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EasyBuild v4.6.1
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@boegel boegel released this 12 Sep 07:54
· 91 commits to develop since this release
easybuild-v4.6.1
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EasyBuild v4.6.1 is primarily a bugfix and update release, but it also includes various minor 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 (***))

  • run python in the same process as eb wrapper script by using exec (which improves startup performance of eb command);

  • reduce the number of command line options for cmake command in CMakeMake generic easyblock;

  • enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when return_output_ec=True is used;

  • updates and enhancements for various software-specific easyblocks: GROMACS, LAMMPS, libQGLViewer, NVHPC, PyTorch;

  • (***) add extra symlinks and sanity checks for libtinfo in ncurses;

  • speed up OpenMPI 4.1.4 configure by not running autogen.pl --force, but only running required Autotools commands;

Prominent bug fixes & changes

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

  • use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (rather than assuming that CMake is loaded as a build dependency);

  • 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;

  • make Amber easyblock aware of FlexiBLAS;

  • tweak Amber(Tools) easyblock to run tests from top-level directory, and enable running of tests for AmberTools v20 + v21;

  • work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong;

  • various fixes for installing PyTorch on POWER systems;

  • (***) 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;

  • (***) use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option);

  • (***) add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs;

  • (***) add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9;

  • simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency;

  • (***) add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 and 2021;

  • (***) fix checksum for Stacks v2.62 (due to silent re-release without version bump);

  • (***) consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs;

  • (***) update Java/11 to 11.0.16 and Java/17 to 17.0.4;

Supported software

Support for installing 37 new software packages has been added, including (but not limited to):

  • BigDFT
  • colossalai
  • Dakota
  • FastFold
  • how_are_we_stranded_here
  • libmad
  • MetaMorpheus
  • muMerge
  • olaFlow
  • OpenFAST
  • OpenFold
  • pyGenomeTracks
  • RheoTool
  • Satsuma2
  • UCC-CUDA
  • VESTA

This brings the total number of supported software packages to 2,773 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AmberTools 22.3
  • BCFtools 1.15.1
  • binutils 2.39
  • BLAST+ 2.13.0
  • CDO 2.0.5
  • CoordgenLibs 3.0.1,
  • Elk 8.5.2,
  • FFmpeg 4.4.2 + 5.0.1
  • FreeSurfer 7.3.2
  • GATE 9.2
  • GCC(core) 12.2.0
  • GDB 12.1
  • gnuplot 5.4.4
  • Graphviz 5.0.0
  • HDF5 1.12.2
  • HTSlib 1.15.1
  • Hypre 2.25.0,
  • jax 0.3.14,
  • LAMMPS 23Jun2022
  • Libint 2.7.2
  • maeparser 1.3.0
  • matplotlib 3.5.2
  • MATSim 14.0
  • medaka 1.6.0
  • Megalodon 2.5.0
  • MetaEuk 6,
  • MUMPS 5.5.1
  • netCDF-Fortran 4.6.0
  • ont-remora 1.0.0
  • OpenFOAM v2206
  • ParaView 5.10.1
  • Perl 5.36.0
  • Pyomo 6.4.2
  • PyStan 3.5.0
  • PyYAML 6.0
  • scikit-bio 0.5.7
  • scikit-learn 1.1.2
  • SCOTCH 7.0.1
  • spglib-python 2.0.0
  • SUMO 1.14.1
  • Valgrind 3.19.0
  • ViennaRNA 2.5.1
  • wxPython 4.1.1
  • zfp 1.0.0

These changes result from various contributions, made by 25 different contributors:

  • 16 merged pull requests for EasyBuild framework
  • 20 merged pull requests for easyblocks
  • 266 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 16240 # use easyconfig from PR #16240

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