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EasyBuild v4.9.3
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@boegel boegel released this 14 Sep 21:19
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easybuild-v4.9.3
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EasyBuild v4.9.3 is primarily a bugfix & update release, but it also includes various enhancements.

The executive summary for this release:

  • Easyconfigs for the foss/2024a and intel/2024a common toolchains;
  • Support for installing 107 (!) new software applications, tools, and libraries, including HERRO, MAGIC, pyMBE, Sagemath, Single-cell-python-bundle, Visit;
  • Easyconfigs for various recent software versions, including AlphaPulldown 2.0.0b4, Clang + LLVM 18.1.8, CUDA 12.5.0 + 12.6.0, FFmpeg 7.0.2, GCC 14.2.0, jax 0.4.25, ORCA 6.0.0, OpenFOAM 12 + v2406, R 4.4.1, SciPy-bundle 2024.05, WRF 4.5.1, and many more;
  • Bug fixes/enhanchements/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 (***))

  • add support for --extra-source-urls to fetch sources from additional URLs;

  • use Intel's oneAPI Fortran compiler by default for version 2024.0.0 and newer;

  • enhancements to generic easyblocks: Cargo, JuliaPackage, PythonBundle, PythonPackage, RPackage, RubyGem;

  • (***) enhance custom easyblock for GCC to use with-arch option for nvptx with 13.1+;

  • additional updates & enhancements to custom easyblocks for Bazel, binutils, Boost, ESMF, Extrae, Geant4, MCR, impi, LAMMPS, OpenFOAM, ORCA, psmpi, PETSc, PyTorch, QuantumESPRESSO, Tensorflow, Tkinter;

  • (***) add additional extensions to R-bundle-CRAN easyconfigs;

  • (***) add Qt support to VTK 9.3.0;

  • (***) also build & install the plugins with OpenFOAM v2406;

Prominent bug fixes & changes

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

  • (***) patch ctypes for Python installations when filtering LD_LIBRARY_PATH + fix path to ldconfig when using alternate sysroot ;

  • merge of the ConfigureMake and CMakeMake versions of the easyblock for QuantumESPRESSO;

  • bug fixes in generic easyblocks: Cargo, CargoPythonPackage, PythonBundle, PythonPackage;

  • bug fixes in custom easyblocks for ANSYS, EasyBuild, Extrae, impi, OCaml, OpenFOAM, OpenMPI, OpenSSL_wrapper, PALM, Python, WPS;

  • (***) add patch to fix implicit function declaration in OpenMPI 4.1.4;

  • (***) disable auto-vectorizer (-ftree-vectorize) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11;

  • (***) add patch for HDF5 v1.14.3 to suppress fp exceptions;

  • (***) fix easyconfigs for recent versions of QuantumESPRESSO;

  • (***) add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection;

  • fix download URLs for old Intel software (2018-2023) by using IRC_NAS instead of irc_nas;

Supported software

Support for installing 107 (!) new software packages has been added, including (but not limited to):

  • absl-py
  • BayesOpt
  • CORSIKA
  • dictys
  • EGA-QuickView
  • fish
  • Flax
  • GPflow
  • HERRO
  • LRBinner
  • MAGIC
  • MBX
  • nifty
  • OpenForceField-Toolkit
  • PEcAn
  • pyMBE
  • Sagemath
  • SharedMeatAxe
  • Single-cell-python-bundle
  • torch-em
  • Visit
  • Zoltan

This brings the total number of supported software packages to 3,656 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AlphaPulldown 2.0.0b4
  • AmberTools 26.3
  • Arrow 16.1.0
  • Biopython 1.84
  • CUDA 12.5.0 + 12.6.0
  • CellOracle 0.18.0
  • Clang 18.1.8
  • cutadapt 4.9
  • dorado 0.7.3
  • Extrae 4.2.0
  • FFmpeg 7.0.2
  • GCC 14.2.0
  • GDAL 3.9.0
  • GLM 1.0.1
  • GPAW 24.6.0
  • genomepy 0.16.1
  • Highway 1.2.0
  • IQ-TREE 2.3.5
  • jax 0.4.25
  • LLVM 18.1.8
  • MPICH 4.2.1
  • MariaDB 11.6.0
  • Mesa 24.1.3
  • matplotlib 3.9.2
  • NanoCaller 3.6.0
  • ORCA 6.0.0
  • OpenFOAM 12 + v2406
  • Optax 0.2.2
  • Perl-bundle-CPAN 5.38.2
  • Pillow-SIMD 10.4.0
  • PostgreSQL 16.4
  • PyAEDT 0.9.9
  • PyWavelets 1.7.0
  • Pygments 2.18.0
  • Python-bundle-PyPI 2024.06
  • pyGenomeTracks 3.9
  • QuantumESPRESSO 7.3.1
  • R-bundle-CRAN 2024.06
  • R 4.4.1
  • RDKit 2024.03.3,
  • ReFrame 4.6.2
  • Rust 1.79.0
  • SciPy-bundle 2024.05
  • SeqKit 2.8.2
  • SingleM 0.16.0
  • SuiteSparse 7.7.0
  • TELEMAC-MASCARET 8p5r0
  • UCX-CUDA 1.16.0
  • WRF 4.5.1
  • X11 20240607
  • XGBoost 2.1.1
  • xarray 2024.5.0

These changes result from various contributions, made by 33 different contributors:

  • 31 merged pull requests for EasyBuild framework;
  • 52 merged pull requests for easyblocks;
  • 367 merged pull requests for easyconfigs;

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

To upgrade to EasyBuild v4.9.3, there are several options.

Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 21412 # use easyconfig from PR #21412

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