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@boegel boegel released this 20 Mar 17:34
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easybuild-v4.7.1
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EasyBuild v4.7.1 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

  • Various small enhancements and bug fixes to EasyBuild framework, easyblocks, and easyconfigs;

  • Easyconfigs for various recent software versions: AlphaFold 2.3.0, HDF5 1.14.0, networkx 3.0, TensorFlow v2.11.0, Trilinos 13.4.1, ...;

  • Additional easyconfigs using the latest 2022b toolchains, incl. SciPy-bundle 2023.02 with gfbf/2022b (subtoolchain of foss/2022b);

  • Support for installing 99 new software applications and libraries;

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 (***))

  • add support for %(start_dir)s easyconfig template;

  • add pre/post extension hook that is triggered before/after individual extension installations;

  • enforce absolute paths as start dir of extensions;

  • updates and enhancements for various generic easyblocks: GoPackage, MesonNinja, PythonPackage;

  • updates and enhancements for various software-specific easyblocks: EasyBuildMeta, ELPA, Maple, Mathematica, NAMD, pybind11, Python, QScintilla, scipy, TensorFlow, Trilinos;

  • (***) add additional extensions to Python 3.10.8 (required for scipy test suite) (see --skip);

  • (***) add extensions to Perl 5.32.1 (see --skip);

  • (***) add additional extensions to R 4.2.1 (see --skip);

  • (***) add additional extensions to Bioconductor 3.15 (see --skip);

  • (***) enhance OpenFold 1.0.1 for standalone usage;

  • (***) add SDL2 dependency for FFmpeg 5.0.1 to build ffplay;

  • (***) add ffnvcodec build dependency to all recent FFmpeg easyconfigs;

  • (***) set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs;

  • (***) add missing zstd dep to Boost;

Prominent bug fixes & changes

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

  • restore initial environment before processing each easystack item (support for easystack files is still experimental);

  • various fixes and improvements for the EasyBuild framework test suite;

  • (***) fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions;

  • (***) fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets;

  • (***) fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x;

  • bug fixes for various generic easyblocks: CMakeMake, CMakePythonPackage, PythonPackage, PythonBundle;

  • bug fixes for various software-specific easyblocks: FlexiBLAS, netCDF, NVHPC, PyTorch;

  • (***) add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug;

  • (***) add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b;

  • (***) replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs;

  • (***) update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (see --skip);

  • (***) replace src include path with installation dir for HDF5;

  • (***) use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API;

  • (***) add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2;

  • (***) fix postinstallcmds in shovill easyconfigs;

  • (***) add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1

  • (***) add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs;

  • (***) enable -fPIC in GEOS 3.11.1 (required by GDAL);

  • add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes);

  • rename some software names in existing easyconfigs, or archive these easyconfigs, to avoid case-insensitive name clashes;

Supported software

Support for installing 99 (!) new software packages has been added, including (but not limited to):

  • CatLearn
  • Cellpose
  • chemprop
  • cuSPARSELt
  • DensPart
  • dorado
  • fastjet
  • finder
  • genomepy
  • grid
  • Health-GPS
  • HiCMatrix
  • Inferelator
  • kineto
  • LASSO-Python
  • netMHCII
  • PfamScan
  • plot1cell
  • PyTorch-Ignite
  • rapidNJ
  • scArches
  • scib
  • smfishHmrf
  • Strainberry
  • VirSorter2
  • YODA

This brings the total number of supported software packages to 2,995 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AlphaFold 2.3.0
  • AUGUSTUS 3.5.0
  • BCFtools 1.17
  • Biopython 1.81
  • Boost 1.81.0
  • CFITSIO 4.2.0
  • CUDA 12.1.0
  • DIAMOND 2.1.0,
  • epiScanpy 0.4.0
  • FFmpeg 5.1.2
  • GDAL 3.6.2
  • GPyTorch 1.9.1
  • h5py 3.8.0
  • HTSlib 1.17
  • Hypre 2.27.0
  • intel/2022.12 (incl. intel-compilers 2023.0.0, impi 2021.8.0, imkl 2023.0.0)
  • jax 0.4.4
  • MaSuRCA 4.1.0
  • MATLAB 2022b
  • MDAnalysis 2.4.2
  • mpi4py 3.1.4
  • NetLogo 6.3.0
  • networkx 3.0
  • numba 0.56.4
  • NVHPC 23.1
  • OpenMPI 4.1.5
  • PLUMED 2.8.1
  • pyGenomeTracks 3.8
  • PySCF 2.1.1
  • Python 3.11.2
  • R 4.2.2
  • ReFrame 4.0.5
  • ROOT 6.22.08
  • SAMtools 1.17,
  • scikit-learn 1.2.1
  • SciPy-bundle 2023.02,
  • SPAdes 3.15.5
  • TensorFlow 2.11.0
  • Trilinos 13.4.1
  • Xerces-C++ 3.2.4

These changes result from various contributions, made by 30 different contributors:

  • 36 merged pull requests for EasyBuild framework
  • 34 merged pull requests for easyblocks
  • 386 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17568 # use easyconfig from PR #17568

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