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EasyBuild v4.9.1

05 Apr 20:32
@boegel boegel
easybuild-v4.9.1
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EasyBuild v4.9.1 Latest
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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

Assets 2

EasyBuild v4.9.0

30 Dec 21:28
@boegel boegel
easybuild-v4.9.0
a0c1159
This commit was signed with the committer’s verified signature.
boegel Kenneth Hoste
GPG key ID: 90C14B582D70E3BE
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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

Assets 2

EasyBuild v4.8.2

29 Oct 19:58
@boegel boegel
easybuild-v4.8.2
a0c1159
This commit was signed with the committer’s verified signature.
boegel Kenneth Hoste
GPG key ID: 90C14B582D70E3BE
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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

Assets 2

EasyBuild v4.8.1

11 Sep 17:58
@boegel boegel
easybuild-v4.8.1
098117c
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EasyBuild v4.8.1

EasyBuild v4.8.1 is primarily a bugfix and update release, but it also includes various enhancements.

The executive summary for this release:

  • Support for various additional hooks that can be used to customize EasyBuild, including pre_run_shell_cmd_hook which allows tweaking shell commands right before they are run by EasyBuild;

  • 2 new custom easyblocks, for sympy and tensorflow-compression;

  • Easyconfigs for various recent software versions, including Clang 16.0.6, CP2K 2023.1, FFmpeg 6.0, GCC 13.2.0, OpenFOAM 11, Pillow 10.0.0, TensorFlow 2.13.0, ...;

  • Support for installing 83 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 (***))

  • support for additional hooks: pre_build_and_install_loop_hook + post_build_and_install_loop_hook, cancel_hook, fail_hook, pre_postiter_hook + post_postiter_hook, and pre_run_shell_cmd_hook + post_run_shell_cmd_hook; see https://docs.easybuild.io/hooks for more information;

  • add --silence-hook-trigger configuration option to suppress printing of a debug message every time a hook is triggered;

  • add support for using fine grained Github tokens;

  • add support for submodule filtering and specifying extra Git configuration in git_config;

  • new custom easyblocks for sympy and tensorflow-compression;

  • add options to MesonNinja generic easyblock to customize build_cmd, install_cmd, build_dir;

  • add support to PerlModule generic easyblock to customize prefix option used in installation command;

  • updates and enhancements to custom easyblocks for Clang, CP2K, CUDA, FreeSurfer, LLVM, Mesa, MXNet, OpenCV, OpenFOAM, PETSc, PyTorch, scipy, Score-P, TensorFlow;

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

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • improve error reporting w.r.t. missing checksums;

  • (***) only add extensions in module file if there are extensions;

  • enhance PythonPackage easyblock to deal with posix_local installation scheme used by Python in recent Debian/Ubuntu versions;

  • (***) improve depot management in JuliaPackage easyblock;

  • (***) set $JULIA_DEPOT_PATH in Julia easyconfigs with default value;

  • bug fixes for various custom easyblocks, incl. imkl-FFTW, Java, (***) MATLAB, Mesa, OpenMPI, STAR-CCM+, TensorFlow;

  • (***) fix regression in GCC 12.1 + 12.2 with wrong warnings;

  • fix installation of Python bindings for recent Arrow easyconfigs;

  • (***) various additional patches for recent PyTorch versions to fix bugs and/or failing tests;

  • (***) additional bug fixes in easyconfigs for Abseil, at-spi2-core, Automake, FreeSurfer, jupyter-server, JupyterHub, LIBSVM, MPFR, RapidJSON, ScaLAPACK, tRNAscan-SE;

  • (***) update Java/11 wrapper to Java/11.0.20;

  • (***) use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with GCCcore/12.2.0;

  • (***) add patch for PMIx 4.x to use lchown so links are not followed;

  • (***) add hpctestlib to the $PYTHONPATH in ReFrame 4.2.0 easyconfig;

  • add alternative checksum for Extrae v4.0.4;

  • (***) disable wx support in gnuplot 5.4.6;

  • set $MUJOCO_PY_FORCE_CPU to avoid that mujoco-py checks for nvidia-smi and aborts installation because /usr/lib/nvidia is not in $LD_LIBRARY_PATH;

Supported software

Support for installing 83 new software packages has been added, including (but not limited to):

  • Ax
  • Boost.Python-NumPy
  • CatBoost
  • ChIPseeker
  • cryptography
  • GAPPadde
  • GenerativeModels
  • hatchling
  • IsoQuant
  • Jupyter-bundle
  • JupyterNoteboo
  • maturin
  • Mikado
  • NanoCaller
  • Omnipose
  • Optax
  • pv
  • Python-bundle-PyPI
  • Sabre
  • scib-metrics
  • scikit-plot
  • setuptools-rust
  • tensorflow-compression
  • torchvf
  • TXR
  • virtualenv

This brings the total number of supported software packages to 3,244 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • ABINIT 9.10.3
  • Arcade-Learning-Envionment 0.8.1
  • archspec 0.2.1
  • Bazel 6.3.1
  • BCFtools 1.18
  • BEDTools 2.31.0
  • Boost 1.82.0
  • CDO 2.2.2
  • Clang 16.0.6
  • CP2K 2023.1
  • CUDA 12.2.2
  • ecBuild 3.8.0
  • FFmpeg 6.0
  • FreeSurfer 7.4.1
  • GCC 13.2.0
  • GHC 9.2.2
  • gnuplot 5.4.8
  • GTK4 4.11.3
  • h5py 3.9.0
  • Horovod 0.28.1
  • Hypre 2.29.0
  • ImageMagick 7.1.1-15
  • magma 2.7.1
  • medaka 1.8.1 + 1.9.1
  • Mesa 23.1.4
  • MXNet 1.9.1
  • OpenAI-Gym 0.26.2
  • OpenCV 4.8.0
  • OpenFOAM 11
  • Pillow 10.0.0
  • PLUMED 2.9.0
  • pocl 4.0
  • QIIME2 2023.5.1
  • Qt5 5.15.10
  • QuantumESPRESSO 7.2
  • SAMtools 1.18
  • SciPy-bundle 2023.07
  • Score-P 8.1
  • sympy 1.12
  • SUNDIALS 6.6.0
  • TensorFlow 2.13.0
  • Valgrind 3.21.0
  • wxPython 4.2.1
  • zarr 2.16.0

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

  • 25 merged pull requests for EasyBuild framework
  • 40 merged pull requests for easyblocks
  • 339 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 18761 # use easyconfig from PR #18761

Assets 2

EasyBuild v4.8.0

07 Jul 21:04
@boegel boegel
easybuild-v4.8.0
f9bfbb3
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
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EasyBuild v4.8.0

EasyBuild v4.8.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

The executive summary for this release:

  • Easyconfigs for the 2023a update of the foss + intel common toolchains;

  • 2 new easyblocks: a generic PerlBundle easyblock, and a custom easyblock for Rust;

  • Easyconfigs for various recent software versions, including elastix 5.0.0, GROMACS 2023.1, PyTorch 1.13.1, VTK 9.2.6, ...;

  • Support for installing 76 new software applications and libraries;

Highlights for this release are listed below. More details are available in the release notes [2] 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 PerlBundle generic easyblock for installing a bundle of Perl modules;

  • add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if --rpath is used;

  • add support for install_cmds in Binary easyblock;

  • update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes;

  • (***) add extra packages to recent R easyconfigs;

  • (***) add extra packages to recent R-bundle-Bioconductor easyconfigs;

  • (***) enable building static libs and check for libexslt.* in libxslt;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • fix regex for extracting glibc version from output of 'ldd --version' in Gentoo Linux;

  • stop running tests with Python 2.7 since it is no longer supported in GitHub Actions;

  • patch CMake's UnixPaths.cmake script if --sysroot is set;

  • use upstream patch for symbol compatibility in XZ 5.2.5;

  • (***) change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a);

  • (***) use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2;

  • (***) stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2;

  • (***) fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530;

  • (***) update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies;

  • (***) fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17);

  • (***) fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b);

  • (***) bump OpenSSL 1.1 wrapper fallback to 1.1.1u;

Supported software

Support for installing 76 new software packages has been added, including (but not limited to):

  • alleleIntegrator
  • BayesPrism
  • Circuitscape
  • DALI
  • DaliLite
  • ecFlow
  • FragPipe
  • GLIMPSE
  • KerasTuner
  • mannkendall
  • MONAI-Label
  • NanoStat
  • pastml
  • Perl-bundle-CPAN
  • PyBioLib
  • PyWBGT
  • Sniffles
  • Tapenade
  • timm
  • wrapt
  • xclip

This brings the total number of supported software packages to 3,161 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • alleleCount 4.2.1
  • BayesTraits 3.0.2
  • Bowtie2 2.5.1
  • Cellpose 2.2.2
  • CUDA 12.1.1 + 12.2.0
  • CVXOPT 1.3.1
  • deepTools 3.5.2
  • DMTCP 3.0.0
  • dorado 0.3.0 + 0.3.1
  • duplex-tools 0.3.3
  • fastp 0.23.4
  • FreeSurfer 7.4.0
  • GATK 4.4.0.0
  • GCC 11.4.0
  • Geant4 11.1.2
  • GROMACS 2023.1
  • Horovod 0.25.0
  • Julia 1.9.0
  • LibLZF 3.6
  • MAGeCK 0.5.9.5
  • MaxQuant 2.4.2.0
  • MMseqs2 14-7e284
  • MuJoCo 2.2.2
  • ncbi-vdb 3.0.5
  • ont-fast5-api 4.1.1
  • openpyxl 3.1.2
  • ParaView 5.11.1
  • Perl 5.36.1
  • PSI4 1.7
  • Pysam 0.21.0
  • Python 3.11.3
  • PyTorch 1.13.1
  • Rust 1.70.0
  • seqtk 1.4
  • SUNDIALS 6.5.1
  • TransDecoder 5.5.0
  • Transformers 4.29.2 + 4.30.2
  • VTK 9.2.6
  • xarray 2023.4.2
  • zlib-ng 2.0.7

These changes result from various contributions, made by 25 different contributors:

  • 9 merged pull requests for EasyBuild framework
  • 13 merged pull requests for easyblocks
  • 301 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.0, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 18282 # use easyconfig from PR #18282

Assets 2

EasyBuild v4.7.2

27 May 23:00
@boegel boegel
easybuild-v4.7.2
d6eacf1
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EasyBuild v4.7.2

EasyBuild v4.7.2 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

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

  • Easyconfigs for various recent software versions, including AlphaFold 2.3.4, CP2K 2022.1, GCC 12.3.0 + 13.1.0, R-bundle-Bioconductor 3.16, ...;

  • Support for installing 89 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 (***))

  • extend (experimental) support for generating container images with Apptainer;

  • 2 new generic easyblocks for installing Rust crates with cargo: Cargo and CargoPythonPackage;

  • (***) enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0;

  • (***) add additional extensions to recent R and R-bundle-Bioconductor easyconfigs;

  • (***) switch bamtofastq + Longshot to Cargo easyblock;

  • (***) add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file;

  • (***) add missing FastTreeMP binary for FastTree;

  • (***) bump versions in Java wrappers to latest builds that include ppc64le;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***)`)

  • fix --check-github as gist url now includes username;

  • (***) force building torchvision with CUDA support if CUDA is included as dependency by setting $FORCE_CUDA;

  • (***) use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0;

  • (***) add missing OpenJPEG dependency for recent GDAL versions;

  • (***) upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues;

  • (***) add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6;

  • (***) FLINT needs BLAS so move it up from GCC level;

  • add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test;

  • exclude flaky test_optim + add patch to fix test_quantization for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent;

  • add make 4.3 as build dependency for recent OpenBLAS versions;

  • add alternative checksum for MONAI 1.0.1;

  • add historical repo paths to install command for old versions of texlive;

Supported software

Support for installing 89 new software packages has been added, including (but not limited to):

  • AGeNT
  • Annocript
  • BoltzTraP2
  • Casanovo
  • CellOracle
  • ColabFold
  • DiCE-ML
  • ESPResSo
  • FunGAP
  • GLI
  • HTSplotter
  • IsoSeq
  • LoRDEC
  • OptaDOS
  • PGPLOT
  • pod5-file-format
  • pytesseract
  • Python-bundle
  • PyTorch-bundle
  • Raven
  • Scalene
  • SoPlex
  • sysbench
  • TOPAS
  • turbinesFoam

This brings the total number of supported software packages to 3,085 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AlphaFold 2.3.4
  • Arrow 11.0.0
  • Clang 15.0.5
  • CP2K 9.1 + 2022.1
  • GCC 12.3.0 + 13.1.0
  • intel/2023.03 (incl. intel-compilers 22023.1.0, impi 2021.9.0, imkl 2023.1.0)
  • OpenMM 8.0.0
  • picard 3.0.0
  • R-bundle-Bioconductor 3.16
  • ReFrame 4.2.0
  • UCC-CUDA 1.1.0

These changes result from various contributions, made by 27 different contributors:

  • 14 merged pull requests for EasyBuild framework
  • 15 merged pull requests for easyblocks
  • 316 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17986 # use easyconfig from PR #17986

Assets 2

EasyBuild v4.7.1

20 Mar 17:34
@boegel boegel
easybuild-v4.7.1
a137b25
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EasyBuild v4.7.1

EasyBuild v4.7.1 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

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

  • Easyconfigs for various recent software versions: AlphaFold 2.3.0, HDF5 1.14.0, networkx 3.0, TensorFlow v2.11.0, Trilinos 13.4.1, ...;

  • Additional easyconfigs using the latest 2022b toolchains, incl. SciPy-bundle 2023.02 with gfbf/2022b (subtoolchain of foss/2022b);

  • Support for installing 99 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

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

  • add support for %(start_dir)s easyconfig template;

  • add pre/post extension hook that is triggered before/after individual extension installations;

  • enforce absolute paths as start dir of extensions;

  • updates and enhancements for various generic easyblocks: GoPackage, MesonNinja, PythonPackage;

  • updates and enhancements for various software-specific easyblocks: EasyBuildMeta, ELPA, Maple, Mathematica, NAMD, pybind11, Python, QScintilla, scipy, TensorFlow, Trilinos;

  • (***) add additional extensions to Python 3.10.8 (required for scipy test suite) (see --skip);

  • (***) add extensions to Perl 5.32.1 (see --skip);

  • (***) add additional extensions to R 4.2.1 (see --skip);

  • (***) add additional extensions to Bioconductor 3.15 (see --skip);

  • (***) enhance OpenFold 1.0.1 for standalone usage;

  • (***) add SDL2 dependency for FFmpeg 5.0.1 to build ffplay;

  • (***) add ffnvcodec build dependency to all recent FFmpeg easyconfigs;

  • (***) set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs;

  • (***) add missing zstd dep to Boost;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • restore initial environment before processing each easystack item (support for easystack files is still experimental);

  • various fixes and improvements for the EasyBuild framework test suite;

  • (***) fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions;

  • (***) fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets;

  • (***) fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x;

  • bug fixes for various generic easyblocks: CMakeMake, CMakePythonPackage, PythonPackage, PythonBundle;

  • bug fixes for various software-specific easyblocks: FlexiBLAS, netCDF, NVHPC, PyTorch;

  • (***) add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug;

  • (***) add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b;

  • (***) replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs;

  • (***) update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (see --skip);

  • (***) replace src include path with installation dir for HDF5;

  • (***) use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API;

  • (***) add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2;

  • (***) fix postinstallcmds in shovill easyconfigs;

  • (***) add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1

  • (***) add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs;

  • (***) enable -fPIC in GEOS 3.11.1 (required by GDAL);

  • add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes);

  • rename some software names in existing easyconfigs, or archive these easyconfigs, to avoid case-insensitive name clashes;

Supported software

Support for installing 99 (!) new software packages has been added, including (but not limited to):

  • CatLearn
  • Cellpose
  • chemprop
  • cuSPARSELt
  • DensPart
  • dorado
  • fastjet
  • finder
  • genomepy
  • grid
  • Health-GPS
  • HiCMatrix
  • Inferelator
  • kineto
  • LASSO-Python
  • netMHCII
  • PfamScan
  • plot1cell
  • PyTorch-Ignite
  • rapidNJ
  • scArches
  • scib
  • smfishHmrf
  • Strainberry
  • VirSorter2
  • YODA

This brings the total number of supported software packages to 2,995 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AlphaFold 2.3.0
  • AUGUSTUS 3.5.0
  • BCFtools 1.17
  • Biopython 1.81
  • Boost 1.81.0
  • CFITSIO 4.2.0
  • CUDA 12.1.0
  • DIAMOND 2.1.0,
  • epiScanpy 0.4.0
  • FFmpeg 5.1.2
  • GDAL 3.6.2
  • GPyTorch 1.9.1
  • h5py 3.8.0
  • HTSlib 1.17
  • Hypre 2.27.0
  • intel/2022.12 (incl. intel-compilers 2023.0.0, impi 2021.8.0, imkl 2023.0.0)
  • jax 0.4.4
  • MaSuRCA 4.1.0
  • MATLAB 2022b
  • MDAnalysis 2.4.2
  • mpi4py 3.1.4
  • NetLogo 6.3.0
  • networkx 3.0
  • numba 0.56.4
  • NVHPC 23.1
  • OpenMPI 4.1.5
  • PLUMED 2.8.1
  • pyGenomeTracks 3.8
  • PySCF 2.1.1
  • Python 3.11.2
  • R 4.2.2
  • ReFrame 4.0.5
  • ROOT 6.22.08
  • SAMtools 1.17,
  • scikit-learn 1.2.1
  • SciPy-bundle 2023.02,
  • SPAdes 3.15.5
  • TensorFlow 2.11.0
  • Trilinos 13.4.1
  • Xerces-C++ 3.2.4

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

  • 36 merged pull requests for EasyBuild framework
  • 34 merged pull requests for easyblocks
  • 386 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17568 # use easyconfig from PR #17568

Assets 2

EasyBuild v4.7.0

09 Jan 19:12
@boegel boegel
easybuild-v4.7.0
a467f23
This commit was signed with the committer’s verified signature.
boegel Kenneth Hoste
GPG key ID: 90C14B582D70E3BE
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EasyBuild v4.7.0

EasyBuild v4.7.0 is primarily a feature release, but it also includes various minor bug fixes and enhancements.

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

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

  • also run unit tests with Python 3.11;

  • add support for checksums specified in external checksums.json file;

  • take into account custom configuration options specified in easystack files - see also docs;

  • add support for using --output-format=md (MarkDown);

  • add support for postinstallmsgs;

  • add gfbf as subtoolchain of foss;

  • make iimkl toolchain aware of intel-compilers;

  • add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage + JuliaBundle;

  • updates and enhancements for various generic easyblocks, incl. ConfigureMake, PythonPackage;

  • (***) updates and enhancements for various software-specific easyblocks: BerkeleyGW, Clang, Clang-AOMP, ESMF, libxml2, LLVM, OpenCV, OpenMPI, PETSc, QScintill, TensorFlow, Xmipp;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • print deprecation warning with running EasyBuild with Python 2;

  • various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format;

  • vendor distutils.version.LooseVersion as easybuild.tools.LooseVersion
    (since distutils is deprecated in Python 3.10, to be removed in Python 3.12);

  • auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0;

  • use -march=x86-64 -mtune=generic instead of -xSSE2 when using Intel oneAPI compilers;

  • drop support for easystack files using 'software' top-level key;

  • make PythonPackage easyblock compatible with --sanity-check-only by loading module early during sanity check step;

  • (***) update HDF5 easyblock to use --enable-threadsafe configure option to make C API thread safe;

  • (***) bug fixes for various software-specific easyblocks: ANSYS, Clang, MRtrix, PyTorch;

Supported software

New version of common toolchains: foss/2022b, intel/2022b

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

  • Alfred
  • bamFilters
  • CAT-BAT
  • CloudCompare
  • COBRApy
  • CUDA-Samples
  • DeepLabCut
  • DRAGMAP
  • ESM-2
  • HighFive
  • IJulia
  • KaHIP
  • LHAPDF
  • Magics
  • MEMOTE
  • MONAI
  • MOOSE
  • MultilevelEstimators
  • napari
  • nf-core-mag
  • OmegaFold
  • pyccel
  • PyDamage
  • pyWannier90
  • scvi-tools
  • SELFIES
  • SISSO++
  • spaCy
  • Squidpy
  • TBA
  • trimesh
  • UCX-ROCm

This brings the total number of supported software packages to 2,904 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • AOCC 4.0.0
  • CDO 2.1.1
  • CubeGUI/CubeLib/CubeWriter 4.8
  • CUDA 11.8.0 + 12.0.0
  • deepdiff 5.8.1
  • FLANN 1.9.1
  • GATK 4.3.0.0
  • GDCM 3.0.20
  • Ghostscript 10.0.0
  • GRASS 8.2.0
  • JasPer 4.0.0
  • libspatialite 5.0.1
  • LLVM 15.0.5
  • Mesa 22.2.4
  • mold 1.7.1
  • MRChem 1.1.1
  • ncbi-vdb 3.0.0
  • nglview 3.0.3
  • nodejs 18.12.1
  • Octave 7.1.0
  • OpenFOAM 10
  • OpenFold 1.0.1
  • OpenMolcas 22.10
  • OpenStackClient 6.0.0
  • PAPI 7.0.0,
  • PETSc 3.17.4
  • pyproj 3.4.0
  • Python 3.10.8
  • PyTorch 1.12.1
  • PyTorch-Geometric 2.1.0
  • QGIS 3.28.1
  • Qt5 5.15.7
  • QtPy 2.2.1
  • ReFrame 3.12.0
  • scanpy 1.9.1
  • Score-P 8.0
  • SignalP 6.0g
  • SLEPc 3.17.2
  • SNAP 2.0.1
  • SpaceRanger 2.0.0
  • SuperLU_DIST 8.1.0
  • tensorboardX 2.5.1
  • TensorFlow 2.8.4
  • tesseract 5.3.0
  • Valgrind 3.20.0
  • Vim 9.0.0950
  • VTK 9.2.2
  • wandb 0.13.6
  • WebKitGTK+ 2.37.1
  • WPS/WRF 4.4
  • wxPython 4.2.0
  • X11 20221110
  • Xmipp 3.22.07

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

  • 42 merged pull requests for EasyBuild framework
  • 36 merged pull requests for easyblocks
  • 469 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.0, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 17065 # use easyconfig from PR #17065

Assets 2

EasyBuild v4.6.2

21 Oct 15:33
@boegel boegel
easybuild-v4.6.2
7f3bce7
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EasyBuild v4.6.2

EasyBuild v4.6.2 is primarily a bugfix and update release, but it also includes various minor enhancements.

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

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

  • enable running of LAPACK tests for recent OpenBLAS easyconfigs;

  • 2 new software-specific easyblocks: CUDA compatibility libraries (CUDAcompat) + mamba;

  • updates and enhancements for various software-specific easyblocks: OpenFOAM, ESMF, netCDF, numexpr;

  • enhance EasyBuildMeta easyblock: auto-enable installing with pip;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • (***) add patch to GCC 11.x + 12.x to fix vectorizer bug;

  • (***) add patch to fix failing LAPACK tests due to use of -ftree-vectorize;

  • correctly count the number of failing tests (not failing test suites) in PyTorch builds;

  • (***) add patches to fix incompatibilites between ASE and other packages in 2022a toolchain;

  • (***) fix execution permissions for bin/ngm* for NextGenMap v0.5.5;

  • (***) add bzip2 and libxml2 as dependencies for netCDF 4.9.0;

  • (***) add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0;

  • make --inject-checksums inject dictionary value for checksums which maps filename to SHA256 checksum;

  • fix trying to generate RPATH wrappers for Clang;

  • update easyconfigs to use SYSTEM template constant instead of True in dependencies;

Supported software

New version of intel toolchain: intel/2022.09

Support for installing 25 new software packages has been added, including (but not limited to):

  • AMAPVox
  • buildingspy
  • CDBtools
  • f90wrap
  • Miller
  • NVSHMEM
  • paladin
  • PyMOL
  • python-irodsclient
  • ruffus
  • TELEMAC-MASCARET
  • x13as

This brings the total number of supported software packages to 2,798 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • ASE 3.22.1
  • biogeme 3.2.10
  • Delly 1.1.5
  • ESMF 8.3.0
  • FDS 6.7.9
  • Go 1.18.3
  • GPAW 22.8.0
  • IPython 8.5.0
  • Julia 1.8.2
  • LIBSVM 3.30
  • netcdf4-python 1.6.1
  • Nipype 1.8.5,
  • OpenCV 4.6.0
  • OpenMM 7.7.0
  • Perl 5.36.0
  • PyTorch 1.12.0
  • PyTorch-Lightning 1.7.7
  • RDFlib 6.2.0
  • SAMtools 1.16.1
  • scikit-learn 1.1.2
  • Score-P 7.1
  • SuiteSparse 5.13.0
  • SUNDIALS 6.3.0
  • sympy 1.11.1
  • torchvision 0.13.1
  • TRIQS 3.1.1
  • UCX 1.13.1
  • VEP 107
  • Wayland 1.21.0
  • wxWidgets 3.2.1

These changes result from various contributions, made by 24 different contributors:

  • 17 merged pull requests for EasyBuild framework
  • 20 merged pull requests for easyblocks
  • 159 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 16465 # use easyconfig from PR #16465

Assets 2

EasyBuild v4.6.1

12 Sep 07:54
@boegel boegel
easybuild-v4.6.1
7ac370c
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EasyBuild v4.6.1

EasyBuild v4.6.1 is primarily a bugfix and update release, but it also includes various minor enhancements.

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

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

  • run python in the same process as eb wrapper script by using exec (which improves startup performance of eb command);

  • reduce the number of command line options for cmake command in CMakeMake generic easyblock;

  • enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when return_output_ec=True is used;

  • updates and enhancements for various software-specific easyblocks: GROMACS, LAMMPS, libQGLViewer, NVHPC, PyTorch;

  • (***) add extra symlinks and sanity checks for libtinfo in ncurses;

  • speed up OpenMPI 4.1.4 configure by not running autogen.pl --force, but only running required Autotools commands;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (rather than assuming that CMake is loaded as a build dependency);

  • don’t enable building of ld.gold when installing binutils on a RISC-V system + don’t configure GCC to use gold as default linker on a RISC-V system;

  • make Amber easyblock aware of FlexiBLAS;

  • tweak Amber(Tools) easyblock to run tests from top-level directory, and enable running of tests for AmberTools v20 + v21;

  • work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong;

  • various fixes for installing PyTorch on POWER systems;

  • (***) replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn’t use odd minor versions of HDF5 which are not stable releases;

  • (***) use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option);

  • (***) add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs;

  • (***) add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9;

  • simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency;

  • (***) add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 and 2021;

  • (***) fix checksum for Stacks v2.62 (due to silent re-release without version bump);

  • (***) consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs;

  • (***) update Java/11 to 11.0.16 and Java/17 to 17.0.4;

Supported software

Support for installing 37 new software packages has been added, including (but not limited to):

  • BigDFT
  • colossalai
  • Dakota
  • FastFold
  • how_are_we_stranded_here
  • libmad
  • MetaMorpheus
  • muMerge
  • olaFlow
  • OpenFAST
  • OpenFold
  • pyGenomeTracks
  • RheoTool
  • Satsuma2
  • UCC-CUDA
  • VESTA

This brings the total number of supported software packages to 2,773 (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 22.3
  • BCFtools 1.15.1
  • binutils 2.39
  • BLAST+ 2.13.0
  • CDO 2.0.5
  • CoordgenLibs 3.0.1,
  • Elk 8.5.2,
  • FFmpeg 4.4.2 + 5.0.1
  • FreeSurfer 7.3.2
  • GATE 9.2
  • GCC(core) 12.2.0
  • GDB 12.1
  • gnuplot 5.4.4
  • Graphviz 5.0.0
  • HDF5 1.12.2
  • HTSlib 1.15.1
  • Hypre 2.25.0,
  • jax 0.3.14,
  • LAMMPS 23Jun2022
  • Libint 2.7.2
  • maeparser 1.3.0
  • matplotlib 3.5.2
  • MATSim 14.0
  • medaka 1.6.0
  • Megalodon 2.5.0
  • MetaEuk 6,
  • MUMPS 5.5.1
  • netCDF-Fortran 4.6.0
  • ont-remora 1.0.0
  • OpenFOAM v2206
  • ParaView 5.10.1
  • Perl 5.36.0
  • Pyomo 6.4.2
  • PyStan 3.5.0
  • PyYAML 6.0
  • scikit-bio 0.5.7
  • scikit-learn 1.1.2
  • SCOTCH 7.0.1
  • spglib-python 2.0.0
  • SUMO 1.14.1
  • Valgrind 3.19.0
  • ViennaRNA 2.5.1
  • wxPython 4.1.1
  • zfp 1.0.0

These changes result from various contributions, made by 25 different contributors:

  • 16 merged pull requests for EasyBuild framework
  • 20 merged pull requests for easyblocks
  • 266 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.1, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 16240 # use easyconfig from PR #16240

Assets 2