Dear EasyBuilders,
We're happy to announce the release of EasyBuild v4.6.1 [1].
An independent jury of experts thoroughly evaluated this release, and
reached the unanimous conclusion that this is the best EasyBuild release
to date!
As usual, there's a lot of attempts to distract you from this, including
soaring gas prices, granting rest to The Queen, and a Belgian 22-year
old brat winning the Vuelta (w00! \o/). What will they think of next...
The executive summary for this release:
- various minor bug fixes for EasyBuild framework;
- various bug fixes and enhancements to existing easyconfigs and
easyblocks;
- easyconfigs for various recent software versions: GATE v9.2,
Graphviz v5.0.0, LAMMPS v23Jun2022, OpenFOAM v2206, ...
- support for installing 37 new software applications and libraries;
EasyBuild v4.6.1 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 [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-v4.6.1)
## Highlighted enhancements
[enhancements that (may) warrant updating existing installations are
marked with (***)]
- run python in the same process as eb wrapper script by using exec
(which improves startup performance of eb command);
- reduce the number of command line options for cmake command in
CMakeMake generic easyblock;
- enhance PythonPackage easyblock to make sure all test command output
makes it to the EasyBuild log, also when return_output_ec=True is used;
- updates and enhancements for various software-specific easyblocks:
GROMACS, LAMMPS, libQGLViewer, NVHPC, PyTorch;
- (***) add extra symlinks and sanity checks for libtinfo in ncurses;
- speed up OpenMPI 4.1.4 configure by not running autogen.pl --force,
but only running required Autotools commands;
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant reinstalling easyconfigs are
marked with (***)]
- use det_cmake_version function to determine CMake version in CMakeMake
generic easyblock (rather than assuming that CMake is loaded as a build
dependency);
- don’t enable building of ld.gold when installing binutils on a RISC-V
system + don’t configure GCC to use gold as default linker on a RISC-V
system;
- make Amber easyblock aware of FlexiBLAS;
- tweak Amber(Tools) easyblock to run tests from top-level directory,
and enable running of tests for AmberTools v20 + v21;
- work around miscompilation of OpenBLAS on POWER by compiling with
-fstack-protector-strong;
- various fixes for installing PyTorch on POWER systems;
- (***) replace HDF5 v1.13.1 with v1.12.1 as dependency, since we
shouldn’t use odd minor versions of HDF5 which are not stable releases;
- (***) use versioned symbols in ncurses built with system toolchain (by
adding --with-versioned-syms configure option);
- (***) add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all
OSs;
- (***) add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9;
- simplify AlphaFold foss/2021a easyconfigs by using a fleshed out
patched OpenMM dependency;
- (***) add patch to fix missing sync in LINCS and SETTLE CUDA kernels
for GROMACS 2020 and 2021;
- (***) fix checksum for Stacks v2.62 (due to silent re-release without
version bump);
- (***) consistently add maeparser + CoordgenLibs dependencies to
OpenBabel 3.1.1 easyconfigs;
- (***) update Java/11 to 11.0.16 and Java/17 to 17.0.4;
## Supported software
Support for installing 37 new software packages has been added,
including (but not limited to):
BigDFT
colossalai
Dakota
FastFold
how_are_we_stranded_here
libmad
MetaMorpheus
muMerge
olaFlow
OpenFAST
OpenFold
pyGenomeTracks
RheoTool
Satsuma2
UCC-CUDA
VESTA
=> This brings the total number of supported software packages to
2,773 (excluding extensions)!
An up-to-date list of supported software is available at [4].
Various software updates have been added, including (but not limited to):
AmberTools 22.3
BCFtools 1.15.1
binutils 2.39
BLAST+ 2.13.0
CDO 2.0.5
CoordgenLibs 3.0.1,
Elk 8.5.2,
FFmpeg 4.4.2 + 5.0.1
FreeSurfer 7.3.2
GATE 9.2
GCC(core) 12.2.0
GDB 12.1
gnuplot 5.4.4
Graphviz 5.0.0
HDF5 1.12.2
HTSlib 1.15.1
Hypre 2.25.0,
jax 0.3.14,
LAMMPS 23Jun2022
Libint 2.7.2
maeparser 1.3.0
matplotlib 3.5.2
MATSim 14.0
medaka 1.6.0
Megalodon 2.5.0
MetaEuk 6,
MUMPS 5.5.1
netCDF-Fortran 4.6.0
ont-remora 1.0.0
OpenFOAM v2206
ParaView 5.10.1
Perl 5.36.0
Pyomo 6.4.2
PyStan 3.5.0
PyYAML 6.0
scikit-bio 0.5.7
scikit-learn 1.1.2
SCOTCH 7.0.1
spglib-python 2.0.0
SUMO 1.14.1
Valgrind 3.19.0
ViennaRNA 2.5.1
wxPython 4.1.1
zfp 1.0.0
These changes result from various contributions, made by 25 different
contributors:
* 16 merged pull requests for EasyBuild framework
* 20 merged pull requests for easyblocks
* 266 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.6.1, there are several options [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 16240 # use easyconfig from PR #16240 [6]
Enjoy!
regards,
Kenneth & Miguel
[1] https://pypi.org/project/easybuild/4.6.1
[2]
https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-6-1-september-12th-2022
[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/16240
