Dear EasyBuilders,
We're happy to announce the release of EasyBuild v4.5.5 [1].
It is beyond doubt that this is the best EasyBuild release so far, so
don't be fooled by the various attemps to distract you from this
memorable event, including:
- people on an island celebrating because someone is getting really old;
- a rich guy pretending that he wants to buy Twitter;
- scientific conferences ignoring science when it comes to the ongoing
pandemic...
EasyBuild v4.5.5 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-v4.5.5)
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant re-installing easyconfigs are
marked with (***)]
- set $FFT(W)_LIB_DIR to imkl-FFTW’s lib path in build environment if
usempi toolchain option is enabled;
- fix 'eb --show-system-info' on Apple M1 system;
- remove system-compiled binutils dirs from $LDFLAGS in binutils easyblock;
- (***) add patch for OpenMPI 4.1.1 to support building using
--with-cuda=internal;
- (***) disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b;
- (***) also symlink cert.pem in from-source OpenSSL installation (if it
exists), to ensure that system certificates are found;
- use x.py to bootstrap Rust so that build options are properly passed
through;
- (***) add hwloc dependency to tbb v2021.4.0;
- (***) define $HHLIB as path to HH-suite installation directory,
required by Perl scripts;
- (***) add missing parallel and tbl2asn dependencies for prokka 1.14.5;
- (***) also build shared library + fix $PYTHONPATH for gmsh 4.9.0;
- add missing dependencies + switch to non-static build for Arriba v2.1.0;
- (***) add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to
foss/2021b toochain;
- (***) update fallback version for OpenSSL 1.1 wrapper to v1.1.1o;
- (***) install sklearn meta-package with scikit-learn v1.0.1;
## Highlighted enhancements & changes
[enhancements that (may) warrant updating existing installations are
marked with (***)]
- change 'eb' command to import easybuild.framework to check if
EasyBuild framework is available;
- add toolchain definitions for nvompi (NVHPC + OpenMPI),
nvpsmpi (NVHPC + ParaStationMPI), and gfbf (GCC, FlexiBLAS, FFTW);
- add support for FFTW.MPI toolchain component;
- add support for customizing EasyBuild command used in jobs via
--job-eb-cmd;
- add support to ConfigureMake for tweaking (first part of) test command
via 'test_cmd';
- 1 new software-specific easyblock for FFTW.MPI;
- updates and enhancements for various software-specific easyblocks:
ABAQUS, Clang, cuDNN, FFTW, LLVM, Mesa, MrBayes, NEURON, OpenMPI,
OpenSSL wrapper, R, SuperLU, TensorFlow;
- don't use gold linker by default for GCC >= 11.3;
- add candidates for 2022a common toolchains: foss/2022.05, intel/2022.05;
- (***) also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0;
- (***) additional extensions for R-bundle-Bioconductor 3.14 and R
v4.1.2 [3];
- (***) update Arrow to use EasyBuild-provided versions of some
dependencies and enable all compression codecs;
- (***) add csh -> tcsh symlink in recent tcsh easyconfigs;
## Supported software
Support for installing 35 new software packages has been added,
including (but not limited to):
Albumentations
arosics
CellTypist
detectron2
EigenExa
FFTW.MPI
FreeBarcodes
GTK4
i7z
ModelTest-NG
OGDF
panito
parameterized
ruamel.yaml
SCGid
scPred
smooth-topk
SPOTPY
UCC
Wayland
XGrafix
XPLOR-NIH
=> This brings the total number of supported software packages to
2,711 (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):
ABAQUS 2022
ARGoS 3.0.0
astropy 5.0.4
Bazel 4.2.2 + 5.1.1
binutils 2.38
BLIS 0.9.0
Boost 1.79.0
cryoDRGN 1.0.0
CUDA 11.7.0
FlexiBLAS 3.2.0
GCC 9.5.0 + 11.3.0 + GCC 12.1.0
Go 1.18.1
GTDB-Tk 2.0.0
GTK3 3.24.33
gzip 1.12,
Hypre 2.24.0
IMB 2021.3
IQ-TREE 2.2.1
jax 0.3.9
libfabric 1.15.1
LLVM 14.0.3
magma 2.6.2
Mathematica 13.0.0
Mesa 22.0.3
mold 1.2.1
MUMPS 5.5.0
Nim 1.6.6
OpenMPI 4.1.4
OSU-Micro-Benchmarks 5.9
Perl 5.34.1
PMIx 4.1.2
Python 3.10.4
R 4.2.0
R-bundle-Bioconductor 3.15
ReFrame 3.11.0
Rust 1.60.0
SAMtools 1.15.1
SciPy-bundle 2022.05
SeqKit 2.2.0
Spack 0.17.2
Spark 3.2.1
SuperLU 5.3.0
ToFu 1.5.0
UCX 1.12.1
X11 2022050
zlib 1.2.12
These changes result from various contributions, made by 21 different
contributors:
* 17 merged pull requests for EasyBuild framework
* 25 merged pull requests for easyblocks
* 272 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.5.5, there are several options [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 15635 # use easyconfig from PR #15635 [6]
Enjoy!
regards,
Kenneth & Sebastian
[1] https://pypi.org/project/easybuild/4.5.5
[2]
https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-5-june-8th-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/15635
