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EasyBuild v4.3.2
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@boegel boegel released this 10 Dec 21:15
· 322 commits to develop since this release
easybuild-v4.3.2
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boegel Kenneth Hoste
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EasyBuild v4.3.2 is primarily a bugfix/update release,
but also includes several interesting 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.

Prominent bug fixes

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

  • fix combination of --copy-ec and --from-pr options;
  • fix regression in apply_regex_substitutions: also accept list of paths to patch;
  • also inject -rpath options for all entries in $LIBRARY_PATH in RPATH wrappers;
  • only configure Python with --enable-optimizations when compiling with (recent) GCC compiler (to fix hanging installations of Python and Tkinter);
  • stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests;
  • fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK;
  • always define $FCCPP in QuantumESPRESSO easyblock (not just when using Intel compilers);
  • fix CPASSERT test faults on RHEL8 in CP2K easyblock;
  • set $UCX_TLS in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file;
  • fix source_urls in Geant4 easyconfigs;
  • add patch for TensorFlow 2.3.1 to fix installation on Arm64;
  • (***) add patch for GCCcore 10.2 to fix __has_include regression (required for building Libint);
  • (***) set $JUPYTER_PATH to make Jupyter find the ipywidgets extension in recent IPython easyconfigs;
  • (***) in-place update to magma 2.5.4 for PyTorch (to fix known bug in magma 2.5.2 which causes e.g. wrong results (NaNs) in PyTorch);
  • (***) add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check;
  • (***) add missing gnuplot dependency in OpenFOAM easyconfigs (just re-generating OpenFOAM module files via --module-only is sufficient);
  • (***) add patch to fix possible memory leak in OpenBLAS 0.3.3+;
  • renamed software to match official name or fix name clashes: Ray-assembler + Ray-project, RStudio-Server, SUMO, XCFun;

Highlighted enhancements

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

  • add (experimental) support for specifying easyconfig files via an "easystack" file;
  • significantly speed up parsing of easyconfig files by only extracting comments from an easyconfig file when they’re actually needed;
  • add support for toolchain options like 'extra_cxxflags' to specify extra compiler options;
  • add support for '%(module_name)s' template value;
  • add support for skipping unit tests (test step) via --skip-test-step;
  • add support for building Clang and GCC with support for OpenMP offloading to GPUs;
  • update TensorFlow easyblock for upcoming TensorFlow 2.4;
  • enhance PyTorch easyblock to ensure it finds MKL;
  • (***) enable NVPTX offload support in GCCcore 10.2.0 easyconfig;
  • (***) add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
  • (***) add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs;

Use "eb --rebuild --skip" to install the missing extensions for R, Bioconductor, or Perl.

Supported software

Easyconfig files for the updated common toolchains are included:

  • foss/2020b
  • fosscuda/2020b
  • intel/2020b
  • intelcuda/2020b

In addition, easyconfigs for the new 'gobff' toolchain are included: gobff/2020.11, gobff/2020.06-amd.

The gobff toolchain includes the following components:

  • GCC + binutils
  • OpenMPI
  • BLIS + libFLAME (BLAS/LAPACK libraries)
  • ScaLAPACK
  • FFTW

The -amd variant uses the AMD forks of the upstream BLIS and libFLAME libraries.

Support for installing 41 new software packages has been added, including:

  • carputils
  • code-server
  • CRISPResso2
  • fgbio
  • IPM
  • LLDB
  • meshalyzer
  • meshtool
  • Metagenome-Atlas
  • MLxtend
  • MRChem
  • nanocompore
  • OpenSees
  • PEST++
  • pyFAI
  • pymca
  • scikit-bio
  • SpaceRanger
  • SWAT+
  • WCT

This brings the total number of supported software packages to 2,175!
An up-to-date list of supported software is available here.

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

  • Boost 1.74.0
  • CUDA 11.1.1
  • CellRanger 5.0.0.eb
  • CheckM 1.1.3
  • Clang 11.0.0
  • cuDNN 8.0.4.30
  • FDS 6.7.5
  • FFmpeg 4.3.1
  • GROMACS 2020.4
  • Geant4 10.6.2
  • GlobalArrays 5.8
  • HDF5 1.10.7
  • h5py 3.1.0
  • magma 2.5.4
  • matplotlib 3.3.3
  • NCCL 2.8.3
  • netCDF-Fortran 4.5.3
  • OpenMolcas 20.10
  • packmol 20.2.2
  • Qt5 5.14.2
  • RAxML-NG 1.0.1
  • SCOTCH 6.1.0
  • SciPy-bundle 2020.11 (incl. numpy 1.19.4, scipy 1.5.4, 1.1.4, ...)
  • StringTie 2.1.4
  • SuperLU 5.2.2
  • scikit-learn 0.23.2
  • snakemake 5.26.1

These changes result from various contributions, made by 27 different contributors:

  • 33 merged pull requests for EasyBuild framework
  • 39 merged pull requests for easyblocks
  • 187 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.3.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release
  • eb --from-pr 11853 # use easyconfig from PR #11853
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