easybuilders/easybuild easybuild-v4.5.1

EasyBuild v4.5.1

on GitHub

EasyBuild v4.5.1 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.

Prominent bug fixes & changes

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

• don't try to ensure absolute path for path part of --repositorypath EasyBuild configuration option;

• only remove lock if it was created in the same EasyBuild session (not if it existed already);

• (***) minor fixes for various software-specific easyblocks: CP2K, MUMmer, netcdf4-python, ORCA, OpenFOAM, OpenMPI, PETSc, SLEPc;

• (***) add patch for libfabric v1.12.1 to fix unknown link width 0x10 warning;

• add patch for GCCcore 9.1-9.3 and 10.1-11.1 to fix compatibility with recent kernel headers;

• (***) add patch to fix CVE-2021-43527 in NSS;

• pass tests on A* GPUs by setting NVIDIA_TF32_OVERRIDE=0 in jax 0.2.19;

• (***) add patch to fix broken (hanging) Mash binaries;

• seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs;

• rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme;

• comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0;

• consistently use 'Grace' software name + sync homepage/source_urls;

Highlighted enhancements

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

• enhancements for experimental feature --parallel-extensions-install:

  • also determine which extensions can be skipped in parallel;
  • fall back to sequential installation for extensions with unknown dependencies;
  • see also https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html;

• allow oversubscription in sanity check for OpenMPI-based toolchains;

• new software-specific easyblock for Clang-AOMP;

• enhanced Rpm generic easyblock;

• updates and enhancements for various software-specific easyblocks: Eigen, GROMACS, Inspector, jaxlib, SAMtools, tbb;

• (***) additional extensions for R-bundle-Bioconductor 3.13;

• (***) additional extensions for R v4.1.x;

Supported software

Support for installing 71 new software packages has been added, including (but not limited to):

• BabelStream
• bamtofastq
• bcbio-gff
• Clang-AOMP
• CMSeq
• dRep
• DUBStepR
• elprep
• epiScanpy
• FMM3D
• HIP
• InChI
• LERC
• libtree
• Megalodon
• nnU-Net
• PPanGGOLiN
• ProFit
• PySide2
• ROCm
• Shasta
• SimNIBS
• SMV (Smokeview)
• ThemisPy
• TOBIAS
• zlib-ng
• Zopfli

This brings the total number of supported software packages to 2,575 (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 2.1.1
• Arrow 6.0.0
• Boost 1.77.0
• Eigen 3.4.0
• ESMF 8.2.0
• Flye 2.9
• Horovod 0.23.0
• ITK 5.2.1
• jax 0.2.24
• NCO 5.0.3
• OpenMPI 4.1.2
• pangolin 3.1.16
• PyTorch 1.10.0
• R 4.1.2
• R-bundle-Bioconductor 3.14
• scikit-learn 1.0.1
• torchvision 0.11.1
• Trycycler 0.5.2
• Unicycler 0.4.9
• UShER 0.5.0
• WPS 4.3.1
• Yambo 5.0.4

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

• 15 merged pull requests for EasyBuild framework
• 19 merged pull requests for easyblocks
• 244 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.1, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release

• eb --from-pr 14545 # use easyconfig from PR #14545