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EasyBuild v4.8.2
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@boegel boegel released this 29 Oct 19:58
· 12 commits to develop since this release
easybuild-v4.8.2
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boegel Kenneth Hoste
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EasyBuild v4.8.2 is primarily a bugfix and update release, but it also includes various enhancements.

The executive summary for this release:

  • Various small enhancements and bug fixes in EasyBuild framework, easyblocks, and easyconfigs;

  • Easyconfigs for various recent software versions, including Cantera 3.0.0, mold 2.3.1, Perl-bundle-CPAN 5.38.0, PyTorch 2.0.1, ...;

  • Support for installing 48 new software applications and libraries, incl. PyTensor, Qt6, SNAP-ESA;

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 & updates

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

  • add dependency_names method to EasyConfig class to get set of names of (direct) dependencies;

  • use more test programs in sanity check step of OpenMPI easyblock;

  • updates and enhancements to various generic easyblocks, including CMake, Conda, ConfigureMake;

  • updates and enhancements to custom easyblocks for imkl, numpy, Perl, PyTorch, WRF, wxPython;

  • add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7;

  • (***) don't disable building of third and fourth derivates in libxc 6.1.0;

  • (***) also build Python bindings for ITK 5.2.1 with foss/2022a;

  • (***) add extensions to recent versions of R and R-bundle-Bioconductor, use "eb --skip --rebuild" to install the missing extensions;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

  • reset tempfile.tempdir to None to avoid that tmpdir path gets progressively deeper with each easystack item;

  • only use -DCMAKE_SKIP_RPATH=ON for CMake < 3.5.0;

  • fix --sanity-check-only and --module-only for UCX plugins;

  • enhance TensorFlow easyblock to avoid use of -mcpu=native for XNNPACK component when building on aarch64;

  • fix the blas/lapack name passed to meson when building recent scipy versions (>= 1.9.0) on top of Intel MKL;

  • (***) add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and GCCcore/12.3.0;

  • (***) add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs;

  • rename ACT to Artemis;

  • rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions;

  • add patch for recent OpenBLAS versions (0.3.23, 0.3.24) to fix flaky and hanging tests;

  • (***) add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3;

  • (***) fix invalid pointer access in UCX 1.11-1.14;

  • (***) statically link Boost 1.75 in Cufflinks v20190706 installed with GCC/11.2.0, so Boost can be changed to build dependency;

  • add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20;

  • (***) add missing dependencies for MONAI to support extras required by MONAI-Label;

  • (***) disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain;

Supported software

Support for installing 48 new software packages has been added, including (but not limited to):

  • ALL
  • bases2fastq
  • biobakery-workflows
  • CLEAR
  • EveryBeam
  • imutils
  • Jmol
  • MACS3
  • MUSCLE3
  • ProBiS
  • PyPy
  • PyTensor
  • Qt6
  • ResistanceGA
  • scCODA
  • SNAP-ESA
  • starparser
  • XBeach

This brings the total number of supported software packages to 3,292 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • Amber 22.4
  • BLAST+ 2.14.1
  • Cantera 3.0.0
  • CapnProto 1.0.1
  • CGAL 5.6
  • CUDA-Samples 12.1.1
  • CuPy 12.1.0
  • FastANI 1.34
  • GDAL 3.7.1
  • GMP 6.3.0
  • GPAW 23.9.1
  • HMMER 3.4
  • IsoSeq 4.0.0
  • libpng 1.6.40
  • libxc 6.2.2
  • MEGAN 6.25.3
  • Mesa 23.1.9
  • mold 2.3.1
  • OpenBLAS 0.3.24
  • OpenCV 4.8.1
  • OpenMPI 4.1.6
  • OrthoFinder 2.5.5
  • ParaView 5.11.2
  • Perl-bundle-CPAN 5.38.0
  • pyEGA3 5.0.2
  • Python 3.11.5
  • PyTorch 2.0.1
  • PyTorch-bundle 1.13.1
  • RagTag 2.1.0
  • RAxML-NG 1.2.0,
  • RDFlib 7.0.0
  • ReFrame 4.3.3
  • Rust 1.73.0
  • scikit-learn 1.3.1
  • TensorRT 8.6.1
  • UCX 1.15.0
  • X11 20231019
  • xtb 6.6.0

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

  • 15 merged pull requests for EasyBuild framework
  • 20 merged pull requests for easyblocks
  • 267 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 19105 # use easyconfig from PR #19105

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