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EasyBuild v4.7.2

27 May 23:00
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easybuild-v4.7.2
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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

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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

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EasyBuild v4.7.0

09 Jan 19:12
@boegel boegel
easybuild-v4.7.0
a467f23
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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

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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

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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

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EasyBuild v4.6.0

08 Jul 10:50
@boegel boegel
easybuild-v4.6.0
2234b62
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EasyBuild v4.6.0

EasyBuild v4.6.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

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 OneAPI compilers using toolchain option 'oneapi';

  • add support for setting environment variables via 'pushenv' with modextravars;

  • fall back to sequential extension install if parallel install is not implemented;

  • one new software-specific custom easyblock for STAR-CCM+;

  • updates and enhancements for various software-specific easyblocks: FFTW, Libint, OpenSSL, Siesta, TensorFlow, WPS;

  • add support for allowing some PyTorch tests to fail + print warning if one or more tests fail;

  • easyconfigs for foss/2022a and intel/2022a common toolchains (see also here);

  • (***) additional extensions for R v4.2.0 (see --skip);

  • (***) add patch for GCCcore 11.3.0 to support using -fuse-ld=mold;

Prominent bug fixes & changes

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

  • tweak 'eb' wrapper script to correctly handle errors when python command being considered fails to run;

  • tweak is_patch_for function to make it more robust;

  • tweak apply_patch function to not create .orig files (by default) when applying patch files;

  • make sure that CMakeMakeCp generic easyblock uses correct build dir;

  • make VEP easyblock compatible with --sanity-check-only;

  • only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension;

  • switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1;

  • (***) avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs;

  • (***) correct configopts in deal.II v9.1.1 easyconfig;

Supported software

Support for installing 24 new software packages has been added, including (but not limited to):

  • fio
  • G-PhoCS
  • Gibbs2
  • Minipolish
  • NetPyNE
  • SISSO
  • sklearn-pandas
  • SWIPE
  • topaz
  • uncertainty-calibration

This brings the total number of supported software packages to 2,736 (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 2.2.2
  • Arrow 8.0.0
  • CellRanger 7.0.0
  • deal.II 9.3.3
  • FSL 6.0.5.1
  • GDAL 3.5.0
  • geopandas 0.11.0
  • GEOS 3.10.3
  • h5py 3.7.0
  • HDF5 1.13.1
  • ImageMagick 7.1.0-37
  • jemalloc 5.3.0
  • Leptonica 1.82.0
  • libRmath 4.2.0
  • libxc 5.2.3
  • MaSuRCA 4.0.9
  • mold 1.3.0
  • netCDF 4.9.0
  • NEURON 7.8.2
  • NLopt 2.7.1
  • nvtop 2.0.2
  • PLUMED 2.8.0,
  • PRISMS-PF 2.2
  • PROJ 9.0.0
  • PyTorch 1.11.0
  • Qt5 5.15.5
  • QuantumESPRESSO 7.1
  • R 4.2.1
  • Ray-project 1.13.0
  • ReFrame 3.11.2
  • SpectrA 1.0.1
  • TensorFlow 2.7.1
  • UCX-CUDA 1.12.1
  • WPS 3.9.1

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

  • 17 merged pull requests for EasyBuild framework
  • 17 merged pull requests for easyblocks
  • 149 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.0, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 15832 # use easyconfig from PR #15832

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EasyBuild v4.5.5

08 Jun 08:52
@boegel boegel
easybuild-v4.5.5
3e4a563
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EasyBuild v4.5.5

EasyBuild v4.5.5 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.

Prominent bug fixes & changes

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

  • set $FFT(W)_LIB_DIR to imkl-FFTW’s lib path in build environment if usempi toolchain option is enabled;

  • fix 'eb --show-system-info' on Apple M1 system;

  • remove system-compiled binutils dirs from $LDFLAGS in binutils easyblock;

  • (***) add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal;

  • (***) disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b;

  • (***) also symlink cert.pem in from-source OpenSSL installation (if it exists), to ensure that system certificates are found;

  • use x.py to bootstrap Rust so that build options are properly passed through;

  • (***) add hwloc dependency to tbb v2021.4.0;

  • (***) define $HHLIB as path to HH-suite installation directory, required by Perl scripts;

  • (***) add missing parallel and tbl2asn dependencies for prokka 1.14.5;

  • (***) also build shared library + fix $PYTHONPATH for gmsh 4.9.0;

  • add missing dependencies + switch to non-static build for Arriba v2.1.0;

  • (***) add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain;

  • (***) update fallback version for OpenSSL 1.1 wrapper to v1.1.1o;

  • (***) install sklearn meta-package with scikit-learn v1.0.1;

Highlighted enhancements & changes

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

  • change 'eb' command to import easybuild.framework to check if EasyBuild framework is available;

  • add toolchain definitions for nvompi (NVHPC + OpenMPI),
    nvpsmpi (NVHPC + ParaStationMPI), and gfbf (GCC, FlexiBLAS, FFTW);

  • add support for FFTW.MPI toolchain component;

  • add support for customizing EasyBuild command used in jobs via --job-eb-cmd;

  • add support to ConfigureMake for tweaking (first part of) test command via 'test_cmd';

  • 1 new software-specific easyblock for FFTW.MPI;

  • updates and enhancements for various software-specific easyblocks: ABAQUS, Clang, cuDNN, FFTW, LLVM, Mesa, MrBayes, NEURON, OpenMPI, OpenSSL wrapper, R, SuperLU, TensorFlow;

  • don't use gold linker by default for GCC >= 11.3;

  • add candidates for 2022a common toolchains: foss/2022.05, intel/2022.05;

  • (***) also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0;

  • (***) additional extensions for R-bundle-Bioconductor 3.14 + R v4.1.2 (see --skip);

  • (***) update Arrow to use EasyBuild-provided versions of some dependencies and enable all compression codecs;

  • (***) add csh -> tcsh symlink in recent tcsh easyconfigs;

Supported software

Support for installing 35 new software packages has been added, including (but not limited to):

  • Albumentations
  • arosics
  • CellTypist
  • detectron2
  • EigenExa
  • FFTW.MPI
  • FreeBarcodes
  • GTK4
  • i7z
  • ModelTest-NG
  • OGDF
  • panito
  • parameterized
  • ruamel.yaml
  • SCGid
  • scPred
  • smooth-topk
  • SPOTPY
  • UCC
  • Wayland
  • XGrafix
  • XPLOR-NIH

This brings the total number of supported software packages to 2,711 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • ABAQUS 2022
  • ARGoS 3.0.0
  • astropy 5.0.4
  • Bazel 4.2.2 + 5.1.1
  • binutils 2.38
  • BLIS 0.9.0
  • Boost 1.79.0
  • cryoDRGN 1.0.0
  • CUDA 11.7.0
  • FlexiBLAS 3.2.0
  • GCC 9.5.0 + 11.3.0 + GCC 12.1.0
  • Go 1.18.1
  • GTDB-Tk 2.0.0
  • GTK3 3.24.33
  • gzip 1.12,
  • Hypre 2.24.0
  • IMB 2021.3
  • IQ-TREE 2.2.1
  • jax 0.3.9
  • libfabric 1.15.1
  • LLVM 14.0.3
  • magma 2.6.2
  • Mathematica 13.0.0
  • Mesa 22.0.3
  • mold 1.2.1
  • MUMPS 5.5.0
  • Nim 1.6.6
  • OpenMPI 4.1.4
  • OSU-Micro-Benchmarks 5.9
  • Perl 5.34.1
  • PMIx 4.1.2
  • Python 3.10.4
  • R 4.2.0
  • R-bundle-Bioconductor 3.15
  • ReFrame 3.11.0
  • Rust 1.60.0
  • SAMtools 1.15.1
  • SciPy-bundle 2022.05
  • SeqKit 2.2.0
  • Spack 0.17.2
  • Spark 3.2.1
  • SuperLU 5.3.0
  • ToFu 1.5.0
  • UCX 1.12.1
  • X11 2022050
  • zlib 1.2.12

These changes result from various contributions, made by 21 different contributors:

  • 17 merged pull requests for EasyBuild framework
  • 25 merged pull requests for easyblocks
  • 272 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.5, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release
  • eb --from-pr 15635 # use easyconfig from PR #15635
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EasyBuild v4.5.4

31 Mar 12:54
@boegel boegel
easybuild-v4.5.4
5b452cc
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EasyBuild v4.5.4

EasyBuild v4.5.4 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.

Prominent bug fixes & changes

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

  • close log after installing a Bundle component, to avoid leaking log files across installations;

  • set $NINJAFLAGS to make sure Ninja doesn’t use all visible cores when building Qt5;

  • replace hardcoded /tmp to make sure that Bazel build respects $TMPDIR;

  • add alternative checksum for norm, optmatch extensions in R 4.1.0 and R 4.1.2 easyconfigs;

  • avoid pollution in the tmp directory when running the AlphaFold tests;

  • (***) downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs;

  • fix GBprocesS easyconfig by switching to source tarball created using git_config;

  • fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON;

  • add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain;

  • (***) configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults;

  • set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs;

  • (***) add patch to fix shared linking in vcflib;

  • fix failing sanity check for PRINSEQ that occurs as a result of adding support to Tarball easyblock for installing extensions;

Highlighted enhancements & changes

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

  • add support for post-install patches;

  • add support for specifying download instructions that are printed when source files are not found and can not be downloaded;

  • also try collecting AMD GPU info (via rocm-smi) for --show-system-info;

  • enable code linting check for all supported Python versions;

  • add gmpit toolchain definition (GCC + MPItrampoline);

  • enhance Tarball easyblock to support using it for installing extensions;

  • (***) build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via $FLEXIBLAS_LIBRARY_PATH;

  • updates, enhancements and fixes for various software-specific easyblocks: Anaconda, Clang-AOMP, Gurobi, imkl, intel-compilers, Java, MRtrix, OpenSSL, Python, TensorFlow, wxPython;

  • add check to verify that patch files touched in PRs have a description in place;

  • (***) additional extensions for Perl v5.34.0, R v4.1.2, R-bundle-Bionconductor v3.14 (see --skip;

  • (***) also install rMATS_P commands in rMATS-turbo easyconfig;

  • (***) add Flask-Session to Flask v1.1.4 and Flask v2.0.2;

  • (***) enhance vcflib easyconfigs to also install scripts;

  • (***) use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3;

  • consistently use system toolchain in EasyBuild easyconfigs;

Supported software

Support for installing 29 new software packages has been added, including (but not limited to):

  • Abseil
  • ArchR
  • CMAverse
  • Devito
  • GraphMap
  • Hydra
  • M1QN3
  • MAGeCK
  • MEGAN
  • ONNX
  • ont-remora
  • Optuna
  • porefoam
  • presto
  • PyFrag
  • skorch
  • SPM
  • STRique

This brings the total number of supported software packages to 2,667 (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 2.1.2
  • AmberTools 21
  • BLIS 3.1
  • DFTB+ 21.1
  • DIRAC 22.0
  • ELPA 2021.11.001
  • FlexiBLAS 3.1.3
  • IgBLAST 1.18.0
  • ITSx 1.1.3
  • Julia 1.7.2,
  • libtree 3.0.3,
  • matplotlib 3.5.1
  • MDAnalysis 1.1.1 + 2.0.0,
  • medaka 1.5.0
  • NLTK 3.7
  • numexpr 2.8.1
  • OpenAI-Gym 0.21.0
  • OpenBLAS 0.3.20
  • PIPITS 2.8
  • pocl 1.8
  • pyEGA3 4.0.0
  • SAMtools 1.15
  • SBCL 2.2.1
  • shovill 1.1.0
  • sympy 1.9
  • VirtualGL 3.0
  • VTK 9.1.0
  • XGBoost 1.5.0

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

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

To upgrade to EasyBuild v4.5.4, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 15214 # use easyconfig from PR #15214

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EasyBuild v4.5.3

11 Feb 11:06
@boegel boegel
easybuild-v4.5.3
2e1572a
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EasyBuild v4.5.3

EasyBuild v4.5.3 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.

Prominent bug fixes & changes

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

  • avoid crash in get_os_version on modern SLES-based OSs;

  • fix get_os_name and get_os_version to avoid reporting UNKNOWN in output of eb --show-system-info;

  • switch to using pip3 for installing EasyBuild in container recipes generated by EasyBuild;

  • (***) add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1;

  • (***) add patch to fix Kraken2 ncbi ftp/https check in rsync_from_ncbi.pl for versions 2.0.9-2.1.1;

  • (***) consistently apply patch for mapDamage 2.2.1 to use external seqtk;

  • fix download URL in UDUNITS v2.2.28 easyconfigs;

  • add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 and R 4.1.2 easyconfigs;

Highlighted enhancements & changes

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

  • new software-specific easyblock for reticulate R package;

  • updates and enhancements for various software-specific easyblocks: CUDA, HDF5, NAMD;

  • (***) set CUDA target architecture(s) for GROMACS based CUDA compute capabilities listed in EasyBuild configuration;

  • (***) also install Python bindings for SHTns 3.5.1;

Supported software

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

  • Arcade-Learning-Environment
  • Bambi
  • CASTEP
  • deepmedic
  • histolab
  • MuJoCo + mujoco-py
  • OpenCensus-python
  • PyEVTK
  • pyradiomics
  • PyTorch-Lightning
  • Redis
  • SoXt
  • SURVIVOR
  • xtensor

This brings the total number of supported software packages to 2,647 (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 3.2.0
  • Bowtie 1.3.1
  • Clang 13.0.1
  • ConnectomeWorkbench 1.5.0
  • CUDA 11.5.1 + 11.6.0
  • dask 2022.1.0
  • deepTools 3.5.0
  • FDS 6.7.7
  • GATE 9.1
  • Geant4 11.0.0
  • Graphviz 2.50.0
  • GROMACS 2021.5
  • JupyterLab 3.2.8
  • MEGA 11.0.10
  • methylpy 1.2.9
  • minimap2 2.24
  • ncbi-vdb 2.11.2
  • OpenCV 4.5.5
  • pyFAI 0.20.0
  • Racon 1.5.0
  • RAxML 8.2.12
  • ReFrame 3.10.1
  • ROOT 6.24.06
  • scikit-image 0.19.1
  • SeqKit 2.1.0
  • Siesta 4.1.5
  • SqueezeMeta 1.5.0
  • torchvision 0.11.3

These changes result from various contributions, made by 21 different contributors:

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

To upgrade to EasyBuild v4.5.3, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release
  • eb --from-pr 14979 # use easyconfig from PR #14979
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EasyBuild v4.5.2

24 Jan 21:33
@boegel boegel
easybuild-v4.5.2
0bfc619
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EasyBuild v4.5.2

EasyBuild v4.5.2 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.

Prominent bug fixes & changes

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

  • fix compatibility with Python 3.10;

  • minor fixes for IntelBase generic easyblocks and various software-specific easyblocks: CP2K, GATE, Perl, Siesta, WRF;

  • (***) add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ...;

  • (***) fix broken patch file for recent GPAW versions;

  • (***) add missing PCRE dependency for pullseq;

  • (***) enforce using internal Boost for bcl2fastq2 with a GCC 10.x toolchain;

  • (***) add patches to fix CVE-2021-23437 for Pillow and Pillow-SIMD;

Highlighted enhancements & changes

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

  • enhance get_cpu_architecture and get_cpu_family to be aware of RISC-V;

  • deprecate use of (actual) patch files that don’t have a filename ending with .patch;

  • add support for enabling sanity checks for specific components in the Bundle easyblock;

  • use all available cores for running Perl test suite;

  • updates and enhancements for various software-specific easyblocks: AOCC, CUDA, Bazel, Gurobi, intel-compilers, itac, LibInt, Mathematica, NAMD, SuiteSparse, WPS;

  • bundle LAPACKE with FlexiBLAS 3.0.4;

  • (***) additional extensions for R-bundle-Bioconductor 3.14;

  • (***) additional extensions for R v4.1.2;

  • (***) update Java 1.8 wrapper to 1.8.0_311 for x86_64;

  • (***) bump nbconvert extension in recent IPython easyconfigs to version 6.4.0;

  • update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain;

Supported software

Support for installing 48 new software packages has been added, including (but not limited to):

  • ANGEL
  • Calcam
  • DyMat
  • ExaML
  • FMPy
  • hivtrace
  • MetaPhlAn
  • mold
  • OpenFace
  • PhyloPhlAn
  • PuLP
  • PyTorch3D
  • SCopeLoomR
  • SHTns
  • TALYS
  • xxHash

This brings the total number of supported software packages to 2,622 (excluding extensions)!
An up-to-date list of supported software is available here.

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

  • intel/2022.00 toolchain
  • antiSMASH 5.2.0
  • BLAST+ 2.12.0
  • CP2K 8.2
  • Extrae 3.8.3
  • gmsh 4.9.0
  • h5py 3.6.0
  • IQ-TREE 2.1.3
  • Java/15 + Java/17
  • libxsmm 1.17
  • MultiQC 1.11
  • numba 0.54.1
  • NVHPC 21.11,
  • openCARP 8.2
  • OpenCV 3.4.1
  • OpenFOAM v2112
  • Pillow + Pillow-SIMD 8.3.2
  • PLUMED 2.7.3
  • Raysect 0.7.1
  • scanpy 1.8.2
  • SqueezeMeta 1.0.0
  • statsmodels 0.13.1

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

  • 16 merged pull requests for EasyBuild framework
  • 23 merged pull requests for easyblocks
  • 199 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.2, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release
  • eb --from-pr 14830 # use easyconfig from PR #14830
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