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@boegel boegel released this 07 Sep 09:11
· 212 commits to develop since this release
easybuild-v4.4.2
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EasyBuild v4.4.2 is mostly a bugfix and update release, but also includes several 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 (***))

  • add --filter-ecs configuration option to filter out easyconfigs from set of easyconfigs to install;

  • also define $BLAS_SHARED_LIBS & co in build environment (analogous to $BLAS_STATIC_LIBS);

  • add get_cuda_cc_template_value method to EasyConfig class;

  • pick up $MODULES_CMD to facilitate using Environment Modules 4.x as modules tool;

  • add 4 new software-specific easyblocks for CRISPR-DAV, jaxlib, ORCA, RepeatModeler;

  • update software-specific easyblocks for ABAQUS, Amber, BerkeleyGW, Clang, CP2K, ESMF, FreeFEM, GROMACS, LAMMPS, numexpr, numpy, Molpro, OpenFOAM, TensorFlow, VTune, WIEN2k;

  • enable make check and sanity check commands for OpenMPI;

  • (***) make sure AOCC commands like clang/flang pick up GCCcore as GCC toolchain;

  • (***) create CMakeConfig files for tbb >= 2020;

  • (***) generate and install pkg-config files for OpenSSL wrapper;

  • added easyconfig for foss/2021.07 (candidate for foss/2021b) and iomkl/2021a toolchains;

  • (***) add various extensions to recent R v4.x easyconfigs;

Prominent bug fixes & changes

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

  • (***) don’t add directory that doesn't include any files to $PATH or $LD_LIBRARY_PATH;

  • make sure git clone with a tag argument actually downloads a tag;

  • honor --ignore-test-failure in PythonPackage easyblock;

  • reset runtest to None in CMakePythonPackage easyblock;

  • let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly;

  • use ${BLAS,LAPACK}_SHARED_LIBS in GROMACS easyblock for FlexiBLAS-based toolchains;

  • (***) add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX);

  • (***) use correct GTK+ version for OpenCV based on dependencies;

  • (***) set $I_MPI_ROOT correctly for 2021.x in impi easyblock (only requires --module-only to fix);

  • (***) keep symlinks in cuDNN installations;

  • (***) fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost;

  • (***) add missing Bio-Search-hmmer dependency for prokka;

  • (***) patch MaxBin2 Perl script to use provided Perl dependency;

  • (***) avoid MPICXX dependency in SimpleElastics ITK;

  • (***) add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault);

  • (***) enable EGL in recent libepoxy easyconfigs;

  • (***) update tensorflow-probability easyconfigs to include --release flag in installopts;

  • (***) fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2;

  • update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check;

  • (***) create libtinfo symlinks in easyconfigs for ncurses with system toolchain;

Other changes

  • simplify Boost easyblock;

  • remove deprecated options from PythonPackage easyblock;

  • use custom ORCA easyblock in easyconfigs for ORCA v4.x;

  • rename NINJA to TWL-NINJA to avoid nameclash;

  • rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda toolchains, to ensure that get_software_root('CUDA') used in easyblocks works;

Supported software

Support for installing 79 new software packages has been added, including (but not limited to):

  • AlphaFold
  • AUTO-07p
  • biogeme
  • CellRank
  • Coin
  • CRISPR-DAV
  • DistributedStream
  • freebayes
  • GIMP (#13216)
  • GOATOOLS
  • GTK2 + GTK3
  • hipSYCL
  • jax
  • Kalign
  • Maude
  • Mish-Cuda
  • OSPRay
  • pandapower
  • pangolin
  • PYPOWER
  • pysamstats
  • QCxMS
  • RepeatModeler
  • SoQt
  • SpectrA
  • SyRI
  • UShER
  • Vampire
  • VisPy
  • Yices

This brings the total number of supported software packages to 2,467!

An up-to-date list of supported software is available here.

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

  • AOCC 3.1.0
  • ASE 3.22.0
  • Biopython 1.79
  • Boost 1.76.0
  • Clang 12.0.1
  • CUDA 11.4.1
  • cuDNN 8.2.2.26
  • DIAMOND 2.0.11
  • ESMF 8.1.1
  • GCC(core) 11.2.0
  • GDRCopy 2.3
  • GenomeTools 1.6.2
  • GPAW 21.6.0
  • GROMACS 2021.3
  • Horovod 0.22.1
  • ImageMagick 7.1.0
  • IMOD 4.11.5
  • IPython 7.26.0
  • Java 16
  • likwid 5.2.0
  • LLVM 12.0.1
  • matplotlib 3.4.2
  • Mesa 21.1.7
  • Metal 2020-05-05
  • MPICH 3.4.2
  • NCCL 2.10.3
  • NCO 5.0.1
  • nodejs 14.17.6
  • NVHPC 21.7
  • OpenBLAS 0.3.17
  • OpenFOAM 9 + OpenFOAM v2106
  • OpenMM 7.5.1
  • OpenMolcas 21.06
  • ParaView 5.9.1
  • Perl 5.34.0
  • PETSc 3.15.1
  • petsc4py 3.15.0
  • PLUMED 2.7.2
  • PMIx 4.1.0
  • PostgreSQL 13.3
  • PyQt5 5.15.4
  • Python 3.9.6
  • R-bundle-Bioconductor 3.13
  • ReFrame 3.8.0
  • Rust 1.54.0
  • Scalasca 2.6
  • SLEPc 3.15.1
  • slepc4py 3.15.1
  • Spack 0.16.2
  • StringTie 2.1.7
  • TensorFlow 2.6.0,
  • UCX 1.11.0 + UCX-CUDA 1.11.0
  • WIEN2k 21.1
  • WPS 4.2
  • WRF 4.3
  • X11 20210802
  • xarray 0.19.0

These changes result from various contributions, made by 23 different contributors:

  • 29 merged pull requests for EasyBuild framework
  • 50 merged pull requests for easyblocks
  • 459 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.4.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 13918 # use easyconfig from PR #13918

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