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EasyBuild v4.7.0
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@boegel boegel released this 09 Jan 19:12
· 36 commits to develop since this release
easybuild-v4.7.0
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boegel Kenneth Hoste
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EasyBuild v4.7.0 is primarily a feature release, but it also includes various minor bug fixes and enhancements.

Highlights for this release are listed below. More details are available in the release notes which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with (***))

  • also run unit tests with Python 3.11;

  • add support for checksums specified in external checksums.json file;

  • take into account custom configuration options specified in easystack files - see also docs;

  • add support for using --output-format=md (MarkDown);

  • add support for postinstallmsgs;

  • add gfbf as subtoolchain of foss;

  • make iimkl toolchain aware of intel-compilers;

  • add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage + JuliaBundle;

  • updates and enhancements for various generic easyblocks, incl. ConfigureMake, PythonPackage;

  • (***) updates and enhancements for various software-specific easyblocks: BerkeleyGW, Clang, Clang-AOMP, ESMF, libxml2, LLVM, OpenCV, OpenMPI, PETSc, QScintill, TensorFlow, Xmipp;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • print deprecation warning with running EasyBuild with Python 2;

  • various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format;

  • vendor distutils.version.LooseVersion as easybuild.tools.LooseVersion
    (since distutils is deprecated in Python 3.10, to be removed in Python 3.12);

  • auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0;

  • use -march=x86-64 -mtune=generic instead of -xSSE2 when using Intel oneAPI compilers;

  • drop support for easystack files using 'software' top-level key;

  • make PythonPackage easyblock compatible with --sanity-check-only by loading module early during sanity check step;

  • (***) update HDF5 easyblock to use --enable-threadsafe configure option to make C API thread safe;

  • (***) bug fixes for various software-specific easyblocks: ANSYS, Clang, MRtrix, PyTorch;

Supported software

New version of common toolchains: foss/2022b, intel/2022b

Support for installing 107 new software packages has been added, including (but not limited to):

  • Alfred
  • bamFilters
  • CAT-BAT
  • CloudCompare
  • COBRApy
  • CUDA-Samples
  • DeepLabCut
  • DRAGMAP
  • ESM-2
  • HighFive
  • IJulia
  • KaHIP
  • LHAPDF
  • Magics
  • MEMOTE
  • MONAI
  • MOOSE
  • MultilevelEstimators
  • napari
  • nf-core-mag
  • OmegaFold
  • pyccel
  • PyDamage
  • pyWannier90
  • scvi-tools
  • SELFIES
  • SISSO++
  • spaCy
  • Squidpy
  • TBA
  • trimesh
  • UCX-ROCm

This brings the total number of supported software packages to 2,904 (excluding extensions)!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

  • AOCC 4.0.0
  • CDO 2.1.1
  • CubeGUI/CubeLib/CubeWriter 4.8
  • CUDA 11.8.0 + 12.0.0
  • deepdiff 5.8.1
  • FLANN 1.9.1
  • GATK 4.3.0.0
  • GDCM 3.0.20
  • Ghostscript 10.0.0
  • GRASS 8.2.0
  • JasPer 4.0.0
  • libspatialite 5.0.1
  • LLVM 15.0.5
  • Mesa 22.2.4
  • mold 1.7.1
  • MRChem 1.1.1
  • ncbi-vdb 3.0.0
  • nglview 3.0.3
  • nodejs 18.12.1
  • Octave 7.1.0
  • OpenFOAM 10
  • OpenFold 1.0.1
  • OpenMolcas 22.10
  • OpenStackClient 6.0.0
  • PAPI 7.0.0,
  • PETSc 3.17.4
  • pyproj 3.4.0
  • Python 3.10.8
  • PyTorch 1.12.1
  • PyTorch-Geometric 2.1.0
  • QGIS 3.28.1
  • Qt5 5.15.7
  • QtPy 2.2.1
  • ReFrame 3.12.0
  • scanpy 1.9.1
  • Score-P 8.0
  • SignalP 6.0g
  • SLEPc 3.17.2
  • SNAP 2.0.1
  • SpaceRanger 2.0.0
  • SuperLU_DIST 8.1.0
  • tensorboardX 2.5.1
  • TensorFlow 2.8.4
  • tesseract 5.3.0
  • Valgrind 3.20.0
  • Vim 9.0.0950
  • VTK 9.2.2
  • wandb 0.13.6
  • WebKitGTK+ 2.37.1
  • WPS/WRF 4.4
  • wxPython 4.2.0
  • X11 20221110
  • Xmipp 3.22.07

These changes result from various contributions, made by 29 different contributors:

  • 42 merged pull requests for EasyBuild framework
  • 36 merged pull requests for easyblocks
  • 469 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.7.0, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17065 # use easyconfig from PR #17065

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