easybuilders/easybuild easybuild-v4.5.2

EasyBuild v4.5.2

on GitHub

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