Dear EasyBuilders,
It's our pleasure to announce the release of EasyBuild v4.5.4 [1].
We figured it was best to push our this release before tomorrow, to
prevent that people assume we're just joking around...
We're not though, since this is our best release to date!
EasyBuild v4.5.4 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-v4.5.4)
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant re-installing easyconfigs are
marked with (***)]
- close log after installing a Bundle component, to avoid leaking log
files across installations;
- set $NINJAFLAGS to make sure Ninja doesn’t use all visible cores when
building Qt5;
- replace hardcoded /tmp to make sure that Bazel build respects $TMPDIR;
- add alternative checksum for norm, optmatch extensions in R 4.1.0 and
R 4.1.2 easyconfigs;
- avoid pollution in the tmp directory when running the AlphaFold tests;
- (***) downgrade dependency on nodejs + use jupyter-server-proxy in
jupyter-matlab-proxy and configurable-http-proxy easyconfigs;
- fix GBprocesS easyconfig by switching to source tarball created using
git_config;
- fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON;
- add patch to fix linking error for imread extension in scikit-image
easyconfigs using intel toolchain;
- (***) configure libffi 3.4.2 with --disable-exec-static-tramp to
prevent segfaults;
- set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA
easyconfigs;
- (***) add patch to fix shared linking in vcflib;
- fix failing sanity check for PRINSEQ that occurs as a result of adding
support to Tarball easyblock for installing extensions;
## Highlighted enhancements & changes
[enhancements that (may) warrant updating existing installations are
marked with (***)]
- add support for post-install patches;
- add support for specifying download instructions that are printed when
source files are not found and can not be downloaded;
- also try collecting AMD GPU info (via rocm-smi) for --show-system-info;
- enable code linting check for all supported Python versions;
- add gmpit toolchain definition (GCC + MPItrampoline);
- enhance Tarball easyblock to support using it for installing extensions;
- (***) build single-file shared libraries for imkl so it can be used as
FlexiBLAS backend via $FLEXIBLAS_LIBRARY_PATH;
- updates, enhancements and fixes for various software-specific
easyblocks: Anaconda, Clang-AOMP, Gurobi, imkl, intel-compilers, Java,
MRtrix, OpenSSL, Python, TensorFlow, wxPython;
- add check to verify that patch files touched in PRs have a description
in place;
- (***) additional extensions for Perl v5.34.0, R v4.1.2,
R-bundle-Bionconductor v3.14 [3];
- (***) also install rMATS_P commands in rMATS-turbo easyconfig;
- (***) add Flask-Session to Flask v1.1.4 and Flask v2.0.2;
- (***) enhance vcflib easyconfigs to also install scripts;
- (***) use typing-extensions from Python v3.9.6 easyconfig in ArviZ and
PyMC3;
- consistently use system toolchain in EasyBuild easyconfigs;
## Supported software
Support for installing 29 new software packages has been added,
including (but not limited to):
Abseil
ArchR
CMAverse
Devito
GraphMap
Hydra
M1QN3
MAGeCK
MEGAN
ONNX
ont-remora
Optuna
porefoam
presto
PyFrag
skorch
SPM
STRique
=> This brings the total number of supported software packages to
2,667 (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):
AlphaFold 2.1.2
AmberTools 21
BLIS 3.1
DFTB+ 21.1
DIRAC 22.0
ELPA 2021.11.001
FlexiBLAS 3.1.3
IgBLAST 1.18.0
ITSx 1.1.3
Julia 1.7.2,
libtree 3.0.3,
matplotlib 3.5.1
MDAnalysis 1.1.1 + 2.0.0,
medaka 1.5.0
NLTK 3.7
numexpr 2.8.1
OpenAI-Gym 0.21.0
OpenBLAS 0.3.20
PIPITS 2.8
pocl 1.8
pyEGA3 4.0.0
SAMtools 1.15
SBCL 2.2.1
shovill 1.1.0
sympy 1.9
VirtualGL 3.0
VTK 9.1.0
XGBoost 1.5.0
These changes result from various contributions, made by 23 different
contributors:
* 19 merged pull requests for EasyBuild framework
* 24 merged pull requests for easyblocks
* 163 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.5.4, there are several options [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 15214 # use easyconfig from PR #15214 [6]
Enjoy!
regards,
Kenneth & Sebastian
[1] https://pypi.org/project/easybuild/4.5.4
[2]
https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-4-march-31st-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/15214
