easybuilders/easybuild easybuild-v4.5.0

EasyBuild v4.5.0

on GitHub

EasyBuild v4.5.0 is primarily a feature release, but it also includes various minor bug fixes 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 (***))

• support for showing progress bars when installing easyconfigs;

  • enabled by default if the Rich Python package (https://pypi.org/project/rich) is installed;
  • see https://docs.easybuild.io/en/latest/Progress_bars.html for more information;

• add initial/experimental support for installing extensions in parallel;

  • currently only supported for R extensions;
  • see https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html for more information;

• add support for checking required/optional EasyBuild dependencies via eb --check-eb-deps;

• add support for --insecure-download configuration option;

• one new software-specific custom easyblock for imkl-FFTW;

• enhance GCC easyblock to add support for AMD GPU offloading;

• enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend;

• enhance imkl easyblock to add support for installing with NVHPC;

• (***) detect problem with compiling CPU detection code in configure output in GROMACS easyblock;

  • only relevant for specific GROMACS versions that were installed using CMake 3.15.3;

• easyconfigs for foss/2021b and intel/2021b common toolchains;

  • see also https://docs.easybuild.io/en/latest/Common-toolchains.html#overview-of-common-toolchains;

Prominent bug fixes & changes

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

• deprecate old toolchain versions (pre-2019a common toolchains);

  • see also https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains;

• refactor EasyBlock to decouple collecting of information on extension source/patch files from downloading them;

• change copy_file function to raise an error when trying to copy non-existing file;

• fix library paths to add to $LDFLAGS for intel-compilers toolchain component;

• restore RPATH wrappers for OpenMPI sanity check;

• (***) don’t use --config=mkl configuration option when installing TensorFlow 2.4+;

  • this fixes some performance related issues for TensorFlow installations, see release notes for more details;

• (***) in-place updates for components of foss/2021b and intel/2021b common toolchains;

  • see release notes for more details;

• (***) add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0;

• (***) add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection;

Supported software

Support for installing 39 new software packages has been added, including (but not limited to):

• ARTS
• bashplotlib
• CIRI-long
• ESL-Bundle
• FreeTDS
• imkl-FFTW
• libSBML
• longread_umi
• MixMHC2pred
• OpenSceneGraph
• pycoQC
• radeontop
• RInChI
• scGeneFit
• TOML-Fortran
• vawk
• VMTK

This brings the total number of supported software packages to 2,506 (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 2.0.1
• artic-ncov2019 2021.06.24
• BerkeleyGW 3.0.1
• CP2K 8.2
• CUDA 11.4.2
• Dalton 2020.0
• ELSI 2.7.1
• FFTW 3.3.10
• jax 0.2.20
• ibxc 5.1.6
• MEME 5.4.1
• OpenBLAS 0.3.18
• OSU-Micro-Benchmarks 5.8
• PyTorch-Geometric 2.0.1
• Qiskit 0.31.0
• QuantumESPRESSO 6.8
• RDKit 2021.03.4
• SAMtools 1.13
• SciPy-bundle 2021.10
• UCX + UCX-CUDA 1.11.2
• Z3 4.8.12

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

• 40 merged pull requests for EasyBuild framework
• 33 merged pull requests for easyblocks
• 225 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.0, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release
• eb --from-pr 14248 # use easyconfig from PR #14248