easybuilders/easybuild easybuild-v4.5.3

EasyBuild v4.5.3

on GitHub

EasyBuild v4.5.3 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 (***))

• avoid crash in get_os_version on modern SLES-based OSs;

• fix get_os_name and get_os_version to avoid reporting UNKNOWN in output of eb --show-system-info;

• switch to using pip3 for installing EasyBuild in container recipes generated by EasyBuild;

• (***) add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1;

• (***) add patch to fix Kraken2 ncbi ftp/https check in rsync_from_ncbi.pl for versions 2.0.9-2.1.1;

• (***) consistently apply patch for mapDamage 2.2.1 to use external seqtk;

• fix download URL in UDUNITS v2.2.28 easyconfigs;

• add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 and R 4.1.2 easyconfigs;

Highlighted enhancements & changes

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

• new software-specific easyblock for reticulate R package;

• updates and enhancements for various software-specific easyblocks: CUDA, HDF5, NAMD;

• (***) set CUDA target architecture(s) for GROMACS based CUDA compute capabilities listed in EasyBuild configuration;

• (***) also install Python bindings for SHTns 3.5.1;

Supported software

Support for installing 25 new software packages has been added, including (but not limited to):

• Arcade-Learning-Environment
• Bambi
• CASTEP
• deepmedic
• histolab
• MuJoCo + mujoco-py
• OpenCensus-python
• PyEVTK
• pyradiomics
• PyTorch-Lightning
• Redis
• SoXt
• SURVIVOR
• xtensor

This brings the total number of supported software packages to 2,647 (excluding extensions)!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

• AOCC 3.2.0
• Bowtie 1.3.1
• Clang 13.0.1
• ConnectomeWorkbench 1.5.0
• CUDA 11.5.1 + 11.6.0
• dask 2022.1.0
• deepTools 3.5.0
• FDS 6.7.7
• GATE 9.1
• Geant4 11.0.0
• Graphviz 2.50.0
• GROMACS 2021.5
• JupyterLab 3.2.8
• MEGA 11.0.10
• methylpy 1.2.9
• minimap2 2.24
• ncbi-vdb 2.11.2
• OpenCV 4.5.5
• pyFAI 0.20.0
• Racon 1.5.0
• RAxML 8.2.12
• ReFrame 3.10.1
• ROOT 6.24.06
• scikit-image 0.19.1
• SeqKit 2.1.0
• Siesta 4.1.5
• SqueezeMeta 1.5.0
• torchvision 0.11.3

These changes result from various contributions, made by 21 different contributors:

• 13 merged pull requests for EasyBuild framework
• 10 merged pull requests for easyblocks
• 156 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.3, there are several options.
Two particularly easy options include:

• eb --install-latest-eb-release
• eb --from-pr 14979 # use easyconfig from PR #14979