easybuilders/easybuild easybuild-v4.5.4

EasyBuild v4.5.4

on GitHub

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:

• 19 merged pull requests for EasyBuild framework
• 24 merged pull requests for easyblocks
• 163 merged pull requests for easyconfigs

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