`#1038 `_), PIL (`#2062 `_), PhyloCSF (`#2018 `_), pycairo (`#2085 `_), pydicom (`#2063 `_), Salmon (`#2051 `_), Samcef (`#1941 `_), scikit-image (`#1974 `_, `#2006 `_), Serf (`#1970 `_), SSAHA2 (`#1039 `_), Subversion (`#1970 `_), SWASH (`#2059 `_), time (`#1954 `_), Trim_Galore (`#1984 `_), Trimmomatic (`#1987 `_), WEKA (`#1986 `_), x264 (`#2017 `_) * added new easyconfigs for existing toolchains: ``gimkl/2.11.5`` (`#2093 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0, ncurses 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, QuantumESPRESSO v5.2.1 * various other enhancements, including: * enable '``pic``' toolchain option in libxml2 easyconfigs (`#1993 `_) * extend list of R libraries included in R v3.2.1 easyconfigs (`#2042 `_, `#2046 `_, `#2067 `_, `#2072 `_) * add Rsubread in Bioconductor easyconfigs (`#1971 `_) * various bug fixes, including: * fix software name for ``BEEF`` (was '``libbeef``') (`#1679 `_) * add patch to install ``qhull.pc`` (pkgconfig) file with Qhull (`#1975 `_) * don't enable experimental nouveau API in libdrm easyconfigs (`#1994 `_) * fix dev version to follow PEP-440, as required by recent setuptools versions (`#1997 `_) * required to avoid that setuptools transforms the version itself * see also https://www.python.org/dev/peps/pep-0440/#developmental-releases * correct homepage in Cufflinks easyconfigs (`#2060 `_) * fix imports for ``set_tmpdir`` in easyblock unit tests after function was moved in EasyBuild framework (`#2097 `_) * add patch for Tk 8.6.4 to fix problem with ``tk.tcl`` not being found (`#2102 `_) * don't use ``%(version)s`` template in toolchain version, causes problems with HierarchicalMNS (`#2104 `_) * fix sanity check paths in several easyconfig (`#2109 `_, `#2120 `_, `#2121 `_, `#2125 `_) * required because of bug fix in ``sanity_check_step`` implementation * CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, Pyke, pandas, pycosat, pyhull, pymatgen, python-dateutils, Seaborn, Theano, XML-LibXML, XML-Simple .. _release_notes_eb230: EasyBuild v2.3.0 (September 2nd 2015) ------------------------------------- feature + bugfix release **framework** * requires vsc-base v2.2.4 or more recent (`#1343 `_) * required for ``mk_rst_table`` function in ``vsc.utils.docs`` * various other enhancements, including: * add support for generating documentation for (generic) easyblocks in ``.rst`` format (`#1317 `_) * preserve comments in easyconfig file in ``EasyConfig.dump()`` method (`#1327 `_) * add ``--cleanup-tmpdir`` option (`#1365 `_) * enables to preserve the used temporary directory via ``--disable-cleanup-tmpdir`` * enhance ``EasyConfig.dump()`` to reformat dumped easyconfig according to style guidelines (`#1345 `_) * add support for extracting ``.iso`` files using 7z (p7zip) (`#1375 `_) * various bug fixes, including: * correctly deal with special characters in template strings in ``EasyConfig.dump()`` method (`#1323 `_) * rework ``easybuild.tools.module_generator`` module to avoid keeping state w.r.t. fake modules (`#1348 `_) * fix dumping of hidden deps (`#1354 `_) * fix use of ``--job`` with hidden dependencies: include ``--hidden`` in submitted job script when needed (`#1356 `_) * fix ``ActiveMNS.det_full_module_name()`` for external modules (`#1360 `_) * fix ``EasyConfig.all_dependencies`` definition, fix tracking of job dependencies (`#1359 `_, `#1361 `_) * fix ``ModulesTool.exist()`` for hidden Lua module files (`#1364 `_) * only call ``EasyBlock.sanity_check_step`` for non-extensions (`#1366 `_) * this results in significant speedup when installing easyconfigs with lots of extensions, but also results in checking the default sanity check paths if none were defined for extensions installed as a module * fix using module naming schemes that were included via ``--include-module-naming-schemes`` (`#1370 `_) **easyblocks** * new easyblocks for 2 software packages that require customized support: * MCR (`#623 `_), Molpro (`#665 `_) * various other enhancements, including: * enhance BWA easyblock to also install man pages (`#650 `_) * enhance tbb easyblock to consider lib dirs in order and also define ``$CPATH``, ``$LIBRARY_PATH``, ``$TBBROOT`` (`#653 `_, `#654 `_) * call ``PythonPackage.configure_step`` in ``ConfigureMakePythonPackage.configure_step`` (`#668 `_) * add '``foldx3b6``' as possible binary name in FoldX easyblock (`#671 `_) * enhance/cleanup MATLAB easyblock (`#672 `_) * move preparing of '``intel``' subdir in ``$HOME`` to ``configure_step`` in ``IntelBase`` easyblock (`#673 `_) * various bug fixes, including: * add missing super call in ``post_install_step`` of imkl easyblock (`#648 `_, `#660 `_) * fix regex used to correct ``I_MPI_ROOT`` in impi ``mpivars.sh`` scripts (`#662 `_) * fix regex used to patch ``.mk`` file in configure step of SuiteSparse easyblock (`#666 `_) * correctly specify installation prefix via ``$GEM_HOME`` in ``RubyGem`` easyblock (`#667 `_) * add custom sanity check in scipy easyblock (`#669 `_) * specify to always use the bfd linker for OpenFOAM, to stay away from using ``ld.gold`` (`#670 `_) **easyconfigs** * added example easyconfig files for 19 new software packages: * ATK (`#1780 `_), Atkmm (`#1780 `_), cairomm (`#1780 `_), GLibmm (`#1780 `_), GlobalArrays (`#1868 `_), gdk-pixbuf (`#1780 `_), gtk+ (`#1780 `_), Gtkmm (`#1780 `_), libbeef (`#1827 `_), libsigc++ (`#1780 `_), libsodium (`#1876 `_), MACS (`#1869 `_), MCR (`#1677 `_), Molpro (`#1880 `_), NFFT (`#1921 `_), p7zip (`#1931 `_), Pangomm (`#1780 `_), pygraphviz (`#1861 `_), pycosat (`#1859 `_) * added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (`#1836 `_), foss/2015b (`#1695 `_), intel/2015b (`#1696 `_) * add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0 * various other enhancements, including: * enhance texinfo easyconfig w.r.t. ``texmf``, only use it as a build dependency (`#1840 `_) * enable building of ``ld.gold`` in binutils 2.25 (`#1885 `_) * various bug fixes, including: * fix enabling MPI support for h5py 2.5.0 (`#1825 `_) * fix versions of Bioconductor packages + add a couple extra (`#1828 `_, `#1852 `_, `#1895 `_, `#1917 `_) * put dummy values in place for ``builddir``/``installdir`` templates in easyconfigs unit tests (`#1835 `_) * fix easyconfigs unit tests w.r.t. changes made in framework (`#1853 `_, `#1870 `_, `#1874 `_, `#1875 `_) * add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (`#1858 `_) * specify installation prefix for SIP (`#1888 `_, `#1892 `_) * add custom sanity check paths in various easyconfigs (`#1889 `_, `#1894 `_, `#1897 `_ - `#1909 `_) * required because of fix in EasyBuild framework, causing default sanity check paths to be considered for extensions that are installed as a module * affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql, evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx, ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn, SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck * don't enable '``static``' toolchain option in SuiteSparse 4.4.3 easyconfig (`#1911 `_) * add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (`#1925 `_) .. _release_notes_eb220: EasyBuild v2.2.0 (July 15th 2015) --------------------------------- feature + bugfix release **framework** * add support for using GC3Pie as a backend for ``--job`` (`#1008 `_) * see also :ref:`submitting_jobs` * add support for ``--include-*`` configuration options to include additional easyblocks, toolchains, etc. (`#1301 `_) * see :ref:`including_additional_python_modules` * add (experimental) support for packaging installed software using FPM (`#1224 `_) * see :ref:`packaging_support` * various other enhancements, including: * use https for PyPI URL templates (`#1286 `_) * add GNU toolchain definition (`#1287 `_) * make bootstrap script more robust (`#1289 `_, `#1325 `_): * exclude 'easyblocks' pkg from ``sys.path`` to avoid that ``setup.py`` for easybuild-easyblocks picks up wrong version * undefine ``$EASYBUILD_BOOTSTRAP*`` environment variables, since they do not correspond with known config options * improve error reporting/robustness in ``fix_broken_easyconfigs.py`` script (`#1290 `_) * reset keep toolchain component class 'constants' every time (`#1294 `_) * make ``--strict`` also a build option (`#1295 `_) * fix purging of loaded modules in unit tests' setup method (`#1297 `_) * promote ``MigrateFromEBToHMNS`` to a 'production' MNS (`#1302 `_) * add support for ``--read-only-installdir`` and ``--group-writable-installdir`` configuration options (`#1304 `_) * add support for *not* expanding relative paths in ``prepend_paths`` (`#1310 `_) * enhance ``EasyConfig.dump()`` method to use easyconfig templates where possible (`#1314 `_), `#1319 `_), `#1320 `_), `#1321 `_) * various bug fixes, including: * fix issue with cleaning up (no) logfile if ``--logtostdout``/``-l`` is used (`#1298 `_) * stop making ``ModulesTool`` class a singleton since it causes problems when multilple toolchains are in play (`#1299 `_) * don't modify values of 'paths' list passed as argument to prepend_paths in ``ModuleGenerator`` (`#1300 `_) * fix issue with ``EasyConfig.dump()`` + cleanup (`#1308 `_), `#1311 `_) * re-enable (and fix) accidentally disabled test (`#1316 `_) **easyblocks** * modified easybuild.easyblocks package declaration to support giving preference to custom easyblocks (`#617 `_) * 2 new generic easyblocks: RubyGem (`#565 `_), SystemCompiler (`#633 `_) * new easyblocks for 5 software packages that require customized support: * NEMO (`#564 `_), pbdMPI (`#612 `_), `#620 `_), pbdSLAP (`#620 `_), PDT (`#624 `_), Ruby (`#565 `_) * various other enhancements, including: * update CUDA easyblock for v6.x (`#476 `_) * make METIS easyblock take into account configopts (`#494 `_) * enable building of EOMIP and EOMEA for NWChem versions 6.5 and up (`#508 `_) * make out-of-source build with CMake truly out-of-source (`#615 `_) * add support in Bundle easyblock to run full sanity check (`#627 `_) * also take platform-specific Python lib dirs into account in PythonPackage easyblock (`#628 `_) * fix mpivars scripts in Intel MPI installation for versions where the installation is moved (`#629 `_) * don't restrict ``det_pylibdir`` function to only EasyBuild-provided Python (`#631 `_), `#641 `_) * support snappy and other optional native libs in Hadoop easyblock (`#632 `_), `#638 `_), `#640 `_), `#642 `_) * various bug fixes, including: * fix Xmipp easyblock, use provided ``install.sh`` script (`#630 `_) * update Clang easyblock to disable tests that may fail when unlimited stack size is used (`#622 `_) * fix setting of ``$INTEL_LICENSE_FILE`` for port@server values (`#635 `_) **easyconfigs** * added example easyconfig files for **62** new software packages: * ADF (`#899 `_), AutoDock_Vina (`#808 `_), bibtexparser (`#1726 `_), Biggus (`#1770 `_), Bismark (`#990 `_), blasr (`#1662 `_), BSMAP (`#1171 `_), Check (`#811 `_), Circuitscape (`#1222 `_), CONTRAfold (`#689 `_), cramtools (`#1741 `_), DBD-Pg (`#1066 `_), DendroPy (`#995 `_), EMAN2 (`#1737 `_), ETSF_IO (`#727 `_), eudev (`#1578 `_), fastqc (`#1636 `_), FDS (`#814 `_), `#1617 `_), `#1625 `_), FPM (`#1440 `_), frealign (`#1619 `_), g2log (`#1035 `_), GC3Pie (`#1692 `_), `#1756 `_), `#1768 `_), GenotypeHarmonizer (`#1672 `_), gensim (`#1762 `_), GraphViz (`#1658 `_), hisat (`#1674 `_), IDBA-UD (`#1045 `_), IMa2 (`#828 `_), IMPUTE2 (`#824 `_), JUBE (`#1396 `_), LAMARC (`#760 `_), libXScrnSaver (`#1653 `_), MATIO (`#1004 `_), MuTect (`#1483 `_), ncdf (`#617 `_), NEMO (`#1640 `_), ngspice (`#1116 `_), ordereddict (`#1774 `_), OSU Micro-Benchmarks (`#1777 `_), Parallel-ForkManager (`#847 `_), pBWA (`#1009 `_), PeakSeq (`#1412 `_), Pillow (`#1702 `_), Pindel (`#1126 `_), PLUMED (`#1596 `_), `#1665 `_), PostgreSQL (`#1066 `_), PROJ (`#1006 `_), PyAMG (`#1222 `_), Pyke (`#1776 `_), rpy2 (`#1775 `_), Sailfish (`#1035 `_), SCANMS (`#1386 `_), Seaborn (`#1763 `_), snpEff (`#1680 `_), SOBAcl (`#1658 `_), SPIDER (`#1624 `_), `#1723 `_), STAR (`#1043 `_), `#1676 `_), system GCC (`#1778 `_), tabix (`#1059 `_), tecplot360ex (`#1100 `_), Vampir (`#512 `_), VampirServer (`#512 `_), verifyBamID (`#1675 `_) * added easyconfigs for 4 new software bundles: * R-bundle-Bioconductor (`#1573 `_), `#1795 `_), R-bundle-devtools (`#1621 `_), `#1759 `_), R-bundle-extra (`#1387 `_), `#1759 `_), R-bundle-pbd (`#1659 `_) * added easyconfigs for new GNU toolchain (`#1346 `_), `#1669 `_) * added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 * various other enhancements, including: * update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (`#1337 `_) * update PDT easyconfigs to use PDT easyblock (`#1687 `_) * add custom ``sanity_check_paths`` in libxml2 easyconfigs (`#1690 `_) * enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (`#1761 `_) * include snappy as dependency in Hadoop easyconfigs (`#1758 `_), `#1773 `_) * enable SSL support in CMake v3.2.3 easyconfigs (`#1784 `_) * add additional extensions in R easyconfigs (`#1637 `_) * various bug fixes, including: * add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (`#631 `_) * fix issue with OpenMPI dependency in ECore easyconfigs (`#777 `_) * don't run the Bloom tests for Jellyfish, they can randomly fail (`#1016 `_) * fix source URLs in BioPerl easyconfigs (`#1075 `_) * patch out svnversion command in Python 2.5.6 to fix build on recent systems (`#1576 `_) * consistently use https for PyPI URLs in homepage/source_urls (`#1616 `_), `#1722 `_) * include Tcl and Tk as dependencies in R easyconfig (`#1623 `_) * add patch for installing paycheck as Py3 extension (`#1629 `_) * add Perl dependency in git 2.x easyconfigs (`#1631 `_) * fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (`#1635 `_) * fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (`#1652 `_) * include Tk as dependency in Python 2.7.9 easyconfigs (`#1654 `_) * include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure '``import Tkinter``' works (`#1655 `_) * drop gpfs versionsuffix and stop using no longer existing ``--enable-gpfs`` configopt for recent HDF5 versions (`#1657 `_) * include missing libxml2 dep in GLib easyconfigs (`#1666 `_) * fix source URLs in Qt easyconfigs (`#1673 `_) * fix source URLs for argparse Python extension (`#1697 `_) * fix source URLs for deap Python extension (`#1699 `_) * fix easyconfigs unit tests after making ModulesTool a non-singleton class (`#1708 `_) * fix names for Xmipp easyconfigs and patches (`#1719 `_) * add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (`#1734 `_) * add M4 as build dep for GCC 5.1.0 (`#1735 `_) * fix Bioconductor extension versions in R 3.1.3 easyconfigs (`#1748 `_) * remove custom exts_filter definition from Python 3.4.3 easyconfig (`#1765 `_) * fix source_urls in netCDF easyconfigs (`#1766 `_) * fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (`#1767 `_) .. _release_notes_eb211: EasyBuild v2.1.1 (May 18th 2015) -------------------------------- bugfix release **framework** * fix issue with missing load statements when ``--module-only`` is used, don't skip ready/prepare steps (`#1276 `_) * enhance ``--search``: only consider actual filename (not entire path), use regex syntax (`#1281 `_) * various other bug fixes, including: * fix ``generate_software_list.py`` script w.r.t. dependencies marked as external modules (`#1273 `_) * only use ``$LMOD_CMD`` value if ``lmod`` binary can't be found in $PATH (`#1275 `_) * fix location of ``module_only`` build option w.r.t. default value (`#1277 `_) * fix combined use of ``--hide-deps`` and ``hiddendependencies`` (`#1280 `_) * remove log handlers that were added during tests, to ensure effective cleanup of log files (`#1282 `_) * this makes the unit test suite run ~3x faster! * define ``$CRAYPE_LINK_TYPE`` if '``dynamic``' toolchain option is enabled for Cray compiler wrappers (`#1283 `_) **easyblocks** * fix compatibility of easyblocks with ``--module-only`` + dedicated unit test module (`#610 `_) * minor enhancements, including: * update GROMACS easyblock for version 5 (`#513 `_) * various other bug fixes, including: * only check compiler being used if FFTW interfaces are being built in Intel MKL easyblock (`#606 `_) **easyconfigs** * added example easyconfig files for **3** new software packages: * networkx (`#1592 `_), Platanus (`#1597 `_), SaguaroGW (`#1600 `_) * added new easyconfigs for existing toolchains: ``ictce/7.3.5``, ``CrayCCE/5.2.40``, ``CrayGNU/5.2.40``, ``CrayIntel/5.2.40`` * added easyconfigs using ``CrayGNU/5.2.25`` and ``CrayGNU/5.2.40`` toolchains (`#1610 `_, `#1611 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 * various bug fixes, including: * enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (`#1590 `_) * use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (`#1595 `_) * only use '``dynamic``' toolchain option, not '``shared``', in easyconfigs using Cray toolchain (`#1609 `_) .. _release_notes_v2.1.0: EasyBuild v2.1.0 (April 30th 2015) ---------------------------------- feature + bugfix release **framework** * requires vsc-base v2.2.0 or more recent * added support for LoggedException (`vsc-base#160 `_, `vsc-base#163 `_, `vsc-base#165 `_, `vsc-base#167 `_) * added support for add_flex action in GeneralOption (`vsc-base#162 `_) * added support to GeneralOption to act on unknown configuration environment variables (`vsc-base#162 `_) * add support for only (re)generating module files: ``--module-only`` (`#1018 `_) * module naming scheme API is enhanced to include det_install_subdir method * see :ref:`module_only` * add support for generating module files in Lua syntax (note: requires Lmod as modules tool) (`#1060 `_, `#1255 `_, `#1256 `_, `#1270 `_) * see ``--module-syntax`` configuration option and :ref:`module_syntax` * deprecate ``log.error`` method in favor of raising ``EasyBuildError`` exception (`#1218 `_) * see :ref:`depr_error_reporting` * add support for using external modules as dependencies, and to provide metadata for external modules (`#1230 `_, `#1265 `_, `#1267 `_) * see :ref:`using_external_modules` * add experimental support for Cray toolchains on top of PrgEnv modules: ``CrayGNU``, ``CrayIntel``, ``CrayCCE`` (`#1234 `_, `#1268 `_) * see https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray * various other enhancements, including: * clear list of checksums when using ``--try-software-version`` (`#1169 `_) * sort the results of searching for files (e.g., ``--search`` output) (`#1214 `_) * enhance test w.r.t. use of templates in cfgfile (`#1217 `_) * define '``%(DEFAULT_REPOSITORYPATH)s``' template for cfgfiles (see ``eb --avail-cfgfile-constants``) (`#1220 `_) * also reset ``$LD_PRELOAD`` when running module commands, in case module defined ``$LD_PRELOAD`` (`#1222 `_) * move location of '``module use``' statements in generated module file (*after* '``module load``' statements) (`#1232 `_) * add support for ``--show-default-configfiles`` (`#1240 `_) * see :ref:`default_configuration_files` * report error on missing configuration files, rather than ignoring them (`#1240 `_) * clean up commit message used in easyconfig git repository (`#1248 `_) * add ``--hide-deps`` configuration option to specify names of software that must be installed as hidden modules (`#1250 `_) * see :ref:`hide_deps` * add support for appending/prepending to ``--robot-paths`` to avoid overwriting default robot search path (`#1252 `_) * see :ref:`robot_search_path_prepend_append` * enable detection of use of unknown ``$EASYBUILD``-prefixed environment variables (`#1253 `_) * see :ref:`configuration_env_vars` * add ``--installpath-modules`` and ``--installpath-software`` configuration options (`#1258 `_) * see :ref:`installpath` * use dedicated subdirectory in temporary directory for each test to ensure better cleanup (`#1260 `_) * get rid of ``$PROFILEREAD`` hack when running commands, not needed anymore (`#1264 `_) * various bug fixes, including: * make bootstrap script robust against having ``vsc-base`` already available in Python search path (`#1212 `_, `#1215 `_) * set default value for unpack_options easyconfig parameter to ``''``, so ``self.cfg.update`` works on it (`#1229 `_) * also copy rotated log files (`#1238 `_) * fix parsing of ``--download-timeout`` value (`#1242 `_) * make ``test_XDG_CONFIG_env_vars`` unit test robust against existing user config file in default location (`#1259 `_) * fix minor robustness issues w.r.t. ``$XDG_CONFIG*`` and ``$PYTHONPATH`` in unit tests (`#1262 `_) * fix issue with handling empty toolchain variables (`#1263 `_) **easyblocks** * replace '``log.error``' with '``raise EasyBuildError``' in all easyblocks (`#588 `_) * one new generic easyblock: ``ConfigureMakePythonPackage`` (`#540 `_) * new easyblocks for 2 software packages that require customized support: * TINKER (`#578 `_), Xmipp (`#581 `_) * various other enhancements, including: * enhance WIEN2k easyblock for recent versions + cleanup (`#486 `_) * define ``$PYTHONNOUSERSITE`` in PythonPackage easyblock so user-installed packages are not picked up (`#577 `_) * add support in CP2K easyblock for building on top of MPICH/MPICH2 (`#579 `_) * enhance Hadoop easyblock to support parallel builds (`#580 `_) * drop ``-noroot`` for recent FLUENT versions, honor ``installopts``, enable ``-debug`` (`#582 `_) * include ``prebuildopts`` in build command for Python packages (`#585 `_) * also install ``rosetta_tools`` subdirectory for Rosetta (`#586 `_) * update SLEPc easyblock for v3.5 + style cleanup (`#593 `_) * minor fix in HPL easyblock w.r.t. checking defined environment variables (`#595 `_) * tweak CP2K easyblock w.r.t. LAPACK/FFTW support (`#596 `_) * minor update to GCC easyblock to support GCC v5.x (`#598 `_) * update sanity check in R easyblock for version 3.2.0 (`#602 `_) * various bug fixes, including: * fix Score-P easyblock for compiler-only toolchains, include Qt as optional dependency (`#552 `_) * fix definition of ``$MKLROOT``, should be set to '``mkl``' subdir of install dir (`#576 `_) * add ``-libmpichf90`` to list of MPI libraries in NWChem easyblock (`#584 `_) * stop using '``$root``' to make easyblocks compatible with module files in Lua syntax (`#590 `_) * also set ``$PYTHONPATH`` before installing Python package in temporary directory in ``test_step`` (`#591 `_) * unset ``buildopts``/``installopts`` before installing Python extensions in Python easyblock (`#597 `_) * allow not including vsc-base sources when installing EasyBuild (gets installed with easybuild-framework) (`#600 `_) * use ``self.initial_environ`` rather than ``self.orig_environ`` in EasyBuildMeta easyblock (`#600 `_) * make GCC easyblock compatible with ``--module-only`` by setting default value for ``self.platform_lib`` in constructor (`#603 `_) **easyconfigs** * added example easyconfig files for **27** new software packages: * AFNI (`#1322 `_, `#1521 `_), BCFtools (`#1492 `_), getdp (`#1518 `_), gmsh (`#1518 `_), gtest (`#1244 `_), hanythingondemand (`#1530 `_), mawk (`#1369 `_), Minimac (`#815 `_), Minimac3 (`#1502 `_), monty (`#1548 `_), Octave (`#1563 `_), pbs_python (`#1530 `_), pigz (`#1036 `_), Pygments (`#1536 `_), pyhull (`#1539 `_), pymatgen (`#1549 `_), PyQt (`#1322 `_, `#1521 `_), Ray (`#1494 `_), requests (`#1536 `_), seqtk (`#1524 `_), SIP (`#1322 `_, `#1521 `_), S-Lang (`#1369 `_), Spark (`#1554 `_), spglib (`#1549 `_), TINKER (`#1465 `_), tmux (`#1369 `_), Xmipp (`#1489 `_) * added easyconfigs for new (Cray-specific) toolchains (`#1538 `_): ``CrayGNU``, ``CrayIntel``, ``CrayCCE`` * initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (`#1558 `_) * see also https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray * added new easyconfigs for existing toolchains: ``goolf/1.5.16``, ``intel/2014.06`` * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 * various other enhancements, including: * include pbr dependency for lockfile Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (`#1462 `_, `#1540 `_) * include SQLite as dependency in Python v2.7.9 easyconfigs (`#1468 `_) * set ``$LD_PRELOAD`` for Hoard and jemalloc (`#1470 `_) * fix homepage in SCOTCH easyconfigs (`#1485 `_) * adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (`#1504 `_, `#1505 `_, `#1506 `_, `#1507 `_, `#1508 `_, `#1509 `_, `#1510 `_) * enable ``pic`` toolchain option in expat easyconfigs (`#1562 `_) * extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (`#1568 `_) * various bug fixes, including: * adding missing zlib dependency in all Tcl easyconfig files (`#1344 `_) * fix homepage in FLUENT easyconfigs (`#1472 `_) * use ``--with-verbs`` rather than deprecated ``--with-openib`` in OpenMPI configure options (`#1511 `_) * stop relying on ``OS_NAME`` constant to specify OS dependencies in OpenMPI easyconfigs (`#1512 `_) * replace use of '``$root``' with '``%(installdir)s``' to ensure compatibility with module files in Lua syntax (`#1532 `_) * stop relying on '``$MKLROOT``' in ROOT easyconfigs (`#1537 `_) * use proper Bundle easyblock for biodeps/PRACE (`#1566 `_) * make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (`#1574 `_) * add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (`#1574 `_) .. _release_notes_v2.0.0: EasyBuild v2.0.0 (March 6th 2015) --------------------------------- feature + bugfix release **framework** * requires vsc-base v2.0.3 or more recent * avoid deprecation warnings w.r.t. use of ``message`` attribute (`vsc-base#155 `_) * fix typo in log message rendering ``--ignoreconfigfiles`` unusable (`vsc-base#158 `_) * removed functionality that was deprecated for EasyBuild version 2.0 (`#1143 `_) * see :ref:`removed_functionality` * the fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (`#1151 `_, `#1206 `_, `#1207 `_) * for more information about this script, see :ref:`fix_broken_easyconfigs_script` * stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (`#1160 `_, `#1194 `_) * vsc-base is automatically installed as a dependency for easybuild-framework, if a Python installation tool is used * see :ref:`required_python_packages` * various other enhancements, including: * add support for Linux/POWER systems (`#1044 `_) * major cleanup in ``tools/systemtools.py`` + significantly enhanced tests (`#1044 `_) * add support for '``eb -a rst``', list available easyconfig parameters in ReST format (`#1131 `_) * add support for specifying one or more easyconfigs in combination with ``--from-pr`` (`#1132 `_) * see :ref:`from_pr_specifying_easyconfigs` * define ``__contains__`` in EasyConfig class (`#1155 `_) * restore support for downloading over a proxy (`#1158 `_) * i.e., use ``urllib2`` rather than ``urllib`` * this involved sacrificing the download progress report (which was only visible in the log file) * let ``mpi_family`` return ``None`` if MPI is not supported by a toolchain (`#1164 `_) * include support for specifying system-level configuration files for EasyBuild via ``$XDG_CONFIG_DIRS`` (`#1166 `_) * see :ref:`default_configuration_files` * make unit tests more robust (`#1167 `_, `#1196 `_) * see :ref:`unit_tests` * add hierarchical module naming scheme categorizing modules by ``moduleclass`` (`#1176 `_) * enhance bootstrap script to allow bootstrapping using supplied tarballs (`#1184 `_) * see :ref:`bootstrap_advanced_options` * disable updating of Lmod user cache by default, add configuration option ``--update-modules-tool-cache`` (`#1185 `_) * for now, only the Lmod user cache can be updated using ``--update-modules-tool-cache`` * use available ``which()`` function, rather than running '``which``' via ``run_cmd`` (`#1192 `_) * fix ``install-EasyBuild-develop.sh`` script w.r.t. vsc-base dependency (`#1193 `_) * also consider robot search path when looking for specified easyconfigs (`#1201 `_) * see :ref:`specifying_easyconfigs` * various bug fixes, including: * stop triggering deprecated/no longer support functionality in unit tests (`#1126 `_) * fix ``from_pr`` test by including dummy easyblocks for HPL and ScaLAPACK (`#1133 `_) * escape use of '``%``' in string with command line options with ``--job`` (`#1135 `_) * fix handling specified patch level 0 (+ enhance tests for fetch_patches method) (`#1139 `_) * fix formatting issues in generated easyconfig file obtained via ``--try-X`` (`#1144 `_) * use ``log.error`` in ``tools/toolchain/toolchain.py`` where applicable (`#1145 `_) * stop hardcoding ``/tmp`` in ``mpi_cmd_for`` function (`#1146 `_, `#1200 `_) * correctly determine variable name for ``$EBEXTLIST`` when generating module file (`#1156 `_) * do not ignore exit code of failing postinstall commands (`#1157 `_) * fix rare case in which used easyconfig and copied easyconfig are the same (`#1159 `_) * always filter hidden deps from list of dependencies (`#1161 `_) * fix implementation of ``path_matches`` function in ``tools/filetools.py`` (`#1163 `_) * make sure plain text keyring is used by unit tests (`#1165 `_) * suppress creation of module symlinks for ``HierarchicalMNS`` (`#1173 `_) * sort all lists obtained via ``glob.glob``, since they are in arbitrary order (`#1187 `_) * stop modifying ``$MODULEPATH`` directly in ``setUp``/``tearDown`` of toolchain tests (`#1191 `_) **easyblocks** * one new generic easyblock for installing a bundle of modules: ``Bundle`` (`#550 `_) * and let the ``Toolchain`` generic easyblock derive from ``Bundle`` * new easyblocks for 2 software packages that require customized support: * GAMESS-US (`#470 `_, `#544 `_, `#558 `_), Hadoop (`#563 `_) * various other enhancements, including: * move support for ``staged_install`` from CPLEX easyblock to generic ``Binary`` easyblock (`#502 `_) * fix sanity check in picard easyblock for v1.119 that doesn't include ``sam.jar`` (`#522 `_) * log warning message when unlinking jellyfish symlink fails in Trinity easyblock (`#534 `_) * revamp ``EB_libint2`` easyblock into ``EB_Libint`` that works for both Libint v1x and v2.x (`#536 `_) * update CP2K easyblock for recent versions (no more '``fes``') (`#537 `_) * update SuiteSparse easyblock for recent versions (`#541 `_) * fix easyblock unit tests after dropping support for deprecated behaviour in framework (`#543 `_) * rework PSI easyblock to support future releases (`#545 `_) * enable always generating a 'verbose' Makefile in the generic CMakeMake easyblock (`#546 `_) * remove functionality in (generic) easyblocks that was deprecated for EasyBuild v2.0 (`#547 `_) * enhance generic RPackage easyblock to support installing extensions in a separate prefix (`#551 `_) * deprecate GenomeAnalysisTK easyblock, since it's basically equivalent to Tarball (`#557 `_) * update SAMtools easyblock for v1.2 (`#562 `_) * take ``preconfigopts`` easyconfig parameter into account in ROOT easyblock (`#566 `_) * update easyblock for installing EasyBuild * to support bootstrapping with provided source tarballs (`#559 `_) * to also cover vsc-base dependency, and verify ``easy-install.pth`` (`#567 `_) * update disabling sanitizer tests for Clang 3.6 (`#570 `_) * various bug fixes, including: * fix handling of LTO in GCC easyblock (`#535 `_) * relocate FDTD RPM to fix installation on SL6 (`#538 `_) **easyconfigs** * added example easyconfig files for **29** new software packages: * bsoft (`#1353 `_), Coot (`#1400 `_), Cuby (`#1258 `_), DSRC (`#1242 `_), Exonerate (`#568 `_), fastqz (`#1242 `_), FSA (`#568 `_), fqzcomp (`#1242 `_), GAMESS-US (`#1153 `_, `#1406 `_), Grep (`#1308 `_), Hadoop (`#1418 `_), Hoard (`#1415 `_), IMB (`#1284 `_), ISL (`#1389 `_), jemalloc (`#1416 `_), libdwarf (`#1283 `_), libelf (`#1283 `_), MPC (`#1310 `_), multitail (`#1327 `_), Pmw (`#1403 `_), Quip (`#1242 `_), rCUDA (`#720 `_), SCALCE (`#1242 `_), SMALT (`#568 `_), STREAM (`#1332 `_), worker (`#1307 `_), Xerces-C++ (`#1370 `_), XQilla (`#1370 `_), ZPAQ (`#1242 `_) * added easyconfigs for new (common) toolchains * ``foss/2015a`` (`#1239 `_), ``gompi/1.5.16`` (`#1380 `_), ``gmvolf/1.7.20`` (`#1397 `_), ``goolf/1.7.20`` (`#1294 `_), intel/2015a (`#1238 `_), ``intel/2015.02`` (`#1393 `_), ``iomkl/2015.01`` (`#1325 `_), ``iomkl/2015.02`` (`#1401 `_) * added new software bundle: ``Autotools`` (`#1385 `_) * various other enhancements, including: * don't define ``$LDSHARED`` in zlib easyconfigs (`#1350 `_) * this fixes the long-standing "``no version information available``" issue with zlib * see also `framework#108 `_ * add unit test to check that all ``extra_options`` keys are defined in ``EasyConfig`` instance (`#1378 `_) * add source MD5 checksums in all GCC easyconfigs (`#1391 `_) * speeding up the unit tests by avoiding rereading of same easyconfig file (`#1432 `_) * fix conflict detection in unit tests by considering build deps separately from runtime deps (`#1447 `_) * fix toolchain for Bison build dep in ``MVAPICH2-1.9-iccifort-2011.13.367.eb`` easyconfig (`#1448 `_) * use ``Bundle`` generic easyblock for HPCBIOS bundles and fix ``moduleclass`` (`#1451 `_) * various bug fixes, including: * revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (`#1144 `_) * added Java dependencies to EMBOSS easyconfigs (`#1167 `_) * don't list '``lto``' as a language in GCC easyconfigs (`#1286 `_) * related to the fixes in the GCC easyblock, see `easyblocks#535 `_ * rename libint2 easyconfigs as Libint v2 easyconfigs (`#1287 `_) * fix mpi4py ``source_urls`` in Python easyconfigs (`#1306 `_) * consistently use CLooG 0.18.0 for GCC 4.8 series (`#1392 `_) * rename GenomeAnalysisTk easyconfigs to GATK (`#1399 `_) * include ``openssl-devel`` SLES11 OS dependency in cURL/MySQL/Python easyconfigs (`#1422 `_) * add missing Perl dependency in parallel easyconfigs (`#1430 `_) * correct name in BLAST+ easyconfigs (`#1443 `_) * fix name for sparsehash easyconfigs (`#1452 `_) EasyBuild v1.16.2 (March 6th 2015) ---------------------------------- bugfix release **framework** `(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)` **easyblocks** * make ``EB_EasyBuildMeta`` easyblock aware of vsc-base to make upgrading to EasyBuild v2.0.0 possible (`#573 `_) **easyconfigs** `(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)` EasyBuild v1.16.1 (December 19th 2014) -------------------------------------- bugfix release **framework** * fix functionality that is broken with ``--deprecated=2.0`` or with ``$EASYBUILD_DEPRECATED=2.0`` * don't include easyconfig parameters for ``ConfigureMake`` in ``eb -a``, since fallback is deprecated (`#1123 `_) * correctly check software_license value type (`#1124 `_) * fix ``generate_software_list.py`` script w.r.t. deprecated fallback to ``ConfigureMake`` (`#1127 `_) * other bug fixes * fix logging issues in tests, sync with vsc-base v2.0.0 (`#1120 `_) **easyblocks** * fix EasyBuild versions for which ``$EASYBUILD_DEPRECATED=1.0`` is set in EasyBuild sanity check (`#531 `_) **easyconfigs** * set default easyblock to ConfigureMake in TEMPLATE.eb (`#1277 `_) EasyBuild v1.16.0 (December 18th 2014) -------------------------------------- feature + bugfix release **framework** * deprecate automagic fallback to ``ConfigureMake`` easyblock (`#1113 `_) * easyconfigs should specify ``easyblock = 'ConfigureMake'`` instead of relying on the fallback mechanism * **note: automagic fallback to** ``ConfigureMake`` **easyblock will be removed in EasyBuild v2.0** * see also `Automagic fallback to ConfigureMake `_ * stop triggering deprecated functionality, to enable use of ``--deprecated=2.0`` (`#1107 `_, `#1115 `_, `#1119 `_) * see `Deprecated functionality `_ for more information * various other enhancements, including: * add script to clean up gists created via ``--upload-test-report`` (`#958 `_) * also use ``-xHost`` when using Intel compilers on AMD systems (as opposed to ``-msse3``) (`#960 `_) * add Python version check in ``eb`` command (`#1046 `_) * take ``versionprefix`` into account in ``HierarchicalMNS`` module naming scheme (`#1058 `_) * clean up and refactor ``main.py``, move functionality to other modules (`#1059 `_, `#1064 `_, `#1075 `_, `#1087 `_) * add check in ``download_file`` function for HTTP return code + show download progress report (`#1066 `_, `#1090 `_) * include info log message with name and location of used easyblock (`#1069 `_) * add toolchains definitions for ``gpsmpi``, ``gpsolf``, ``impich``, ``intel-para``, ``ipsmpi`` toolchains (`#1072 `_, `#1073 `_) * support for Parastation MPI based toolchains * enforce that ``hiddendependencies`` is a subset of ``dependencies`` (`#1078 `_) * this is done to avoid that site-specific policies w.r.t. hidden modules slip into contributed easyconfigs * enable use of ``--show_hidden`` for ``avail`` subcommand with recent Lmod versions (`#1081 `_) * add ``--robot-paths`` configure option (`#1080 `_, `#1093 `_, `#1095 `_, `#1114 `_) * support use of ``%(DEFAULT_ROBOT_PATHS)s`` template in EasyBuild configuration files (`#1100 `_) * see also `Controlling the robot search path `_ * use ``-xHost`` rather than ``-xHOST``, to match Intel documentation (`#1084 `_) * update and cleanup ``README`` file (`#1085 `_) * deprecate ``self.moduleGenerator`` in favor of ``self.module_generator`` in ``EasyBlock`` (`#1088 `_) * also support ``MPICH`` MPI family in ``mpi_cmd_for`` function (`#1098 `_) * update documentation references to point to http://easybuild.readthedocs.org (`#1102 `_) * check for OS dependencies with *both* ``rpm`` and ``dpkg`` (if available) (`#1111 `_) * various bug fixes, including: * fix picking required software version specified by ``--software-version`` and clean up ``tweak.py`` (`#1062 `_, `#1063 `_) * escape ``$`` characters in module load message specified via ``modloadmsg`` easyconfig parameter) (`#1068 `_) * take available hidden modules into account in dependency resolution (`#1065 `_) * fix hard crash when using patch files with an empty list of sources (`#1070 `_) * fix Intel MKL BLACS library being used for MPICH/MPICH2-based toolchains (`#1072 `_) * fix regular expression in ``fetch_parameter_from_easyconfig_file`` function (`#1096 `_) * don't hardcode queue names when submitting a job (`#1106 `_) * fix affiliation/mail address for Fotis in headers (`#1105 `_) * filter out ``/dev/null`` entries in patch file in ``det_patched_files`` function (`#1108 `_) * fix ``gmpolf`` toolchain definition, to have ``gmpich`` as MPI components (instead of ``gmpich2``) (`#1101 `_) * 'MPICH' refers to MPICH v3.x, while MPICH2 refers to MPICH(2) v2.x (MPICH v1.x is ancient/obsolete) * **note**: this requires to reinstall the ``gmpolf`` module, using the updated easyconfig from `easybuild-easyconfigs#1217 `_ **easyblocks** * new easyblocks for **2** software packages that requires customized support: * Chimera (`#524 `_), GATE (`#518 `_) * fix use of deprecated functionality, enhance unit tests to check for it (`#523 `_) * various other enhancements, including: * update PETSc easyblock for recent versions (v3.5) (`#446 `_) * only include major/minor version numbers for FLUENT subdir (`#480 `_) * factor out 'move after install' code from impi easyblock to ``IntelBase``, use it for itac (`#487 `_) * support custom easyconfig parameters in ``EB_impi`` easyblock to correct behavior of MPI wrapper commands (`#493 `_) * consider both ``lib`` and ``lib64`` in sanity check for GROMACS (`#501 `_) * take ``preinstallopts`` and ``installopts`` into account in ``Binary`` easyblock (`#503 `_) * add sanity check command ``abaqus information=all`` for ABAQUS (`#504 `_) * update and clean up ``README``, refer to http://easybuild.readthedocs.org documentation (`#505 `_, `#516 `_) * rename deprecated ``self.moduleGenerator`` to ``self.module_generator`` (`#506 `_) * see also `easybuild-framework#1088 `_ * check whether specified ``type`` value is a known value (``psmp`` or ``popt``) in CP2K easyblock (`#509 `_) * add support to ``SAMtools`` easyblock for installing recent versions (v1.x) (`#512 `_) * fix version check + sanity check in Geant4 easyblock + style fixes (`#517 `_) * added ``$root/modlib`` to ``$PYTHONPATH`` guesses in Modeller easyblock (`#525 `_) * mark ``license`` custom easyconfig parameter as deprecated in ``IntelBase`` (`#527 `_) * various bug fixes, including: * fix Libxc version check in CP2K easyblock (`#478 `_) * correctly specify ``mkl_libs`` when building *numpy* with GCC and imkl (`#485 `_) * extend noqa for OpenFOAM-Extend in build_step (`#488 `_, `#520 `_) * correctly set ``$LD_LIBRARY_PATH``, ``$LIBRARY_PATH`` and ``$PKG_CONFIG_PATH`` for ``R`` (`#495 `_) * fix default value for ``files_to_copy`` in ``MakeCp`` easyblock (`#500 `_) * treat ``MPICH`` MPI family as MPICH v3.x instead of MPICH v1.x (`#519 `_) * see also `easybuild-framework#1112 `_ * fix affiliation/mail address for Fotis in headers (`#521 `_) * clean up in ``extra_options`` methods, avoid casting return value to ``dict`` or returning via parent (`#528 `_) **easyconfigs** * added example easyconfig files for **39** new software packages: * ANTs (`#1232 `_), BEOPS (`#1264 `_), Chhimera (`#1255 `_), ctffind (`#1249 `_), DBD-SQLite (`#1064 `_), DBD-mysql (`#1063 `_), DIALIGN-TX (`#668 `_), ffmpeg (`#1088 `_), GObject-Introspection (`#1079 `_), GTS (`#1079 `_), Graphviz (`#1079 `_), GraphViz2 (`#1079 `_), grace (`#1131 `_), HarfBuzz (`#1079 `_), HTSlib (`#1161 `_), GSSAPI (`#1048 `_), Kerberos_V5 (`#1048 `_), libevent (`#1063 `_), libXdmcp (`#1129 `_), libXft (`#1017 `_), libXinerama (`#1017 `_), libXrender (`#1017 `_), Maven (`#1094 `_), MySQL (`#1063 `_), Net-LibIDN (`#1060 `_), OpenCV (`#1088 `_), OpenMD (`#1105 `_), Qhull (`#1105 `_), Pango (`#1079 `_), psmpi (`#1245 `_, `#1246 `_), RELION (`#1017 `_), renderproto (`#1017 `_), rjags (`#1125 `_), runjags (`#1125 `_), SPRNG (`#1138 `_, `#1141 `_), xineramaproto (`#1017 `_), XML-Dumper (`#1061 `_), XML-Parser (`#1061 `_), XML-Twig (`#1061 `_) * added easyconfigs for new toolchains * ``intel/2014.10`` & ``intel/2014.11`` (`#1219 `_), ``intel-para/2014.12`` (`#1246 `_), ``gpsolf/2014.12`` (`#1245 `_), ``iompi/6.6.4`` (`#1215 `_) * include ``easyblock = 'ConfigureMake'`` in relevant easyconfigs to deal with deprecation of automagic fallback to ``ConfigureMake`` (`#1248 `_) * see also `easybuild-framework#1113 `_ and `Automagic fallback to ConfigureMake `_ * clean up use of deprecated functionality in existing easyconfigs (`#1252 `_, `#1259 `_) * stop using deprecated ``makeopts``, ``premakeopts`` and ``shared_lib_ext`` * check for use of deprecated functionality in easyconfigs unit tests * see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters * various other enhancements, including: * also build ``fftw3_threads`` libraries, and enhance sanity checks (`#1013 `_) * add unit test to verify specified ``sanity_check_paths`` (`#1119 `_) * update and clean up ``README``, refer to http://easybuild.readthedocs.org documentation (`#1184 `_, `#1224 `_) * various bug fixes, including: * fix unit tests w.r.t. changes in framework (`#1146 `_) * remove unnecessary build dependencies for OpenMPI (`#1168 `_) * remove duplicate line in OpenMPI easyconfigs (`#1207 `_) * fix affiliation/mail address for Fotis in headers (`#1237 `_) * fix permissions of easyconfig files for consistency (`#1210 `_) * disable symbol lookup feature in cairo to fix build on SL6 (`#1241 `_) * fix easyconfig ``gmpolf`` toolchain w.r.t. MPICH software name (`#1217 `_) * see also `easybuild-framework#1112 `_ * fix ``source_urls`` for WRF and WPS (`#1225 `_) * fix and clean up GATE easyconfigs (`#1228 `_) * fix broken CLHEP builds by including ``-gcc`` in ``$CXXFLAGS`` (`#1254 `_) * add patch to fix broken test in Go (`#1257 `_) * fix name of GMAP easyconfigs, should be GMAP-GSNAP (`#1268 `_) * fix easyconfig filenames, enhance unit test to check easyconfig filenames (`#1271 `_) EasyBuild v1.15.2 (October 7th 2014) ------------------------------------ bugfix release **framework** * fix ``$MODULEPATH`` extensions for Clang/CUDA, to make ``goolfc``/``cgoolf`` compatible with ``HierarchicalMNS`` (`#1050 `_) * include ``versionsuffix`` in module subdirectory with ``HierarchicalMNS`` (`#1050 `_, `#1055 `_) * fix unit tests which were broken with bash patched for ShellShock bug (`#1051 `_) * add definition of gimpi toolchain, required to make gimkl toolchain compatible with ``HierarchicalMNS`` (`#1052 `_) * don't override ``COMPILER_MODULE_NAME`` obtained from ``ClangGCC`` in Clang-based toolchains (`#1053 `_) * fix wrong code in ``path_to_top_of_module_tree`` function (`#1054 `_) * because of this, load statements for compilers were potentially included in higher-level modules under ``HierarchicalMNS`` **easyblocks** * only disable sanitizer tests for recent Clang versions (`#481 `_, `#482 `_) * pass down installopts to CUDA install command (`#483 `_) **easyconfigs** * disable parallel build for slalib (`#968 `_) * fix compatibility of goolfc with HierarchicalMNS by using GCC toolchain for installing CUDA (`#1106 `_, `#1115 `_) * fix zlib OS dependency spec for Debian in Boost easyconfigs (`#1109 `_) * fix compatibility of gimkl with HierarchicalMNS by using gimpi subtoolchain (`#1110 `_) * make both GCC and Clang first-class members in Clang-based toolchains to fix compatibility with HierarchicalMNS (`#1113 `_) EasyBuild v1.15.1 (September 23rd 2014) --------------------------------------- bugfix release **framework** * take into account that multiple modules may be extending ``$MODULEPATH`` with the same path, when determining path to top of module tree (see `#1047 `_) * this bug caused a load statement for either ``icc`` or ``ifort`` to be included in higher-level modules installed with an Intel-based compiler toolchain, under the ``HierarchicalMNS`` module naming scheme * make ``HierarchicalMNS`` module naming scheme compatible with ``cgoolf`` and ``goolfc`` toolchain (`#1049 `_) * add definition of ``iompi`` (sub)toolchain to make ``iomkl`` toolchain compatible with ``HierarchicalMNS`` (`#1049 `_) **easyblocks** `(no changes compared to v1.15.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** * minor bug fixes, including: * use SHLIB_EXT in GMP/MPFR easyconfigs (`#1090 `_) * fix TopHat homepage and source_urls since page moved (`#1092 `_) * make iomkl toolchain compatible with HierarchicalMNS (`#1099 `_) EasyBuild v1.15.0 (September 12th 2014) --------------------------------------- feature + bugfix release **framework** * various other enhancements, including: * fetch extension sources in fetch_step to enhance ``--stop=fetch`` (`#978 `_) * add ``iimpi`` toolchain definition (`#993 `_) * prepend robot path with download location of files when ``--from-pr`` is used (`#995 `_) * add support for excluding module path extensions from generated modules (`#1003 `_) * see ``include_modpath_extensions`` easyconfig parameter * add support for installing hidden modules and using them as dependencies (`#1009 `_, `#1021 `_, `#1023 `_) * see ``--hidden`` and ``hiddendependencies`` easyconfig parameter * stop relying on ``conflict`` statement in module files to determine software name of toolchain components (`#1017 `_, `#1037 `_) * instead, the ``is_short_modname_for`` method defined by the module naming scheme implementation is queried * improve error message generated for a missing easyconfig file (`#1019 `_) * include path where tweaked easyconfigs are placed in robot path (`#1032 `_) * indicate forced builds in ``--dry-run`` output (`#1034 `_) * fix interaction between ``--force`` and ``--try-toolchain --robot`` (`#1035 `_) * add ``--software`` option, disable recursion for ``--try-software(-X)`` (`#1036 `_) * various bug fixes, including: * fix ``HierarchicalMNS`` crashing when MPI library is installed with a dummy toolchain (`#986 `_) * fix list of FFTW wrapper libraries for Intel MKL (`#987 `_) * fix stability of unit tests (`#988 `_, `#1027 `_, `#1033 `_) * make sure ``$SCALAPACK_INC_DIR`` (and ``$SCALAPACK_LIB_DIR``) are defined when using ``imkl`` (`#990 `_) * fix error message on missing FFTW wrapper libs (`#992 `_) * fix duplicate toolchain elements in ``--list-toolchains`` output (`#993 `_) * filter out load statements that extend the ``$MODULEPATH`` to make the module being installed available (`#1016 `_) * fix conflict specification included in module files (`#1017 `_) * avoid ``--from-pr`` crashing hard unless ``--robot`` is used (`#1022 `_) * properly quote GCC version string in archived easyconfig (`#1028 `_) * fix issue with ``--repositorypath`` not honoring ``--prefix`` (`#1031 `_) * sync with latest vsc-base version to fix log order (`#1039 `_) * increase # commits per page for ``--from-pr`` (`#1040 `_) **easyblocks** * added support for **2** new software packages that requires customized support: * Modeller (`#392 `_), NAMD (`#397 `_) * various enhancements, including: * fix locale used for running Perl unit tests (`#425 `_) * fix Rmpi easyblock to correctly configure for Intel MPI (`#435 `_) * add support in generic Rpackage easyblock for handling patches (`#435 `_) * enhance OpenFOAM easyblock: fix building MPI build of Pstream and (pt)scotchDecomp + overall cleanup (`#436 `_) * enhance NWChem easyblock for version 6.3, clean up running of test cases (`#441 `_) * enhance noqa for interactive configuration of Qt build procedure (`#447 `_) * add custom sanity check for R in easyblock (`#449 `_) * make perlmodule take into account ``(pre){config,build,install}opts`` (`#450 `_) * add support for specifying an activation key after installing Mathematica (`#452 `_) * consider both ``lib`` and ``lib64`` directories in netCDF sanity check (`#453 `_) * fix sanity check for ANSYS for v15.0.x (`#458 `_) * fix Trilinos easyblock for recent version (`#462 `_) * enhance impi easyblock to handle install subdir for impi v5.0.1 and future version (`#465 `_, `#472 `_) * include $CFLAGS in linker flags for HPL (`#466 `_) * update sanity test checks for GROMACS 5.x (`#471 `_) * various bug fixes: * fix building of FFTW wrappers for Intel MKL v11.1.x + cleanup of imkl easyblock (`#445 `_) **easyconfigs** * added example easyconfig files for **13** new software packages: * Circos (`#780 `_), DB_File (`#913 `_), Emacs (`#970 `_), evmix (`#1077 `_), GD (`#780 `_), gsl (`#1077 `_), IOR (`#949 `_), JAGS (`#1076 `_), libgd (`#780 `_), MethPipe (`#1070 `_), Modeller (`#825 `_), NAMD (`#835 `_), netCDF-C++4 (`#1015 `_) * added easyconfigs for new toolchains (`#986 `_, `#1051 `_): * gimkl/1.5.9, ictce/7.1.2 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ... * various enhancements, including: * make existing ictce/intel toolchains compatible with HierarchicalMNS (`#1069 `_) * this involves installing impi with an iccifort toolchain, and imkl with an iimpi toolchain * various bug fixes, including: * download link for Perl modules changed to use cpan.metapan.org * fix missing MPI-based OpenFOAM libraries (``Pstream``, ``(pt)scotchDecomp``), make sure provided SCOTCH is used (`#957 `_) EasyBuild v1.14.0 (July 9th 2014) --------------------------------- feature + bugfix release **framework** * important changes * required Lmod version bumped to v5.6.3 (`#944 `_) * required due to enhancements and bug fixes in Lmod, e.g. making ``--terse avail`` significantly faster, and correctly handling a ``prepend-path`` statement that includes multiple directories at once * required Tcl/C environment modules version set to 3.2.10 ( * hard requirement due to fixed ``modulecmd`` segmentation fault bug, that only tends manifests itself when making a large amount of changes in the environment (e.g. ``module load ``) * renamed ``EasyBuildModuleNamingScheme`` to ``EasyBuildMNS`` * enhanced custom module naming schemes functionality to support hierarchical module naming schemes (`#953 `_, `#971 `_, `#975 `_) * extended API for custom module naming schemes to allow tweaking different aspects of module naming * see ``easybuild/tools/module_naming_scheme/mns.py`` for abstract ``ModuleNamingScheme`` class * an example hierarchical module naming scheme is included, see ``HierarchicalMNS`` * split up full module names into a module subdirectory part, which becomes part of ``$MODULEPATH``), and a 'short' module name (is exposed to end-users) * example: ``GCC/4.7.2`` in ``Core`` subdir, ``OpenMPI/1.6.5`` in ``Compiler/GCC/4.7.2`` subdir * make ``ModuleNamingScheme`` class a singleton, move it into ``easybuild.tools.module_naming_scheme.mns`` module * implement ``ActiveMNS`` wrapper class for querying active module naming scheme * implement toolchain inspection functions that can be used in a custom module naming scheme * ``det_toolchain_compilers``, ``det_toolchain_mpi`` in ``easybuild.tools.module_naming_scheme.toolchain`` * significant code cleanup & enhanced unit tests * enhance & clean up ``tools/modules.py`` (`#944 `_, `#953 `_, `#963 `_, `#964 `_, `#969 `_) * make ``ModulesTool`` a singleton to avoid repeating module commands over & over again needlessly * use ``module use``, ``module unuse`` rather than fiddling with ``$MODULEPATH`` directly * improve debug logging (include full stdout/stderr output of module commands) * remove deprecated functionality (``add_module``, ``remove_module``, indirect module load) * various other enhancements, including: * added toolchain definitions for 'common' toolchains: ``intel`` and ``foss`` (`#956 `_) * implement caching for easyconfig files, parsed easyconfigs and toolchains (`#953 `_) * enable ``--ignore-osdeps`` implicitly when ``-D``, ``--dry-run`` or ``--dep-graph`` are used (`#953 `_) * flesh out ``use_group`` and ``det_parallelism`` function, include them in ``easybuild.tools.systemtools`` (`#953 `_) * make symlinking of module files part of module naming scheme API (`#973 `_) * list of symlinks paths can be controlled using ``det_module_symlink_paths()`` method * added support for new configuration options: * tweaking compiler flags triggered by ``optarch`` toolchain options using ``--optarch`` (`#949 `_) * filtering out dependencies from easyconfig files using ``--filter-deps`` (`#957 `_) * filtering environment included in test reports with ``--test-report-env-filter`` (`#959 `_) e.g. ``--test-report-env-filter='^SSH|USER|HOSTNAME|UID|.*COOKIE.*'`` * made suffix used for module files install path configurable, using ``--suffix-modules-path`` (`#973 `_) * added support for additional easyconfig parameters: * define aliases in module files (``modaliases``) (`#952 `_) * add print message on module load (``modloadmsg``) and Tcl footer (``modtclfooter``) in module files (`#954 `_, `#974 `_) * various bug fixes, including: * don't try to tweak generated easyconfigs when using ``--try-X`` (`#942 `_) * currently create symlinks to module files modules/all under a custom module naming scheme (`#953 `_) * restore traceback error reporting on hard crashes (`#965 `_) **easyblocks** * added **one** new `generic` easyblock: CmdCp (`#395 `_) * added support for **2** new software packages that requires customized support: * ANSYS (`#398 `_), HPCG (`#408 `_) * various enhancements, including: * updated ABAQUS easyblock so that it works for version 13.2 (`#406 `_) * enhance BLAT easyblock by using ``super``'s ``build_step`` and ``prebuildopts``/``buildopts`` (`#423 `_) * enhance Mothur easyblock to guess correct start dir for recent versions (`#424 `_) * replace use of deprecated (pre)makeopts with (``pre``)``buildopts`` in all easyblocks (`#427 `_) * fix poor mans version of toolchain compiler detection in imkl easyblock (`#429 `_) * various bug fixes: * only check for ``idb`` for older versions of icc (`#426 `_) * fix issues with installing RPMS when ``rpmrebuild`` is required (`#433 `_) * correctly disable parallel build for ATLAS (`#434 `_) * fix sanity check for Intel MPI v5.x (only provides bin64) (`#432 `_) * add ``$MIC_LD_LIBRARY_PATH`` for MKL v11.x (`#437 `_) **easyconfigs** * added example easyconfig files for **17** new software packages: * ANSYS (`#836 `_), Beast (`#912 `_), ELPH (`#910 `_, `#911 `_), FastTree (`#900 `_, `#947 `_), GEM-library (`#858 `_), HPCG (`#853 `_), mdtest (`#925 `_), ncview (`#648 `_), PRANK (`#917 `_), RDP-Classifier (`#903 `_), SDPA (`#955 `_), SIBELia (`#886 `_), SOAPaligner (`#857 `_), SPAdes (`#884 `_), stemming (`#891 `_), WHAM (`#872 `_), YAXT (`#656 `_) * added easyconfigs for new toolchains (`#935 `_, `#944 `_, `#948 `_): * foss/2014b, ictce/6.3.5, intel/2014b * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * various enhancements, including: * replace use of deprecated ``(pre)makeopts`` with ``(pre)buildopts`` in all easyblocks (`#954 `_) * disable running embossupdate on installation of EMBOSS (`#963 `_) * various bug fixes, including: * really enable OpenMP support in FastTree easyconfigs (`#947 `_) * fix easyconfigs unit tests after changes in framework (`#958 `_) EasyBuild v1.13.0 (May 29th 2014) --------------------------------- feature + bugfix release **framework** * make ``--try-X`` command line options work recursively (i.e. collaborate with ``--robot``) (`#922 `_) * EasyBuild will first build a full dependency graph of the specified easyconfigs, and then apply the ``--try`` specifications * the elements of the dependency graph for the used toolchain and its dependencies are left untouched * this makes ``eb foo-1.0-goolf-1.4.10.eb --try-toolchain=ictce,5.5.0 --robot`` also work when ``foo`` has dependencies * caveat: the specified easyconfig files must all use the same toolchain (version) * add support for testing easyconfig pull requests from EasyBuild command line (`#920 `_, `#924 `_, `#925 `_, `#932 `_, `#933 `_, `#938 `_) * add ``--from-pr`` command line option for downloading easyconfig files from pull requests * add ``--upload-test-report`` command line option for uploading a detailed test report to GitHub as a gist * this requires specifying a GitHub username for which a GitHub token is available, using ``--github-user`` * with ``--dump-test-report``, the test report can simply be dumped to file rather than being uploaded to GitHub * see also https://github.com/easybuilders/easybuild/wiki/Review-process-for-contributions#testing-result * the ``makeopts`` and ``premakeopts`` easyconfig parameter are deprecated, and replaced by ``buildopts`` and ``prebuildopts`` (`#918 `_) * both ``makeopts`` and ``premakeopts`` will still be honored in future EasyBuild v1.x versions, but should no longer be used * various other enhancements, including: * add ``--disable-cleanup-builddir`` command line option, to keep the build dir after a (successful) build (`#853 `_) * the build dir is still cleaned up by default for successful builds, i.e. ``--cleanup-builddir`` is the default * also consider lib32 in paths checked for ``$LD_LIBRARY_PATH`` and ``$LIBRARY_PATH`` (`#912 `_) * reorganize support for file/git/svn repositories into ``repository`` package, making it extensible (`#913 `_) * add support for ``postinstallcmds`` easyconfig parameter, to specify commands that need to be run after the install step (`#918 `_) * make ``VERSION=`` part in version of C environment modules tool optional, which is required for older versions (`#930 `_) * various bug fixes, including: * fix small issues in bootstrap script: correctly determine EasyBuild version and make sure modules path exists (`#915 `_) * fix github unit tests (`#916 `_) * disable useless debug logging for unit tests (`#919 `_) * fix unit test for ``--skip`` (`#929 `_) * make sure ``start_dir`` can be set based on location of unpacked first source file (`#931 `_) * the ``vsc`` package shipped with easybuild-framework is synced with vsc-base v1.9.1 (`#935 `_) * fancylogger (used for logging in EasyBuild) is now robust against strings containing UTF8 characters * the ``deprecated`` logging function now does a non-strict version check (rather than an erroneous strict check) * the ``easybuild.tools.agithub`` module is removed, ``vsc.utils.rest`` now provides the required functionality * fix support for unpacking gzipped source files, don't unpack ``.gz`` files in-place in the source directory (`#936 `_) **easyblocks** * added support for **1** new software package that requires customized support: * Go (`#417 `_) * various enhancements, including: * enhance OpenFOAM easyblock so OpenFOAM-Extend fork can be built too + style fixes (`#253 `_, `#416 `_) * enhance CPLEX easyblock by adding support for staged installation (`#372 `_) * include support for ``configure_cmd_prefix`` easyconfig parameter in ConfigureMake generic easyblock (`#393 `_) * enhance GCC easyblock for building v4.9.0 and versions prior to v4.5 (`#396 `_, `#400 `_) * enhance easyblocks for Intel ipp and itac to support recent versions (`#399 `_) * enhance Clang easyblock: install static analyzer (`#402 `_), be more robust against changing source dir names (`#413 `_) * enhance FoldX easyblock, update list of potential FoldX binaries to support recent versions (`#407 `_) * add runtime patching in Boost easyblock to fix build issue with old Boost versions and recent glibc (> 2.15) (`#412 `_) * enhance ``MakeCp`` generic easyblock: use location of 1st unpacked source as fallback base dir for ``files_to_copy`` (`#415 `_) * various bug fixes: * fix installing Mathematica when X forwarding is enabled (make sure ``$DISPLAY`` is unset) (`#391 `_) * fix permissions of installed files in SAMtools easyblock, ensure read/execute for group/other (`#409 `_) * fix implementation of ``det_pylibdir`` function in PythonPackage generic easyblock (`#419 `_, `#420 `_) * determine Python lib dir via ``distutils`` Python, which works cross-OS (as opposed to hardcoding ``lib``) **easyconfigs** * added example easyconfig files for **32** new software packages: * APBS (`#742 `_), BayesTraits (`#770 `_), bc (`#888 `_), BitSeq (`#791 `_), CEM (`#789 `_), CVS (`#888 `_), eXpress (`#786 `_), file (`#888 `_), GEMSTAT (`#861 `_), GMAP (`#594 `_), Go (`#887 `_), iscp (`#602 `_), IsoInfer (`#773 `_), Jellyfish (`#868 `_), less (`#888 `_), libcircle (`#883 `_), mcpp (`#602 `_), MMSEQ (`#795 `_), MUSTANG (`#800 `_), OpenFOAM-Extend (`#437 `_), popt (`#759 `_), pscom (`#759 `_), psmpi2 (`#759 `_), QuadProg++ (`#773 `_), rSeq (`#771 `_), RSEQtools (`#870 `_), Ruby (`#873 `_), segemehl (`#792 `_), SOAPec (`#879 `_), SOAPdenovo2 (`#874 `_), SRA-Toolkit (`#793 `_), texinfo (`#888 `_) * added easyconfig for new toolchain goolfc/1.4.10 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * e.g., older versions of Boost (1.47.0), GCC (4.1-4.4), & recent versions of Clang, GCC, Lmod, etc. * various enhancements, including: * add OpenSSL dependency for cURL, to enable HTTPS support (`#881 `_) * also install esl-X binaries for HMMER (`#889 `_) * various bug fixes, including: * properly pass down compiler flags for ParMGridGen (`#437 `_) * specify proper make options for PLINK, fixing the build on SL6 (`#594 `_, `#772 `_) * fix netloc version (0.5 rather than 0.5beta) (`#707 `_) * remove Windows-style line ending in netCDF patch file (`#796 `_) * bump version of OpenSSL dep for BOINC (`#882 `_) EasyBuild v1.12.1 (April 25th 2014) ----------------------------------- bugfix release **framework** * return to original directory after executing a command in a subdir (`#908 `_) * fix bootstrap with Lmod, fix issue with module function check and Lmod (`#911 `_) **easyblocks** `(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** `(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)` EasyBuild v1.12.0 (April 4th 2014) ---------------------------------- feature + bugfix release **framework** * various enhancements, including: * completed support for custom module naming schemes (`#879 `_, `#904 `_) * a fully parsed easyconfig file is now passed to the ``det_full_module_name`` function * this does require that an easyconfig file matching the dependency specification is available * added more features to better support using a shared install target with multiple users (`#902 `_, `#903 `_, `#904 `_) * further development on support for new easyconfig format (v2.0) (`#844 `_, `#848 `_) * not considered stable yet, so still requires using ``--experimental`` * enhanced bootstrap script to also support Lmod and ``modulecmd.tcl`` module tools (`#869 `_) * added support to ``run_cmd_qa`` function to supply a list of answers (`#887 `_) * detect mismatch between definition of ``module`` function and selected modules tool (`#871 `_) * allowing mismatch now requires ``--allow-modules-tool-mismatch``; an empty ``module`` function is simply ignored * provide lib64 fallback option for directories in default sanity check paths (`#896 `_) * add support for adding JAR files to ``$CLASSPATH`` (`#898 `_) * enhanced and cleaned up unit tests (`#877 `_, `#880 `_, `#884 `_, `#899 `_, `#901 `_) * code cleanup and refactoring * get rid of global variable for configuration settings in ``config.py``, use singleton instead (`#874 `_, `#888 `_, `#890 `_, `#892 `_) * track build options via singleton in ``config.py`` rather than passing them around all over (`#886 `_, `#889 `_) * avoid parsing easyconfig files multiple times by passing a parsed easyconfig to the easyblock (`#891 `_) * deprecate list of tuples return type of ``extra_options`` static method (`#893 `_, `#894 `_) * move OS dependency check to ``systemtools.py`` module (`#895 `_) * bug fixes, including: * fix linking with ``-lcudart`` if CUDA is part of the toolchain, should also include ``-lrt`` (`#882 `_) **easyblocks** * various enhancements, including: * also run ``Perl Build build`` for Perl modules (usually not required, but sometimes it is) (`#380 `_) * added glob support in generic makecp block (`#367 `_, `#384 `_) * enhance sanity check in GCC easyblock such that it also passes/works on OpenSuSE (`#365 `_) * add multilib support in GCC easyblock (`#379 `_) * various bug fixes: * Clang: disable sanitizer tests when vmem limit is set (`#366 `_) * make sure all libraries are installed for recent Intel MKL versions (`#375 `_) * fix appending Intel MPI include directories to ``$CPATH`` (`#371 `_) * statically link readline/ncurses libraries in Python and NWChem easyblocks (`#370 `_, `#383 `_, `#385 `_) * fix easyblock unit tests after changes in framework (`#376 `_, `#377 `_, `#378 `_) **easyconfigs** * added example easyconfig files for **6** new software packages: * CLooG (`#653 `_), ELPA (`#738 `_), LIBSVM (`#788 `_), netaddr (`#753 `_), netifcas (`#753 `_), slalib-c (`#750 `_) * added easyconfigs for new toolchains: * ClangGCC/1.3.0 (`#653 `_), goolf/1.4.10-no-OFED (`#749 `_), goolf/1.5.14(-no-OFED) (`#764 `_, `#767 `_), ictce/6.2.5 (`#726 `_), iomkl (`#747 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * various enhancements, including: * tweak BOINC easyconfig to make use of ``glob`` support available for ``files_to_copy`` (`#781 `_) * enable ``-fPIC`` for libreadline, so it can be linked into shared libs (e.g. ``libpython2.x.so``) (`#798 `_) * various bug fixes, including: * fix Qt source_urls (`#756 `_) * enable ``-fPIC`` in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others (`#801 `_) * fix unit tests after changes to framework (`#763 `_, `#766 `_, `#769 `_) EasyBuild v1.11.1 (February 28th 2014) -------------------------------------- bugfix release **framework** * various bug fixes, including: * fix hard crash when ``$LMOD_CMD`` specified full path to lmod binary, but ``spider`` binary is not in ``$PATH`` (`#861 `_, `#873 `_) * fix bug in initialisation of repositories, causing problems when a repository subdirectory is specified (`#852 `_) * avoid long wait when dependency resolution fails if ``--robot`` is not specified (`#875 `_) **easyblocks** `(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)` **easyconfigs** `(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)` EasyBuild v1.11.0 (February 16th 2014) -------------------------------------- feature + bugfix release **framework** * various enhancements, including: * add checksum support for extensions (`#807 `_) * make checksum functionality more memory efficient by reading in blocks (`#836 `_) * rewrite of dependency solving for speed and better reporting of missing dependencies (`#806 `_, `#818 `_) * refactoring of ``main.py`` (`#815 `_, `#828 `_) * function/method signatures to pass down build options * move functions from main.py into easybuild.framework.X or easybuild.tools * provide better build statistics (`#824 `_) * add --experimental, ``--deprecated`` and ``--oldstyleconfig`` command line options (`#838 `_) * with ``--experimental``, new but incomplete (or partially broken) features are enabled * with ``--deprecated``, removed of deprecated functionality can be tested (anything deprecated will fail hard) * with ``--disable-oldstyleconfig``, support for the old style configuration is disabled * define ``$LIBRARY_PATH`` in generated module files (`#832 `_) * more constants for source URLs (e.g. for downloads from bitbucket) (`#831 `_) * prefer ``$XDG_CONFIG_HOME`` and ``~/.config/easybuild`` over ``~/.easybuild`` for configuration files (`#820 `_) * add support for specifying footers to be appended to generated module files (`#808 `_) * see ``--modules-footer`` command line option * track version of modules tool + cleanup of ``modules.py`` (`#839 `_) * move actual ``run_cmd`` and ``run_cmd_qa`` implementations from ``tools.filetools`` into ``tools.run`` (`#842 `_, `#843 `_) * add support for generating modules that support recursive unloading (`#830 `_) * see ``--recursive-module-unload`` command line option * add flexibility support for specifying OS dependencies (`#846 `_) * alternatives can be specified, e.g. (``openssl-devel``, ``libssl-dev``) * initial (incomplete) support for easyconfig files in new format (v2.0) (`#810 `_, `#826 `_, `#827 `_, `#841 `_) * requires ``--experimental`` to be able to experiment with format v2 easyconfig files * various bug fixes, including: * fix problems with use of new-style configuration file (`#821 `_) * fix removal of old build directories, unless ``cleanupoldbuild`` easyconfig parameter is set (`#809 `_) * fix support for different types of repository path specifications (`#814 `_) * fix unit tests sensitive to ``$MODULEPATH`` and available easyblocks (`#845 `_) **easyblocks** * added **one** new `generic` easyblock: ``VSCPythonPackage`` (`#348 `_) * added support for **1** new software package that requires customized support: * netcdf4-python (`#347 `_) * various enhancements, including: * add support for installing recent tbb versions (`#341 `_) * use ``makeopts`` in the build step of the generic ``PythonPackage`` easyblock (`#352 `_) * define the ``$CMAKE_INCLUDE_PATH`` and ``$CMAKE_LIBRARY_PATH`` in the generic ``CMakeMake`` easyblock (`#351 `_, `#360 `_) * update Clang easyblock to support v3.4 (`#346 `_) * make sure Python is built with SSL support, adjust Python easyblock to pick up OpenSSL dep (`#359 `_) * note: providing OpenSSL via an OS package is still recommended, such that security updates are picked up * add support for recent netCDF versions (`#347 `_) * update SuiteSparse easyblock for new versions, and clean it up a bit (`#350 `_) * various bug fixes: * fix name of ``VersionIndependentPythonPackage`` easyblock, deprecate ``VersionIndependendPythonPackage`` easyblock (`#348 `_) * fix detection of machine architecture in FSL easyblock (`#353 `_) * fix bug in NWChem easyblock w.r.t. creating local dummy ``.nwchem`` file (`#360 `_) * make sure ``$LIBRARY_PATH`` is set for Intel compilers and Intel MPI, fix 64-bit specific paths (`#360 `_) **easyconfigs** * added example easyconfig files for **30** new software packages: * argtable (`#669 `_), Clustal-Omega (`#669 `_), Coreutils (`#582 `_), GMT (`#560 `_), gperftools (`#596 `_), grep (`#582 `_), h4toh5 (`#597 `_), libunwind (`#596 `_), Lmod (`#600 `_, `#692 `_), Lua (`#600 `_, `#692 `_), MAFFT (`#654 `_), Molekel (`#597 `_), NEdit (`#597 `_), netcdf4-python (`#660 `_), nodejs (`#678 `_), OCaml (`#704 `_), patch (`#582 `_), PhyML (`#664 `_), PRACE Common Production Environment (`#599 `_), protobuf (`#680 `_), python-dateutil (`#438 `_), sed (`#582 `_), sickle (`#651 `_), Tesla-Deployment-Kit (`#489 `_), TREE-PUZZLE (`#662 `_), VCFtools (`#626 `_), Vim (`#665 `_), vsc-mympirun-scoop (`#661 `_), vsc-processcontrol (`#661 `_), XZ (`#582 `_) * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * OpenSSL with ictce toolchain (`#703 `_) * various enhancements, including: * using more constants and templates (`#613 `_, `#615 `_) * specify OS dependency for SSL support, with OpenSSL dependency as fallback (`#703 `_) * various bug fixes, including: * fix unit tests after (internal) framework API changes (`#667 `_, `#672 `_) * fix homepage in vsc-mympirun easyconfig file (`#681 `_) * align OpenMPI easyconfigs (`#650 `_) * add additional source URL in Qt easyconfigs (`#676 `_) * specify correct $PATH specification and define ``$CHPL_HOME`` for Chapel (`#683 `_) EasyBuild v1.10.0 (December 24th 2013) -------------------------------------- feature + bugfix release **framework** * various enhancements, including: * set unique default temporary directory, add ``--tmpdir`` command line option (`#695 `_) * add support for computing and verifying source/patch file checksums (`#774 `_, `#777 `_, `#779 `_, `#801 `_, `#802 `_) * cfr. ``checksums`` easyconfig parameter * add support for `eb --confighelp`, which prints out an example configuration file (`#775 `_) * add initial support for ``eb`` tab completion in bash shells (`#775 `_, `#797 `_, `#798 `_) * see also https://github.com/easybuilders/easybuild/wiki/Setting-up-tab-completion-for-bash * note: may be quite slow for now * enhancements for using Lmod as modules tool (`#780 `_, `#795 `_, `#796 `_): * ignore Lmod spider cache by setting ``$LMOD_IGNORE_CACHE`` (requires Lmod 5.2) * bump required Lmod version to v5.2 * get rid of slow workaround for detecting module directories (only required for older Lmod versions) * fix version parsing for Lmod release candidates (rc) * improve integration with `lmod spider` by adding ``Description: `` prefix to ``module-whatis`` field of module * add ``--dry-short-short``/``-D`` and ``--search-short``/``-S`` command line options (`#781 `_) * add toolchain definition for 'gompic', intended for using with CUDA-aware OpenMPI (`#783 `_) * add support for specifying multiple robot paths (`#786 `_) * add various source URL constants, add support for ``%(nameletter)s`` and ``%(nameletterlower)s`` templates (`#793 `_) * add ``buildininstalldir`` easyconfig parameter (`#794 `_) * add ``--ignore-osdeps`` command line option (`#799 `_, `#802 `_) * various bug fixes, including: * enable ``-mt_mpi`` compiler flag if both ``usempi`` and ``openmp`` toolchain options are enabled (`#771 `_) * only use ``libmkl_solver*`` libraries for Intel MKL versions prior to 10.3 (`#776 `_) * fix toolchain support for recent Intel tools (`#785 `_) * code style fixes in ``main.py`` to adhere more to PEP8 (`#789 `_) * make sure ``easyblock`` easyconfig parameter is listed in ``eb -a`` (`#791 `_) * fix error that may pop up when using ``skipsteps=source`` (`#792 `_) **easyblocks** * added **one** new `generic` easyblock: ``VersionIndependendPythonPackage`` (`#329 `_, `#334 `_) * added support for **2** new software packages that require customized support: * Charmm (`#318 `_), GROMACS (`#335 `_, `#339 `_) * various enhancements, including: * fix support for recent SAMtools version (>= 0.1.19) (`#320 `_) * fix support for recent Intel tools (icc, ifort, imkl, impi) (`#325 `_, `#327 `_, `#338 `_) * enhance generic easyblock for installing RPMs (`#332 `_) * pick up ``preinstallopts`` in generic ``PythonPackage`` easyblock (`#334 `_) * enhance CP2K easyblock (libxc support, new versions) + style cleanup (`#336 `_) * various bug fixes: * use unwanted env var functionality to unset ``$MKLROOT`` rather than failing with an error (`#273 `_) * always include ``-w`` flag for preprocessor to suppress warnings that may break QuantumESPRESSO configure (`#317 `_) * link with multithreaded LAPACK libs for ESMF (`#319 `_) * extend ``noqanda`` list of patterns in CUDA easyblock (`#328 `_, `#337 `_) * add ``import _ctypes`` to Python sanity check commands to capture a common build issue (`#329 `_) * bug fixes in generic ``IntelBase`` easyblock (`#331 `_, `#333 `_, `#335 `_) * remove broken symlink ``$HOME/intel`` if present * fix use of gettempdir to obtain a common (user-specific) tmp dir to symlink ``$HOME/intel`` to * fix build of recent scipy versions with GCC-based toolchain (`#334 `_) * fix use of gettempdir to obtain common (user-specific) tmp dir for ``$HOME/.nwchemrc`` symlink (`#340 `_, `#342 `_) * extend ``noqanda`` list in Qt easyblock (`#342 `_) **easyconfigs** * added example easyconfig files for **18** new software packages: * BEDTools (`#579 `_, `#632 `_, `#635 `_), CAP3 (`#548 `_), CHARMM (`#584 `_), cutadapt (`#620 `_), ErlangOTP (`#556 `_, `#630 `_), Ghostscript (`#547 `_, `#632 `_), HTSeq (`#554 `_, `#632 `_), Jansson (`#545 `_), libjpeg-turbo (`#574 `_), Molden (`#566 `_), netloc (`#545 `_), o2scl (`#633 `_), packmol (`#566 `_), PP (`#405 `_), qtop (`#500 `_), TAMkin (`#566 `_), vsc-base (`#621 `_), vsc-mympirun (`#621 `_) * added easyconfigs for new toolchains (`#545 `_, `#609 `_, `#629 `_): * gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, ictce/6.1.5 * added additional easyconfigs for various supported software packages: version updates, different toolchains, ... * new versions of icc, ifort, imkl, impi (`#609 `_, `#629 `_) * large collection of ictce/5.3.0 easyconfigs (`#627 `_) * various enhancements, including: * extended list of Python packages as extensions to Python (`#625 `_) * add MPI-enabled version of GROMACS + easyconfigs using ictce (`#606 `_, `#636 `_) * clean up templating of ``source_urls`` (`#637 `_) * various bug fixes, including: * provide alternative download URL for Mesa (`#532 `_) * add Python versionsuffix in OpenBabel filenames (`#566 `_) * apply no-gets patch in all M4 v1.4.16 easyconfigs (`#623 `_) * fix patching of Python w.r.t. ``libffi``/``_ctypes`` issues (`#625 `_, `#642 `_) * bug fixes in GROMACS easyconfigs (`#606 `_) * change versionsuffix for non-MPI GROMACS easyconfigs to ``-mt`` * stop using 'CMakeMake' easyblock for GROMACS now that there's a dedicated GROMACS easyblock, which correctly specifies building against external BLAS/LAPACK libraries * fix Qt dependency for CGAL (`#642 `_) * fix libctl, libmatheval, Meep, PSI build issues caused by full paths in ``guile-config``/``python-config`` shebang (`#642 `_) * make sure HDF easyconfigs specify dedicated ``include/hdf`` include dir (`#642 `_) * this is required to avoid build issues with NCL, because HDF ships it's own ``netcdf.h`` * this also triggered removal of patch files for NCL that rewrote ``include/hdf`` to ``include`` * fix WPS v3.5.1 patch file after upstream source tarball was changed, supply checksum for verification (`#642 `_) EasyBuild v1.9.0 (November 17th 2013) ------------------------------------- feature + bugfix release **framework** * add support for Tcl environment modules (``modulecmd.tcl``) (`#728 `_, `#729 `_, `#739 `_) * special care was taken to make sure also the DEISA variant of ``modulecmd.tcl`` can be used * code refactoring to prepare for supporting two formats for easyconfig files (`#693 `_, `#750 `_) * this prepares the codebase for supporting easyconfig format v2.0 * some initial work on adding support for the new easyconfig format is included, but it's by no means complete yet * the current easyconfig format (now dubbed v1.0) is still the default and only supported format, for now * for more details, see https://github.com/easybuilders/easybuild/wiki/Easyconfig-format-two * various other enhancements, including: * include a full version of vsc-base (see the ``vsc`` subdirectory) (`#740 `_) * this is a first step towards switching to using vsc-base as a proper dependency * implement get_avail_core_count function in systemtools module that takes cpusets and co into account (`#700 `_) * the ``get_core_count`` function is now deprecated * add ``impmkl`` toolchain definition (`#736 `_) * make regtest more robust: put holds on jobs without dependencies, release holds once all jobs are submitted (`#751 `_) * add support for specifying multiple alternatives for sanity check paths (`#753 `_) * add ``get_software_libdir`` function to modules.py (along with unit tests) (`#758 `_) * add support for more file extensions and constants w.r.t. sources (`#738 `_, `#760 `_, `#761 `_) * add MPICH2 support in ``mpi_cmd_for`` function (`#761 `_) * various bug fixes, including: * fix checking of OS dependencies on Debian/Ubuntu that have ``rpm`` command available (`#732 `_) * make unit tests more robust w.r.t. non-writeable ``/tmp`` and loaded modules prior to starting unit tests (`#752 `_, `#756 `_) * also call ``EasyBlock``'s sanity check in ``ExtensionEasyblock`` if paths/commands are specified in easyconfig (`#757 `_) * set compiler family for dummy compiler, add definition of toolchain constant for dummy (`#759 `_) * other * add build status badges for master/develop branches to ``README`` (`#742 `_) * add scripts for installing EasyBuild develop version or setting up git development environment (`#730 `_, `#755 `_) **easyblocks** * added support for **8** new software packages that require customized support: * Allinea DDT/MAP (`#279 `_), ARB (`#291 `_), GenomeAnalysisTK (`#278 `_), OpenBabel (`#305 `_, `#309 `_), picard (`#278 `_), PyQuante (`#297 `_), Scalasca v1.x (`#304 `_), Score-P (`#304 `_) * the Score-P easyblock is also used for Cube 4.x, LWM2, OTF2, and Scalasca v2.x * various enhancements, including: * add support building ScaLAPACK on top of MPICH2, required for gmpolf toolchain (`#274 `_) * add support to ConfigureMake easyblock to customize configure ``--prefix`` option (`#287 `_) * add support for specifying install command in Binary easyblock (`#288 `_) * enhance CMakeMake easyblock to specify srcdir via easyconfig parameter, and to perform out-of-source builds (`#303 `_) * various bug fixes: * use correct configure flag for Szip in HDF5 easyblocks, should be ``--with-szlib`` (`#286 `_, `#301 `_) * add support for serial HDF5 builds (`#290 `_, `#301 `_) * enhance robustness of Qt easyblock w.r.t. interactive configure (`#295 `_, `#302 `_) * enhance support for picking up license specification via environment variables (`#298 `_, `#307 `_) * extend list of values for ``$CPATH`` in libint2 easyblock (`#300 `_) * fix ``extra_options`` ``super`` call in Clang easyblock (`#306 `_) * add support in Boost easyblock to specify toolset in easyconfig file (`#308 `_) * other: * add build status badges for master/develop branches to README (`#289 `_) **easyconfigs** * added example easyconfig files for **58** new software packages: * Allinea (`#468 `_), ARB + dependencies (`#396 `_, `#493 `_, `#495 `_), arpack-ng (`#451 `_, `#481 `_), CDO (`#484 `_, `#521 `_), Cube (`#505 `_), ed (`#503 `_), FLTK (`#503 `_), GenomeAnalysisTK (`#467 `_), GIMPS (`#527 `_), GTI (`#511 `_), IPython (`#485 `_, `#519 `_), LWM2 (`#510 `_), MPICH2 (`#460 `_), MUST (`#511 `_), ncdf (`#496 `_, `#522 `_), OPARI2 (`#505 `_), OpenBabel (`#504 `_, `#524 `_), OTF (`#505 `_), OTF2 (`#505 `_), PandaSEQ (`#475 `_), ParaView (`#498 `_, `#514 `_), ParFlow (`#483 `_, `#520 `_), PCC (`#486 `_, `#528 `_), PDT (`#505 `_), picard (`#467 `_), PnMPI (`#511 `_), PyQuante (`#499 `_, `#523 `_), pysqlite (`#519 `_), Scalasca (`#505 `_), Score-P (`#505 `_), SDCC (`#486 `_, `#528 `_), Silo (`#483 `_, `#520 `_), Stride (`#503 `_), SURF (`#503 `_), TCC (`#486 `_, `#528 `_) * ARB dependencies (23): fixesproto, imake, inputproto, kbproto, libICE, libSM, libX11, libXau, libXaw, libXext, libXfixes, libXi, libXmu, libXp, libXpm, libXt, lynx, motif, printproto, Sablotron, xbitmaps, xextproto, xtrans * added easyconfigs for new gmpich2/1.4.8, gmpolf/1.4.8 and goolf/1.6.10 toolchains (`#460 `_, `#525 `_, `#530 `_) * added additional easyconfigs for various software packages (list too long to include here) * version updates, different toolchains, ... * various bug fixes, including: * enable building of shared libraries for MPICH (`#482 `_) * fix HDF configure option for Szip, should be ``--with-szlib`` (`#533 `_) * for HDF5, this issue is fixed in the HDF5 easyblock * other * add build status badges for master/develop branches to README (`#490 `_) EasyBuild v1.8.2 (October 18th 2013) ------------------------------------ bugfix release **framework** * fix regular expression used for obtaining list of modules from ``module avail`` (`#724 `_) * modules marked as default were being hidden from EasyBuild, causing problems when they are used as dependency **easyblocks** * fix installing of EasyBuild with a loaded EasyBuild module (`#280 `_) * this is important to make upgrading to the latest EasyBuild version possible with a bootstrapped EasyBuild **easyconfigs** * port thread pool patch to PSI 4.0b4 and include it to avoid hanging tests (`#471 `_) EasyBuild v1.8.1 (October 14th 2013) ------------------------------------ bugfix release * various bug fixes, including: * fix bugs in regtest procedure (`#713 `_) * force 2nd and 3rd attempt of build in case 1st attempt failed * fix copying of install log to install directory (`#716 `_) * only create first source path if multiple paths are specified (`#718 `_) * detect failed PBS job submission by checking obtained job ID for ``None`` value (`#713 `_, `#717 `_, `#719 `_, `#720 `_) **easyblocks** * various bug fixes: * fix problems in PSI easyblock causing build to fail (`#270 `_) * fix issues with running NWChem test cases, fail early in case broken symlink is present (`#275 `_) **easyconfigs** * added additional easyconfigs for various software packages (`#457 `_): * Boost, bzip2, libreadline, ncurses, PSI, Python, zlib * various bug fixes, including: * fix faulty easyconfig file names for HPCBIOS_Math, MUSCLE, XML-LibXML and YAML-Syck (`#459 `_, `#462 `_) * stop (re)specifying default maximum ratio for failed tests in NWChem easyconfig (`#457 `_) EasyBuild v1.8.0 (October 4th 2013) ----------------------------------- feature + bugfix release **framework** * add support for using alternative module naming schemes (`#679 `_, `#696 `_, `#705 `_, `#706 `_, `#707 `_) * see https://github.com/easybuilders/easybuild/wiki/Using-a-custom-module-naming-scheme for documentation * module naming scheme classes that derive from the 'abstract' ``ModuleNamingScheme`` class can be provided to EasyBuild * the Python module providing the class must be available in the ``easybuild.tools.module_naming_scheme`` namespace * a function named ``det_full_module_name`` must be implemented, that determines the module name in the form of an string based on the supplied dictionary(-like) argument * the active module naming scheme is determined by EasyBuild configuration option ``--module-naming-scheme`` * for now, only the ``name``/``version``/``versionsuffix``/``toolchain`` easyconfig parameters are guaranteed to be provided * consistently providing all easyconfig parameters (i.e., also for dependencies) requires more work (see `#687 `_) * implementing this involved a number of intrusive changes: * the API of the modules.py module needed to be changed, breaking backward compatibility * the function for which the signatures were modified are considered to be internal to the framework, so this should have very minor impact w.r.t. easyblocks not included with EasyBuild * affected functions include: ``available``, ``exists``, ``show``, ``modulefile_path``, ``dependencies_for`` * the format for specifying dependencies was extended, to allow for specifying a custom toolchain * this allows to fix inaccurate dependency specifications, for example: ``('OpenMPI', '1.6.4-GCC-4.7.2')" to "('OpenMPI', '1.6.4', '', ('GCC', '4.7.2'))`` * see also `easyconfigs#431 `_ * the recommended version for Lmod was bumped to v5.1.5 * using earlier 5.x version still works, but may be very slow when 'available' is used, due to bugs and a missing feature in Lmod versions prior to v5.1.5 on which we rely * various other enhancements, including: * only (try to) change group id if it is different from what is wanted (`#685 `_) * added toy build unit test (`#688 `_) * support for specifying a list of source paths in EasyBuild configuration (`#690 `_, `#702 `_) * add function to determine CPU clock speed in ``systemtools.py`` (`#694 `_, `#699 `_) * various bug fixes, including: * avoid importing toolchain modules over and over again to make toolchain constants available in toolchain module (`#679 `) * only change the group id if current gid is different from what we want in ``adjust_permissions`` function (`#685 `) * restore original environment after running 'module purge' (`#698 `) * important sidenote: this results in resetting the entire environment, and has impact on the sanity check step; * any environment variables that are set before the EasyBlock.sanity_check_step method fires, are no longer there when the sanity check commands are run (cfr. `easyblocks#268 `_) **easyblocks** * added **one** new `generic` easyblock: ``BinariesTarball`` (`#255 `_) * added support for **5** new software packages that require customized support: * DB (`#226 `_), FDTD Solutions (`#239 `_), FoldX (`#256 `_), Mathematica (`#240 `_), MUMPS (`#262 `_) * various enhancements, including: * support optionally running configure in generic ``MakeCp`` easyblock (`#252 `_) * enhanced Clang easyblock to support building Clang 3.3 (`#248 `_) * add support for ``$INTEL_LICENSE_FILE`` specifying multiple paths (`#251 `_) * enhanced ATLAS easyblock to support building ATLAS 3.10.1 (`#258 `_) * various bug fixes: * add zlib lib dir in link path dirs for WPS (`#249 `_) * stop using deprecated ``add_module`` function in imkl easyblock (`#250 `_) * fixed PSI easyblock w.r.t. support for building plugins (`#254 `_, `#269 `_) * move OS check for Clang to ``check_readiness_step``, to allow a build job to be submitted from SL5 (`#263 `_, `#264 `_) * enable verbose build for DOLFIN, to allow for proper debugging if the build fails (`#265 `_) * make sure ``$LDFLAGS`` and ``$INSTANT_*_DIR`` env vars are set for DOLFIN sanity check commands (`#268 `_) * this is required after resetting the environment after running module purge (see framework release notes) * don't try to load module in LAPACK test-only build (`#264 `_, `#266 `_) **easyconfigs** * added example easyconfig files for **9** new software packages: * BOINC (`#436 `_), DB (`#343 `_, `#449 `_), fastahack (`#374 `_), FDTD Solutions (`#387 `_), FoldX (`#440 `_, `#442 `_), Mathematica (`#394 `_), Mesquite (`#447 `_), MUMPS (`#447 `_), ParMGridGen (`#447 `_) * added additional easyconfigs for goalf, gompi, ClangGCC, cgmvapich2, cgmvolf toolchains (`#350 `_, `#441 `_) * added additional easyconfigs for various software packages: * ATLAS, Bison, bzip2, Clang, CMake, cURL, EasyBuild, expat, FFTW, GDB, gettext, git, HPL, LAPACK, libreadline, M4, METIS, MVAPICH2, Mercurial, ncurses, OpenBLAS, OpenMPI, ParMETIS, Python, ScaLAPACK, SCOTCH, Valgrind, zlib * various 'bug' fixes, including: * fix source URL for lockfile in Python easyconfigs (`#428 `_) * correct dependency specifications w.r.t. versionsuffix and toolchain (`#431 `_) * this is required to support building the affected easyconfigs with a custom module naming scheme * correct PSI patch file to avoid errors w.r.t. memcpy not being in scope (`#446 `_) * fix gettext build with adding ``--without-emacs`` configure options, add gettext as dependency for a2ps (`#448 `_) * exclude EMACS support in a2ps because of build failures (`#452 `_) EasyBuild v1.7.0 (September 2nd 2013) ------------------------------------- feature + bugfix release **framework** * various enhancements, including: * also search for patch files in directory where easyconfig file is located (`#667 `_) * reduce false positives in reporting of possible errors messages (`#669 `_) * make module update ``$ACLOCAL`` if a share/aclocal subdir is found (`#670 `_) * add ``unwanted_env_vars`` easyconfig parameter to list environment variables to unset during install procedure (`#673 `_) * add support for updating list easyconfig values (next to string values) (`#676 `_) * add ``--dry-run`` command line option which prints installation overview for specified easyconfig files (`#677 `_) * various bug fixes, including: * ensure that all extensions are listed in ``$EBEXTSLISTX`` set by module, also when using ``--skip`` (`#671 `_) * report reason for failed sanity check for extensions (`#672 `_, `#678 `_) * fix ``--list-toolchains`` command line option (`#675 `_) **easyblocks** * added support for **3** new software packages that require customized support: * Libint2 (`#236 `_), Qt (`#210 `_), Rosetta (`#218 `_) * various enhancements, including: * allow building OpenFOAM without 3rd party tools (`#230 `_) * also add sitelib path to ``$PERL5LIB``, refactor code to add generic ``get_site_suffix`` function (`#232 `_, `#233 `_) * support building imkl FFT wrappers using MVAPICH2 MPI library (`#234 `_) * remove libnpp from CUDA sanity check to support installing CUDA v5.5 (`#238 `_) * pick up ``$INTEL_LICENSE_FILE`` for Intel tools, if it is set (`#243 `_) * note: gets preference over ``license_file`` easyconfig parameter * various bug fixes: * call WRF build script with '``tcsh