EasyBuild v4.3.2 Release Notes

Release Date: 2020-12-10 // over 3 years ago

Previous changes from v4.3.1

  • EasyBuild v4.3.1 is primarily a bugfix/update release,
    but also includes some minor enhancements.

    ๐Ÿš€ All details are available in the release notes, with links to the respective pull requests.

    ๐Ÿ›  Prominent bug fixes

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

    • ๐Ÿ›  fix compatibility of EasyBuild with Python 3.9;
    • ๐Ÿ›  fix various issues when using "sources" to specify extension sources;
    • (***) add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS 0.3.3 through 0.3.9;
    • (***) fix source for SQLite 3.31.1;
      => incorrect source URL and filename caused SQLite 3.29.0 to be installed instead;
    • (***) configure OpenMPI 4.x (foss/2020a) with --without-verbs when using UCX;
      ๐Ÿ‘€ => this fixes a warning message that occurs when using OpenMPI on systems with Infiniband, see also https://www.open-mpi.org/faq/?category=all#ofa-device-error;
    • (***) add patch for OpenMPI 3.1.4 (foss/2019b) adding device parameters for ConnectX-6;
      โš  => fixes warning about missing device parameters on systems with recent Infiniband cards;
    • (***) enhance OpenFOAM easyblock to add symlinks for libraries to ensure MPI versions have preference over dummy versions;
      ๐Ÿ”ง => fixes broken tools (like snappyHexMesh) in OpenFOAM installation if EasyBuild was configured to use RPATH linking (via --rpath);
    • (***) patch out bug in collective primitive in TensorFlow 2.2.0;
    • (***) remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (so pip can find SIP);
    • (***) remove GLog and GFlags dependencies from PyTorch easyconfigs (known to cause problems on POWER);
    • (***) fix dependency on Bowtie of v0.x in seq2HLA easyconfigs;
    • (***) add protobuf-python as a dependency for PyTorch 1.6 (required by caffe2.python module);
    • (***) add ncurses runtime dependency to Clang easyconfigs;
    • (***) fix PyVCF easyconfig, only supports Python 2;
    • (***) remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0;
    • ๐Ÿ‘‰ make OpenBLAS installation procedure respect the parallelism set by EasyBuild;
    • ๐Ÿ›  fix checksum in NAMD 2.12 easyconfigs + add source URL;
    • ๐Ÿ“‡ rename jupyterhub to JupyterHub;

    Highlighted enhancements

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

    • โœ… publish test reports to easybuild-easyblocks pull request when --include-easyblocks-from-pr is used without --from-pr;
    • โž• add support for including easyblocks from multiple PRs at once via --include-easyblocks-from-pr;
    • โšก๏ธ update TensorFlow easyblock to:
      • put Bazel build files in build directory;
      • avoid unnecessary runtime patching;
      • add XLA build support;
      • leverage installed OpenSSL/BoringSSL when cURL is used as a dependency;
    • ๐Ÿ”ง make easyblock for installing CMake aware of --sysroot EasyBuild configuration setting;
    • โšก๏ธ update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0);
    • (***) use more EasyBuild installed dependencies for TensorFlow 2.2.0;
    • (***) add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a);
    • (***) add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
      โœ… => use "eb --rebuild --skip" to install the missing extensions;
    • (***) make libtirpc easier to use as replacement of rpc in glibc (for RHEL8);
    • (***) build LibTIFF with -fPIC;

    ๐Ÿ‘Œ Supported software

    ๐Ÿ‘Œ Support for installing 75 new software packages has been added, including:

    • CFDEMcoupling
    • COMSOL
    • DIRAC
    • โœ… FRUIT (Fortran Unit Test Framework)
    • GDRCopy
    • mauveAligner
    • MyCC
    • Nek5000
    • ๐Ÿ‘ NVHPC (NVIDIA HPC SDK) + support using it as a toolchain
    • OPERA-MS
    • PyOpenCL
    • QtPy
    • SeqKit

    ๐Ÿ“ฆ This brings the total number of supported software packages to 2,134!
    โœ… An up-to-date list of supported software is available here.

    Easyconfigs for fosscuda/2020a and intelcuda/2020a toolchains have been added.

    โšก๏ธ Various software updates have been added, including:

    • ABINIT 9.2.1
    • Bazel 3.6.0
    • CUDA 11.0.2
    • GROMACS 2020.3
    • GTK+ 3.24.23
    • HMMER 3.3.1
    • Horovod 0.20.3
    • IPython 7.18.1
    • LLVM 11.0.0
    • medaka 1.1.3
    • Mesa 20.2.1
    • PSI4 1.3.2
    • PyQt5 5.15.1
    • PyRETIS 2.5.0
    • Python 3.8.6
    • ReFrame 3.2
    • Spyder 4.1.5
    • Taiyaki 5.1.0
    • TINKER 8.8.1
    • TensorFlow 2.3.1 (with foss/2019b, fosscuda/2019b, foss/2020a)
    • TRIQS 3.0.0
    • UCX 1.9.0
    • X11 20201008

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

    • ๐Ÿ”€ 21 merged pull requests for EasyBuild framework
    • ๐Ÿ”€ 32 merged pull requests for easyblocks
    • ๐Ÿ”€ 287 merged pull requests for easyconfigs

    ๐Ÿš€ Thanks to everyone who contributed to this release in one way or another!

    โšก๏ธ To upgrade to EasyBuild v4.3.1, there are several options.
    Two particularly easy options include:

    • ๐Ÿš€ eb --install-latest-eb-release
    • eb --from-pr 11590 # use easyconfig from PR #11590