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@boegel boegel released this 05 Apr 20:32
· 7 commits to develop since this release
easybuild-v4.9.1
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EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements.

Executive summary

  • Support for --from-commit and --include-easyblocks-from-commit;

  • 1 new sofware-specific easyblocks for DualSPHysics;

  • Support for installing 101 (!) new software applications, tools, and libraries;

  • Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more;

  • Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below);

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 (***))

  • new software-specific easyblock for DualSPHysics;

  • enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage;

  • updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k;

  • (***) significant improvements to QuantumESPRESSO easyblock, incl. running the test suite;

  • enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems;

  • (***) add extensions to R-bundle-CRAN v2023.12 (use --rebuild --skip);

  • (***) add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency;

  • (***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use --rebuild --skip);

Prominent bug fixes & changes

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

  • bug fixes for generic easyblocks: Cargo, CMakeMake,

  • bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision;

  • (***) fix link order in PETSc easyblock for SCOTCH >= 7.x;

  • (***) do not rename GCC's include-fixed directory by default + add script to regenerate it;
    Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0, see easyblocks PR #3254 for more info.

  • (***) add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component;
    We recommend re-installing OpenMPI 4.1.x to pick up this fix.

  • (***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support;

  • (***) add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin;

  • add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs;

  • (***) move setuptools_scm extension from hatchling to Python easyconfig;
    We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.5-GCCcore-13.2.0 using eb --rebuid --skip (or the reinstall these modules).

  • add patches for PyTorch v2.1.2 to fix test failures;

  • add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+;

  • (***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency;

Supported software

Support for installing 101 (!) new software packages has been added, including (but not limited to):

  • AMICA
  • Circlator
  • Clarabel.rs
  • DeepLoc
  • devbio-napari
  • EpiSCORE
  • ExtremeLy
  • GenomeComb
  • GRASP-suite
  • IDG
  • IonQuant
  • libspectre
  • MLflow
  • MSFragger
  • noise
  • PAGAN2
  • phyluce
  • python-casacore
  • QuPath
  • RHEIA
  • SemiBin
  • Sentence-Transformers
  • SQLAlchemy
  • Vamb
  • zUMIs

This brings the total number of supported software packages to 3,470 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • anvio 8
  • arrow-R 14.0.0.2
  • BerkeleyGW 3.1.0 + 4.0
  • Cartopy 0.22.0
  • Clang-Python-bindings 16.0.6
  • CUDA 12.3.2 + 12.4.0
  • CuPy 13.0.0
  • CVXPY 1.4.2
  • DeepLabCut 2.3.6
  • EggLib 3.3.0
  • ESMF 8.4.2
  • FDS 6.8.0
  • Flask 3.0.0
  • FLINT 3.1.1
  • GATK 4.5.0.0
  • GLFW 3.4
  • GROMACS 2024.1
  • Gurobi 11.0.0
  • HeFFTe 2.4.0
  • LAMMPS 2Aug2023_update2
  • likwid 5.3.0
  • matplotlib 3.8.2
  • medaka 1.11.3
  • MOABB 1.0.0
  • MONAI 1.3.0
  • NCCL 2.20.5
  • NGSpeciesID 0.3.0
  • NLTK 3.8.1
  • NVHPC 24.1
  • OCaml 4.14.0
  • ONNX 1.15.0
  • OpenFOAM v2306 + v2312
  • OpenSSL/3 (wrapper)
  • PAPI 7.1.0
  • ParaView 5.12.0
  • PETSc 3.20.3
  • plotly.py 5.18.0
  • PyQt5 5.15.10
  • PyTables 3.9.2
  • pytest-rerunfailures 14.0
  • python-irodsclient 2.0.0,
  • PyTorch-Lightning 2.2.1
  • Qt5 5.15.13
  • Qt6 6.6.3
  • QuantumESPRESSO 7.3
  • R 4.3.3
  • R-bundle-Bioconductor 3.18
  • rMATS-turbo 4.2.0
  • Ruby 3.3.0
  • Rust 1.76.0
  • scikit-learn 1.4.0
  • Score-P 8.4,
  • SLEPc 3.20.1
  • timm 0.9.7
  • VEP 111
  • WIEN2k 23.2
  • wrf-python 1.3.4.1
  • YODA 1.9.9

These changes result from various contributions, made by 34 different contributors:

  • 28 merged pull requests for EasyBuild framework
  • 43 merged pull requests for easyblocks
  • 575 (!) merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 20299 # use easyconfig from PR #20299

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