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@boegel boegel released this 12 Jun 16:57
easybuild-v4.9.2
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EasyBuild v4.9.2 is primarily a bugfix & update release, but it also includes various enhancements.

The executive summary for this release:

  • EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;

  • Bug fix for --from-commit, so easyconfigs for dependencies are found if they're available in the commit;

  • 4 new sofware-specific easyblocks: AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;

  • Support for installing 82 new software applications, tools, and libraries;

  • Easyconfigs for various recent software versions, including BLIS 1.0, Clang 17.0.6, GCC 13.3.0 + 14.1.0, IOR 4.0.0, OCaml 5.1.1, OpenMPI 5.0.3, PyTorch-bundle 2.1.2, Python 3.12.3, TensorFlow 2.15.1, and many more;

  • Bug fixes/changes to easyblocks/easyconfigs that require reinstallation (more info below, marked with (***));

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 (***))

  • implement EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;

  • 4 software-specific easyblock for AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;

  • enhancement to PythonPackage generic easyblock;

  • add a sanity check for OpenFOAM's wmake to make sure it finds the compiler commands;

  • refactor GAMESS-US easyblock to directly write install.info;

  • additional updates & enhancements to custom easyblocks for ABAQUS, Clang, CUDA, FFTW, Java, Mesa, OpenMPI, OpenSSL, torchvision, UCX-Plugins;

  • (***) additional extensions for R-bundle-CRAN v2023.12;

Prominent bug fixes & changes

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

  • symlink downloaded repo at specified commit when using --from-commit so easyconfigs for dependencies are found;

  • bug fixes for CargoPythonBundle generic easyblock;

  • bug fixes in custom easyblocks for intel-compilers and Python;

  • (***) add patch to fix CVE-2024-27322 in R v3.6.x, v4.0.x, v4.1.x, v4.2.x, v4.3.x;

  • (***) fix detection of CC/CXX compilers for wmake in OpenFOAM v2306 + v2312;

  • (***) change arrow-R dependency of R-bundle-Bioconductor v3.18 to v14.0.1;

  • (***) add dependencies required for GUI in Cellpose 2.2.2 easyconfigs;

  • (***) add missing dependencies for funannotate;

  • (***) make sure mummerplot can use gnuplot if available for recent MUMmer;

  • remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (see here);

Supported software

Support for installing 82 new software packages has been added, including (but not limited to):

  • AEDT
  • AMGX
  • Cassiopeia
  • CheckM2
  • Compass
  • CVX
  • EasyMocap
  • FDMNES
  • HiGHS
  • HOMER
  • LangChain
  • libabigail
  • LIBSVM-MATLAB
  • Lightning
  • MetalWalls
  • ml-collections
  • MOFA2
  • orthAgogue
  • planarity
  • PRRTE
  • PSM2
  • PyHMMER
  • PyVista
  • SCReadCounts
  • TF-COMB
  • TorchIO
  • VAMPIRE-ASM
  • WGDgc

This brings the total number of supported software packages to 3,552 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AFNI 24.0.02
  • alevin-fry 0.9.0
  • BCFtools 1.19
  • BLIS 1.0
  • BWA 0.7.18
  • Boost 1.85.0
  • CGAL 5.6.1
  • CellRank 2.0.2
  • Clang 17.0.6
  • dask 2024.5.1
  • deal.II 9.5.2
  • dorado 0.5.3
  • ESPResSo 4.2.2
  • FMM3D 1.0.4
  • GAMESS-US 20220930-R2 + 20230930-R2
  • GCC 13.3.0 + 14.1.0
  • GOATOOLS 1.4.5
  • GTDB-Tk 2.4.0
  • gemmi 0.6.5
  • gmsh 4.12.2,
  • HDDM 0.9.9
  • HTSlib 1.19.1
  • HyPhy 2.5.60
  • h5py 3.11.0
  • IOR 4.0.0
  • Jupyter-bundle 20240522 (incl. JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, ...)
  • Kalign 3.4.0
  • kallisto 0.50.1
  • MATSim 15.0
  • MetaMorpheus 1.0.5
  • MuJoCo 3.1.4
  • mold 2.31.0
  • NanoPlot 1.42.0
  • nglview 3.1.2
  • nvtop 3.1.0
  • OCaml 5.1.1
  • OpenMPI 5.0.3
  • PhyML 3.3.20220408
  • PyTorch-bundle 2.1.2
  • Python 3.12.3
  • petsc4py 3.20.3
  • polars 0.20.2
  • py3Dmol 2.1.0
  • pyiron 0.5.1
  • ROOT 6.30.06
  • Rust 1.78.0
  • SAMtools 1.19.2
  • SentencePiece 0.2.0
  • Seurat 5.1.0
  • SimNIBS 4.0.1
  • Spack 0.21.2
  • Squidpy 1.4.1
  • SymEngine 0.11.2
  • scikit-learn 1.4.2
  • TensorFlow 2.15.1
  • Transformers 4.39.3
  • tokenizers 0.15.2
  • UCX 1.16.0
  • Valgrind 3.23.0
  • VisPy 0.14.1
  • zlib-ng 2.1.6

These changes result from various contributions, made by 29 different contributors:

  • 16 merged pull requests for EasyBuild framework
  • 27 merged pull requests for easyblocks
  • 326 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.2, there are several options.

Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 20801 # use easyconfig from PR #20801

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