easybuilders/easybuild easybuild-v4.5.5

EasyBuild v4.5.5

on GitHub

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