Skip to content

EasyBuild v4.3.4
Compare
Choose a tag to compare
@boegel boegel released this 09 Apr 09:06
· 276 commits to develop since this release
easybuild-v4.3.4
d9e1582
This commit was signed with the committer’s verified signature. The key has expired.
boegel Kenneth Hoste
GPG key ID: 90C14B582D70E3BE
Expired
Verified
Learn about vigilant mode.

EasyBuild v4.3.4 is primarily a bugfix/update release, but also includes several useful 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 reinstalling easyconfigs are marked with (***)]

  • sort output of eb --search in natural order (respecting numbers);

  • enhance eb command to ensure that easybuild.main can be imported before settling on python* command to use;

  • deprecate --accept-eula configuration option, renamed to --accept-eula-for;

  • fix problem with downloading large files when running EasyBuild with a recent Python 3 version, by passing file-like object to write_file in download_file so that the data is read is chunks;

  • (***) set $R_LIBS_SITE rather than $R_LIBS when installing R packages;

  • make WRF and WPS easyblocks aware of (pre)configopts;

  • remove PYPI_SOURCE source URL from easyconfigs using PythonPackage or PythonBundle;

  • (***) enhance BWA and g2clib easyblocks to pass down compiler flags;

  • (***) avoid 0.0.0 install version for various Python apps, including carputils, deepdiff, EMU, maze, Open-Cube-Core, pytest, Spyder, suave;

  • (***) bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0;

  • (***) update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages;

  • (***) bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error;

  • (***) fix numpy tests for recent SciPy-bundle easyconfig on POWER;

  • (***) add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI;

  • (***) revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0;

  • (***) use -D_USE_METIS_5p1 in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0;

  • (***) rename opencv_contrib and update to OpenCV v3.4.1 with contrib versionsuffix;

Highlighted enhancements

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

  • avoid running expensive module use and module unuse commands when using Lmod as modules tool, update $MODULEPATH directly instead;

  • also accept regular expression value for --accept-eula-for;

  • update validate_github_token function to accept GitHub token in new format;

  • enhance cuDNN and CUDA easyblocks to support aarch64;

  • use PYPI_SOURCE as the default for source_urls of PythonPackage;

  • enhance PythonPackage easyblock to catch faulty version (0.0.0) for installed Python packages;

  • updated easyblocks for AOCC, CP2K, GROMACS, LAPACK, OpenCV, PETSc, PyTorch, VMD, VTune;

  • (***) add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a;

  • (***) add extensions to R-bundle-Bioconductor 3.12: motifmatchr (#12390), OUTRIDER + FRASER;

  • (***) add DMCfun + linkcomm + rnetcarto extensions to R v4.0.3;

Use "eb --rebuild --skip" to install the missing extensions for R and R-bundle-Bioconductor.

Supported software

Additional easyconfig file for existing goblf toolchain: goblf/2020b

Support for installing 41 new software packages has been added, including:

  • BEEF
  • CDAT
  • DL_POLY_4
  • ESMPy
  • GPyOpt
  • LncLOOM
  • LPJmL
  • MetaEuk
  • Myokit
  • PyOD
  • Ratatosk
  • scikit-cuda
  • Seeder
  • YACS

This brings the total number of supported software packages to 2,288!
An up-to-date list of supported software is available here.

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

  • AOCC 3.0.0
  • BUSCO 5.0.0
  • CP2K 8.1
  • CellRanger 6.0.0
  • Clang 11.0.1
  • dask 2021.2.0
  • Extrae 3.8.0
  • GROMACS 2021
  • Hypre 2.20.0
  • Kent_tools 411
  • LAPACK 3.9.1
  • libxc 5.1.3
  • MUMPS 5.3.5
  • NVHPC 21.2
  • OpenCV 4.5.1
  • PETSc 3.14.4
  • PLUMED 2.7.0
  • PyCUDA 2020.1
  • PyOpenCL 2021.1.2
  • PyTorch-Geometric 1.6.3
  • pocl 1.6
  • preCICE 2.2.0
  • pymatgen 2022.0.4
  • R 4.0.4
  • RDFlib 5.0.0
  • ReFrame 3.5.1
  • Ruby 2.7.2
  • SIMPLE 3.0.0
  • SUNDIALS 5.7.0
  • Seurat 4.0.1
  • Spark 3.1.1
  • tensorboardX 2.1
  • VTK 9.0.1

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

  • 29 merged pull requests for EasyBuild framework
  • 26 merged pull requests for easyblocks
  • 220 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.3.4, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release
  • eb --from-pr 12554 # use easyconfig from PR #12554
Assets 2
Loading