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EasyBuild v4.3.1
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@boegel boegel released this 29 Oct 21:04
· 345 commits to develop since this release
easybuild-v4.3.1
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EasyBuild v4.3.1 is primarily a bugfix/update release,
but also includes some minor enhancements.

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

Prominent bug fixes

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

  • fix compatibility of EasyBuild with Python 3.9;
  • 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;
    => 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;
    => 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;
    => 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;
  • make OpenBLAS installation procedure respect the parallelism set by EasyBuild;
  • fix checksum in NAMD 2.12 easyconfigs + add source URL;
  • rename jupyterhub to JupyterHub;

Highlighted enhancements

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

  • publish test reports to easybuild-easyblocks pull request when --include-easyblocks-from-pr is used without --from-pr;
  • add support for including easyblocks from multiple PRs at once via --include-easyblocks-from-pr;
  • 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;
  • make easyblock for installing CMake aware of --sysroot EasyBuild configuration setting;
  • 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;
    => 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;

Supported software

Support for installing 75 new software packages has been added, including:

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

This brings the total number of supported software packages to 2,134!
An up-to-date list of supported software is available here.

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

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:

  • 21 merged pull requests for EasyBuild framework
  • 32 merged pull requests for easyblocks
  • 287 merged pull requests for easyconfigs

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

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

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