Dear EasyBuilders,
I'm happy to announce the release of EasyBuild v4.3.4 [1].
As usual, the world has come up with creative ways of distracting you
from the many improvements that are available in this release, like a
way too big container ship blocking the Suez canal...
What will they think of next?!
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 [2] which includes links to the respective pull
requests for more detailed information.
(this information is also available at
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.3.4)
## 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 (see [3]);
## 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 at [4].
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 [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 12554 # use easyconfig from PR #12554 [6]
Enjoy!
regards,
Kenneth & Miguel
[1] https://pypi.org/project/easybuild/4.3.4
[2]
https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-3-4-apr-9th-2021
[3]
https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip
[4]
https://docs.easybuild.io/en/latest/version-specific/Supported_software.html
[5]
https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation
[6] https://github.com/easybuilders/easybuild-easyconfigs/pull/12554/files
