Dear EasyBuilders,
We're pleased to announce the release of EasyBuild v4.8.1 [1].
Somehow several bugs were found in previous versions of EasyBuild, which
were resolved in EasyBuild v4.8.1.
We are as flabbergasted as you are by this...
This does make this release the best release ever though (you know,
because the bugs are fixed).
As usual, various attempts to distract you from this wonderful event
have been made, including a Belgian youngster visiting Spain who is one
day able to ride a bike like the wind, the next day pretending to have
no idea how a bike works, only to then blow away the competition again
the day after. Yeah, it's weird.
EasyBuild v4.8.1 is primarily a bugfix and update release, but it also
includes various enhancements.
The executive summary for this release:
- Support for various additional hooks that can be used to customize
EasyBuild, including pre_run_shell_cmd_hook which allows tweaking shell
commands right before they are run by EasyBuild;
- 2 new custom easyblocks, for sympy and tensorflow-compression;
- Easyconfigs for various recent software versions, including Clang
16.0.6, CP2K 2023.1, FFmpeg 6.0, GCC 13.2.0, OpenFOAM 11, Pillow 10.0.0,
TensorFlow 2.13.0, ...;
- Support for installing 83 new software applications and libraries;
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-v4.8.1)
## Highlighted enhancements & updates
[enhancements or updates that (may) warrant updating existing
installations are marked with (***)]
- support for additional hooks: pre_build_and_install_loop_hook +
post_build_and_install_loop_hook, cancel_hook, fail_hook,
pre_postiter_hook + post_postiter_hook, and pre_run_shell_cmd_hook +
post_run_shell_cmd_hook; see https://docs.easybuild.io/hooks for more
information;
- add --silence-hook-trigger configuration option to suppress printing
of a debug message every time a hook is triggered;
- add support for using fine grained Github tokens;
- add support for submodule filtering and specifying extra Git
configuration in git_config;
- new custom easyblocks for sympy and tensorflow-compression;
- add options to MesonNinja generic easyblock to customize build_cmd,
install_cmd, build_dir;
- add support to PerlModule generic easyblock to customize prefix option
used in installation command;
- updates and enhancements to custom easyblocks for Clang, CP2K, CUDA,
FreeSurfer, LLVM, Mesa, MXNet, OpenCV, OpenFOAM, PETSc, PyTorch, scipy,
Score-P, TensorFlow;
- add extensions to recent versions of R (tabletools, flextables) and
R-bundle-Bioconductor (UCell, decoupleR, RnBeads), use "eb --skip
--rebuild" to install the missing extensions [3] (***);
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant re-installing easyconfigs are
marked with (***)]
- improve error reporting w.r.t. missing checksums;
- only add extensions in module file if there are extensions (***);
- enhance PythonPackage easyblock to deal with posix_local installation
scheme used by Python in recent Debian/Ubuntu versions;
- improve depot management in JuliaPackage easyblock (***);
- set $JULIA_DEPOT_PATH in Julia easyconfigs with default value (***);
- bug fixes for various custom easyblocks, incl. imkl-FFTW, Java, MATLAB
(***), Mesa, OpenMPI, STAR-CCM+, TensorFlow;
- fix regression in GCC 12.1 + 12.2 with wrong warnings (***);
- fix installation of Python bindings for recent Arrow easyconfigs;
- various additional patches for recent PyTorch versions to fix bugs
and/or failing tests (***);
- additional bug fixes in easyconfigs for Abseil, at-spi2-core,
Automake, FreeSurfer, jupyter-server, JupyterHub, LIBSVM, MPFR,
RapidJSON, ScaLAPACK, tRNAscan-SE (***);
- update Java/11 wrapper to Java/11.0.20 (***);
- use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7
with GCCcore/12.2.0 (***);
- add patch for PMIx 4.x to use lchown so links are not followed (***);
- add hpctestlib to the $PYTHONPATH in ReFrame 4.2.0 easyconfig (***);
- add alternative checksum for Extrae v4.0.4;
- disable wx support in gnuplot 5.4.6 (***);
- set $MUJOCO_PY_FORCE_CPU to avoid that mujoco-py checks for nvidia-smi
and aborts installation because /usr/lib/nvidia is not in $LD_LIBRARY_PATH;
## Supported software
Support for installing 83 new software packages has been added,
including (but not limited to):
Ax
Boost.Python-NumPy
CatBoost
ChIPseeker
cryptography
GAPPadde
GenerativeModels
hatchling
IsoQuant
Jupyter-bundle
JupyterNoteboo
maturin
Mikado
NanoCaller
Omnipose
Optax
pv
Python-bundle-PyPI
Sabre
scib-metrics
scikit-plot
setuptools-rust
tensorflow-compression
torchvf
TXR
virtualenv
=> This brings the total number of supported software packages to
3,244 (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):
ABINIT 9.10.3
Arcade-Learning-Envionment 0.8.1
archspec 0.2.1
Bazel 6.3.1
BCFtools 1.18
BEDTools 2.31.0
Boost 1.82.0
CDO 2.2.2
Clang 16.0.6
CP2K 2023.1
CUDA 12.2.2
ecBuild 3.8.0
FFmpeg 6.0
FreeSurfer 7.4.1
GCC 13.2.0
GHC 9.2.2
gnuplot 5.4.8
GTK4 4.11.3
h5py 3.9.0
Horovod 0.28.1
Hypre 2.29.0
ImageMagick 7.1.1-15
magma 2.7.1
medaka 1.8.1 + 1.9.1
Mesa 23.1.4
MXNet 1.9.1
OpenAI-Gym 0.26.2
OpenCV 4.8.0
OpenFOAM 11
Pillow 10.0.0
PLUMED 2.9.0
pocl 4.0
QIIME2 2023.5.1
Qt5 5.15.10
QuantumESPRESSO 7.2
SAMtools 1.18
SciPy-bundle 2023.07
Score-P 8.1
sympy 1.12
SUNDIALS 6.6.0
TensorFlow 2.13.0
Valgrind 3.21.0
wxPython 4.2.1
zarr 2.16.0
These changes result from various contributions, made by 33 different
contributors:
* 25 merged pull requests for EasyBuild framework
* 40 merged pull requests for easyblocks
* 339 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.8.1, there are several options [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 18761 # use easyconfig from PR #18761 [6]
Enjoy!
regards,
Kenneth & Sebastian
[1] https://pypi.org/project/easybuild/4.8.1
[2] https://docs.easybuild.io/release-notes/#release_notes_eb481
[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/18761
