Dear EasyBuilders,
Small update: a workaround has been implemented for the divergent name
of source tarballs on PyPI for EasyBuild v4.9.2 that is caused by a
change in recent versions of setuptools and made "eb
--install-latest-eb-release" fail unless an updated custom easyblock for
installing EasyBuild with EasyBuild was being pulled in, see
https://github.com/easybuilders/easybuild-easyconfigs/pull/20818.
Long story short: "eb --install-latest-eb-release" will now work as
expected when running it with EasyBuild v4.9.1 (or prior) to install
EasyBuild v4.9.2 .
regards,
Kenneth
On 12/06/2024 18:57, Kenneth Hoste wrote:
Dear EasyBuilders,
It's our pleasure to announce the release of EasyBuild v4.9.2 [1].
Much to our surprise, we found a couple of bugs in earlier versions of
EasyBuild, but this time we're confident: this is the best EasyBuild
release to date!
EasyBuild v4.9.2 is primarily a bugfix & update release, but it also
includes various enhancements.
* Note: to install EasyBuild v4.9.2 with an earlier version of
EasyBuild, you will need to pull in a fix for the custom easyblock that
is used to install EasyBuild with EasyBuild, due to a change in
setuptools that has resulting in different names for the source tarballs
for EasyBuild v4.9.2 that have been uploaded to PyPI. More info below...
The executive summary for this release:
- EasyBuild API version checks to avoid mixing major versions across
the EasyBuild components;
- Bug fix for --from-commit, so easyconfigs for dependencies are
found if they're available in the commit;
- 4 new sofware-specific easyblocks: AEDT, MetalWalls, optiSLang,
QuantumESPRESSO with CMake;
- Support for installing 82 new software applications, tools, and
libraries;
- Easyconfigs for various recent software versions, including BLIS
1.0, Clang 17.0.6, GCC 13.3.0 + 14.1.0, IOR 4.0.0, OCaml 5.1.1, OpenMPI
5.0.3, PyTorch-bundle 2.1.2, Python 3.12.3, TensorFlow 2.15.1, and many
more;
- Bug fixes/changes to easyblocks/easyconfigs that require
reinstallation (more info below, marked with (***));
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-v4.9.2>>
## Highlighted enhancements & updates
[enhancements or updates that (may) warrant updating existing
installations are marked with (***)]
- implement EasyBuild API version checks to avoid mixing major versions
across the EasyBuild components;
- 4 software-specific easyblock for AEDT, MetalWalls, optiSLang,
QuantumESPRESSO with CMake;
- enhancement to PythonPackage generic easyblock;
- add a sanity check for OpenFOAM's wmake to make sure it finds the
compiler commands;
- refactor GAMESS-US easyblock to directly write install.info;
- additional updates & enhancements to custom easyblocks for ABAQUS,
Clang, CUDA, FFTW, Java, Mesa, OpenMPI, OpenSSL, torchvision, UCX-Plugins;
- (***) additional extensions for R-bundle-CRAN v2023.12;
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant re-installing easyconfigs are
marked with (***)]
- symlink downloaded repo at specified commit when using --from-commit
so easyconfigs for dependencies are found;
- bug fixes for CargoPythonBundle generic easyblock;
- bug fixes in custom easyblocks for intel-compilers and Python;
- (***) add patch to fix CVE-2024-27322 in R v3.6.x, v4.0.x, v4.1.x,
v4.2.x, v4.3.x;
- (***) fix detection of CC/CXX compilers for wmake in OpenFOAM v2306 +
v2312;
- (***) change arrow-R dependency of R-bundle-Bioconductor v3.18 to
v14.0.1;
- (***) add dependencies required for GUI in Cellpose 2.2.2 easyconfigs;
- (***) add missing dependencies for funannotate;
- (***) make sure mummerplot can use gnuplot if available for recent
MUMmer;
- remove easyconfigs for CellBender v0.3.1, since this version has been
redacted due to a serious bug (see
https://github.com/broadinstitute/CellBender/issues/306>>
## Supported software
Support for installing 82 new software packages has been added,
including (but not limited to):
AEDT
AMGX
Cassiopeia
CheckM2
Compass
CVX
EasyMocap
FDMNES
HiGHS
HOMER
LangChain
libabigail
LIBSVM-MATLAB
Lightning
MetalWalls
ml-collections
MOFA2
orthAgogue
planarity
PRRTE
PSM2
PyHMMER
PyVista
SCReadCounts
TF-COMB
TorchIO
VAMPIRE-ASM
WGDgc
This brings the total number of supported software packages to 3,552
(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):
AFNI 24.0.02
alevin-fry 0.9.0
BCFtools 1.19
BLIS 1.0
BWA 0.7.18
Boost 1.85.0
CGAL 5.6.1
CellRank 2.0.2
Clang 17.0.6
dask 2024.5.1
deal.II 9.5.2
dorado 0.5.3
ESPResSo 4.2.2
FMM3D 1.0.4
GAMESS-US 20220930-R2 + 20230930-R2
GCC 13.3.0 + 14.1.0
GOATOOLS 1.4.5
GTDB-Tk 2.4.0
gemmi 0.6.5
gmsh 4.12.2,
HDDM 0.9.9
HTSlib 1.19.1
HyPhy 2.5.60
h5py 3.11.0
IOR 4.0.0
Jupyter-bundle 20240522 (incl. JupyterHub 4.1.5, JupyterLab 4.2.0,
JupyterNotebook 7.2.0, ...)
Kalign 3.4.0
kallisto 0.50.1
MATSim 15.0
MetaMorpheus 1.0.5
MuJoCo 3.1.4
mold 2.31.0
NanoPlot 1.42.0
nglview 3.1.2
nvtop 3.1.0
OCaml 5.1.1
OpenMPI 5.0.3
PhyML 3.3.20220408
PyTorch-bundle 2.1.2
Python 3.12.3
petsc4py 3.20.3
polars 0.20.2
py3Dmol 2.1.0
pyiron 0.5.1
ROOT 6.30.06
Rust 1.78.0
SAMtools 1.19.2
SentencePiece 0.2.0
Seurat 5.1.0
SimNIBS 4.0.1
Spack 0.21.2
Squidpy 1.4.1
SymEngine 0.11.2
scikit-learn 1.4.2
TensorFlow 2.15.1
Transformers 4.39.3
tokenizers 0.15.2
UCX 1.16.0
Valgrind 3.23.0
VisPy 0.14.1
zlib-ng 2.1.6
These changes result from various contributions, made by 29 different
contributors:
* 16 merged pull requests for EasyBuild framework
* 27 merged pull requests for easyblocks
* 326 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.9.2, there are several options [5].
Two particularly easy options include:
* eb --include-easyblocks-from-pr 3358 --install-latest-eb-release
* eb --include-easyblocks-from-pr 3358 --from-pr 20801 #
use easyconfig from PR #20801 [6]
Note: due to a change in setuptools that affects the name of the source
tarballs for the different EasyBuild components that have been uploaded
to PyPI, you will need to instruct EasyBuild to pull in an updated
version of the custom easyblock that is used for installing EasyBuild
with EasyBuild, by running "eb --include-easyblocks-from-pr 3358".
This is only relevant when installing EasyBuild with EasyBuild, not when
installing EasyBuild with pip or another mechanism;
For more information, see [7].
Enjoy!
regards,
Kenneth, Sebastian, Miguel
[1]
https://pypi.org/project/easybuild/4.9.2>> [2]
https://docs.easybuild.io/release-notes/#release_notes_eb492>> [3]
https://docs.easybuild.io/partial-installations/#partial_installation_skip>> [4]
https://docs.easybuild.io/version-specific/supported-software>> [5]
https://docs.easybuild.io/installation/#updating>> [6]
https://github.com/easybuilders/easybuild-easyconfigs/pull/20801>> [7]
https://github.com/easybuilders/easybuild-easyblocks/pull/3358>
