EasyBuild v5.1.2

EasyBuild v5.1.2 is primarily a bugfix/update release, but it also includes various minor enhancements and support for new software (versions).

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 amdgcn-capabilities configuration option (equivalent to cuda-compute-capabilities for AMD GPUs);

• (***) various improvements to custom easyblock for LLVM;

• update various software-specific easyblocks to support new software versions, including for Amber(Tools), DualSPHysics, jax(lib), Mesa, MUMPS, ORCA, TensorFlow;

• add easyconfigs for foss/2025b and intel/2025b common toolchains;

Prominent bug fixes & changes

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

• test if all extensions support parallel install before attempting parallel extension install;
• fix error when adding files to existing PR with --update-pr;
• fixes for RPATH wrapper script;
• keep ModuleTool.mod_paths in sync with $MODULEPATH in ModuleTool.load(), to fix problems with using a hierarchical module naming schemes with Environment Modules as modules tool;
• don't log variables (un)set + raw output of module command when cleaning up fake module;
• load module in Bundle easyblock instead of components;
• (***) various fixes for custom easyblock for LLVM;
• (***) add back configure options for PETSc dependencies with generic --with options;
• (***) additional fixes for various other software-specific easyblocks, including for ELPA, HPL, Java, OpenCV, OpenBLAS, OpenFOAM, PETSc, pybind11, WPS;
• increase the default for the maximum number of failed PyTorch tests to 10;
• limit parallelism of OpenBLAS tests with parallel property;
• deprecate the Clang Easyblock in favor of the LLVM one for newer (>=18.1.6) versions of Clang;

Supported software

Support for installing 81 new software packages has been added, including (but not limited to):

• autoCAS
• CHARM++
• GAlib
• HPCToolkit
• MACE
• MFEM
• nvbandwidth
• Planet
• QCMaquis
• SnapATAC2

This brings the total number of supported software packages to 2,917 (excluding extensions)!
An up-to-date list of supported software is available here.

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

• AmberTools 25.2
• ASE 3.26.0
• BLIS 2.0
• CGAL 6.0.1
• CUDA 12.9.1 + 13.0.0
• GATE 10.0.2
• GCC 15.2.0
• GROMACS 2025.2
• Highway 1.3.0
• jax 0.6.2 + 0.7.0
• libxc 7.0.0
• likwid 5.4.1
• lxml 6.0.0
• magma 2.9.0
• MUST 1.11.1
• numba 0.62.0
• Octave 10.1.0
• OpenCV 4.11.0
• PETSc 3.23.5
• pocl 7.0
• Python-bundle-PyPI 2025.07
• PyTorch 2.6.0
• QuantumESPRESSO 7.5
• SciPy-bundle 2025.07
• Score-P 9.2
• Siesta 5.4.1
• SLiM 5.0
• SUNDIALS 7.0.0
• X11 20250608

These changes result from various contributions, made by 30 different contributors:

• 33 merged pull requests for EasyBuild framework
• 81 merged pull requests for easyblocks
• 503 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v5.1.2, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release
• eb --from-pr 24024 # use easyconfig from PR #24024

EasyBuild v5.1.1

EasyBuild v5.1.1 is primarily a bugfix/update release, but it also includes various minor enhancements and support for new software.

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 pre/post easyblock hook (see also https://docs.easybuild.io/hooks);

• enhance generic Bundle easyblock to also run test step for each bundle component;

• new custom easyblock for BLIS;

• update numpy easyblock to support installing numpy >= 2.0

Prominent bug fixes & changes

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

• (***) also copy patches for extensions and bundle components to installation directory;

• (***) various fixes (and enhancements) for custom easyblock for LLVM;

• (***) configure Rust to use stable channel;

• disable trace output when unpacking crates in Cargo easyblock;

• archive old easyconfigs to separate easybuild-easyconfigs-archive Git repository;

Supported software

Support for installing 105 new software packages has been added, including (but not limited to):

• ASAGI
• cowsay
• easi
• FUNAERO
• Ginkgo
• IMAS-Python
• Juicebox
• mumax3
• PyMDE
• SeisSol
• TRIQS-som
• WarpX
• XeniumRanger

This brings the total number of supported software packages to 2,835 (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 24.3 + AmberTools 24.10
• BindCraft 1.5.1
• CMake 4.0.3
• DeltaLake 0.25.5
• Flink 2.0.0
• GPyTorch 1.11
• JupyterHub 5.3.0
• MAQAO 2025.1.0
• mpi4py 4.1.0
• NLopt 2.10.0
• openCARP 18.0
• polars 1.28.1
• preCICE 3.2.0
• Python 3.13.5
• rocm-smi 7.6.0 w/ ROCm 6.4.1
• SciPy-bundle 2025.06
• Siesta 5.4.0
• TensorFlow 2.18.1
• X11 20250521

These changes result from various contributions, made by 32 different contributors:

• 31 merged pull requests for EasyBuild framework
• 55 merged pull requests for easyblocks
• 446 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v5.1.1, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release
• eb --from-pr 23340 # use easyconfig from PR #23340

EasyBuild v5.1.0

EasyBuild v5.1.0 is primarily a feature release that includes a couple of new features, but it also includes various bug fixes (including for some regressions introduced in EasyBuild v5.0.0), minor enhancements, and support for new software.

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 (***))

• print summary at the end of EasyBuild session to show which installations were successful, which failed, and which were skipped;

• extra sanity check to verify if device code of CUDA binaries/libraries matches with cuda-compute-capabilities configuration setting + a couple of related additional configuration settings (cuda-sanity-check-*);

• support for data installations (installpath-data and sourcepath-data EasyBuild configuration settings, data_sources easyconfig parameter, ...);

• reduced trace output for sanity check commands for extensions;

• new generic Dataset easyblock;

• 2 new software-specific easyblocks for Term::Readline::Gnu Perl module and VSCode + restored software-specific eaasyblock for fastStructure (got removed in EasyBuild v5.0.0);

• add easyconfigs for foss/2025a and intel/2025a (see also overview of common toolchains);

• (***) add extensions to recent R-bundle-CRAN and R-bundle-Bioconductor easyconfigs (can be added via --skip);

Prominent bug fixes & changes

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

• obtain PR/commit diff via GitHub API (rather than downloading *.diff file via github.com);

• run pip check only once for PythonBundle and Python installations;

• (***) various fixes and enhancements for custom easyblock for LLVM;

• (***) configure Rust to use stable channel;

• (***) rebuild C++ API for Gurobi;

• deprecate JAR easyblock, Binary easyblock should be used instead;

• (***) update version of pRolocdata and RnBeads.hg38 extensions in R-bundle-Bioconductor 3.20 (since source tarball for previous versions are no longer available);

• (***) update to latest Java versions for Java/8, Java/11, Java/17, Java/21, Java/23;

Supported software

Support for installing 64 new software packages has been added, including (but not limited to):

• Boltz-1
• cooltools
• HEEDS
• KrakenTools
• LST-AI
• porefoam
• PySide6
• SQUID
• SQuIRE
• STITCH
• TSEBRA
• uv

This brings the total number of supported software packages to 2,899 (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 2.0.3
• Amber 24.0
• CUDA 12.9.0
• GCC 14.3.0 + 15.1.0
• LLVM 20.1.5
• NVHPC 25.3
• openCARP 17.0
• OpenFold 2.0.0
• PETSc 3.22.5
• PyTorch 2.3.0
• Python-bundle-PyPI 2025.04
• Rust 1.85.1
• QIIME2 2024.10.1
• Score-P 9.0
• StringTie 3.0.0
• SuiteSparse 7.10.1
• VTK 9.3.1

These changes result from various contributions, made by 30 different contributors:

• 48 merged pull requests for EasyBuild framework
• 53 merged pull requests for easyblocks
• 304 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v5.1.0, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release
• eb --from-pr 22953 # use easyconfig from PR #22953

EasyBuild v5.0.0

EasyBuild v5.0.0 is a major release, which includes various backwards-incompatible changes.

Overview of changes

A high-level overview of changes in EasyBuild v5.0.0 is available in the EasyBuild documentation .
The pages and sections to which the entries in the high-level overview link will be updated in the next couple of days with more information, so stay tuned...

A detailed list of all changes with links to the pull requests in which these changes were implemented is available in the release notes.

This release includes support for 148 new software packages!

Installation

There are several ways of installing EasyBuild v5.0.0, including:

• Via pip install (or other standard Python tools), see also here

• Via eb --install-latest-eb-release, which downloads the easyconfig file for EasyBuild v5.0.0 from the develop branch of the easybuild-easyconfigs repository .

Note that installing EasyBuild v5.0.0 with EasyBuild v4.x using "eb --from-pr" will not work shortly after the release of EasyBuild v5.0.0, because the develop branch of the easybuild-easyconfigs repository will be updated, and recent EasyBuild versions don't allow "cross-version" installations via --from-pr .

Contributions

This release includes contributions made by 25 different contributors:

• 245 merged pull requests for EasyBuild framework;
• 341 merged pull requests for easyblocks;
• 778 merged pull requests for easyconfigs;

That's 1,364 merged pull requests in total!

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

Best release ever?

While this release includes breaking changes + changes to the default configuration of EasyBuild, the EasyBuild maintainers are confident that this version of EasyBuild is stable and ready for production, since it has been thoroughly tested.

If you find any unexpected problems or bugs, please report them (via Slack, GitHub, mailing list, etc.) so we can publish a (quick) bugfix release, should that be required.

So for once: let's take some time to conclude whether this really is the best EasyBuild release ever.
We're pretty sure it is, but do make your own assessment after taking it for a spin...

EasyBuild v4.9.4

EasyBuild v4.9.4 is primarily a bugfix & update release, but it also includes various enhancements.

The main motivation for this quick release is a bug in the custom easyblock for GCC that led to a crash in EasyBuild unless the cuda-compute-capabilities configuration option was specified; see easybuilders/easybuild-easyblocks#3449 for more details.

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 (***))

• (***) enhance custom easyblock for NCCL: add licence to NCCL installation;

Prominent bug fixes & changes

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

• implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6;

• take into account alternate sysroot for /bin/bash used by run_cmd;

• fix crash in GCC easyblock when cuda-compute-capabilities EasyBuild configuration option is not set;

Supported software

Support for installing 14 new software packages has been added, including (but not limited to):

• Biotite
• cramino
• ESM3
• MOKIT
• PyBullet
• xskillscor

This brings the total number of supported software packages to 3,670 (excluding extensions)!
An up-to-date list of supported software is available here.

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

• BiG-SCAPE-1.1.9
• GATE 9.4
• HarfBuzz 9.0.0
• LDC 1.39.0
• NanoPlot 1.43.0
• pocl 6.0
• RHEIA 1.1.11,
• SNAP-ESA 10.0.0
• VirtualGL 3.1.1

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

• 6 merged pull requests for EasyBuild framework;
• 8 merged pull requests for easyblocks;
• 71 merged pull requests for easyconfigs;

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

To upgrade to EasyBuild v4.9.4, there are several options.

Two particularly easy options include:

• eb --install-latest-eb-release

• eb --from-pr 21465 # use easyconfig from PR #21465

EasyBuild v4.9.3

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

EasyBuild v4.9.2

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

EasyBuild v4.9.1

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

EasyBuild v4.9.0

EasyBuild v4.9.0 is primarily a feature release, mainly because it includes the 2023b version of the common toolchains (foss + intel), but it also includes various bug fixes, and much more.

The executive summary for this release:

• improved support for using recent version of Environment Modules as modules tool;

• new generic CargoPythonBundle easyblock;

• 3 new custom easyblocks: for flook, HPCC, and PALM;

• easyconfigs for foss/2023b and intel/2023b;

• Easyconfigs for various recent software versions, including GROMACS 2023.3, NWChem 7.2.2, Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, SciPy-bundle 2023.11, Spark 3.5.0, VTK 9.3.0, ...;

• Support for installing 77 new software applications and libraries;

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 generic CargoPythonBundle easyblock;

• 3 new software-specific easyblocks for flook, HPCC, PALM;

• update easyblocks for intel-compilers, impi, imkl to support latest versions;

• update numpy easyblock for v1.26+;

• updates and enhancements to custom easyblocks for Ferret, SuiteSparse;

• add easyconfigs for foss/2023b and intel/2023b (see also common toolchains overview);

Prominent bug fixes & changes

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

• fix support for Environment Modules as modules tool to pass unit tests with v4.2+;

• adapt module function check for Environment Modules v4+;

• disable LLVM build downloads from CI in Rust;

• update SuiteSparse easyblock to only install SuiteSparse libraries with make install;

• fix specifying path to SuiteSparse header files and libraries in numpy, Trilinos, PETSc easyblocks;

• add support for allowing version mismatch + consider versionsuffix when creating .modulerc in ModuleRC easyblock;

• fix det_pylibdir provided by PythonPackage easyblock for Python 3.12+;

• bug fixes for custom easyblocks for Clang, CUDA, numpy, NWChem, PETSc, PyTorch, Rust, SuiteSparse, TensorFlow, Trilinos

• add patch to fix regression in GCC 12.x on AVX512 systems (***);

• add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (***);

• add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23;

• fix OpenBLAS 0.3.20+ on newer Intel CPUs;

• add patch to fix [cz]asums in OpenBLAS 0.3.24 (***);

• add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (***);

• change toolchain in json-fortran easyconfigs to GCC, since it includes Fortran modules (***);

• use GCC toolchain in kim-api, since it includes Fortran modules (***);

• allow ITK legacy code and Python wrappers in ITK v5.2.1 (***);

Supported software

Support for installing 77 new software packages has been added, including (but not limited to):

• BRiAl
• CellBender
• DIA-NN
• EUKulele
• FACE
• GFF3-toolkit
• HPCC
• iperf
• LoopTools
• MitoHiFi
• PFFT
• PySINDy
• R-bundle-CRAN
• scikit-lego
• SEACells
• solo
• Triton
• waLBerla

This brings the total number of supported software packages to 3,369 (excluding extensions)!
An up-to-date list of supported software is available here.

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

• Arrow 14.0.1
• Boost 1.83.0
• CellRanger 7.2.0
• CUDA 12.3.0
• f90wrap 0.2.11
• FPM 1.15.1
• GPyTorch 1.10
• GROMACS 2023.3
• ITK 5.3.0,
• LinBox 1.7.0
• magma 2.7.2,
• Molden 7.3
• NWChem 7.2.2
• phonopy 2.20.0
• PostgreSQL 16.1,
• Python-bundle-PyPI 2023.10
• PyTorch 2.1.2
• R 4.3.2
• SciPy-bundle 2023.11
• Seurat 4.4.0
• Spark 3.5.0
• SuiteSparse 7.1.0
• UCX-CUDA 1.15.0
• VTK 9.3.0
• XGBoost 2.0.2

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

• 21 merged pull requests for EasyBuild framework
• 26 merged pull requests for easyblocks
• 276 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.0, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release

• eb --from-pr 19464 # use easyconfig from PR #19464

EasyBuild v4.8.2

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