Dear EasyBuilders,
It's my pleasure to announce the first EasyBuild release of 2021 (a.k.a.
the year after the infamous year 2020): EasyBuild v4.3.3 [1]
Not only is this the best release of 2021 so far, it's also the best
EasyBuild version ever!
It's so good that everybody in Clubhouse is talking about it, and that
there again were multiple distraction attempts, including delayed
COVID-19 vaccines, Daft Punk posting a confusing video that seems to
suggest they're throwing the towel (*gasp*), and other
software-who-shall-not-be-named (*) also pushing out a new release...
EasyBuild v4.3.3 is primarily a bugfix/update release,
but also includes several useful 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.
## Prominent bug fixes & changes
[bug fixes or changes that (may) warrant reinstalling easyconfigs are
marked with (***)]
- (***) filter out duplicate paths in RPATH wrapper script;
- fix UTF-8 encoding errors when running EasyBuild with Python 3.0.x-3.6.x;
- fix adding extra compiler flags via toolchainopts;
- fix OpenFOAM sanity check on POWER;
- fix Boost sanity check on POWER + aarch64;
- read MATLAB configuration file in binary mode to avoid UTF-8 encoding
errors when using Python 3.6;
- fix download issues for expat, GDRCopy, Hypre in PETSc, libspatialite,
MAGMA, UDUNITS;
- (***) use library search paths of compiler for RPATH when building
binutils with system compiler;
- (***) fix vector mul and div with broadcasts in -masm=intel mode in
GCCcore v9.3.0;
- (***) add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x;
- (***) don’t disable optarch for Clang 11.0.0;
- (***) pass down compilation flags from build environment for ESMF and PDT;
- (***) add patch for Boost 1.74.0 to fix missing include file;
- (***) add missing ESMF dependency in NCO easyconfigs;
- (***) add patch to fix version for bam-readcount 0.8.0;
- (***) add missing mkl-service dependency for Theano built with
intel/2019b + enhance sanity check;
- (***) fix lack of optimization for SHAPEIT4 v4.1.3;
- (***) add patches to fix test problems with p4est 2.2;
- (***) add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6;
- (***) replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a
single easyconfig for BioPP v2.4.1;
## Highlighted enhancements
[enhancements that (may) warrant updating existing installations are
marked with (***)]
- support for using customized HTTP headers in when downloading files,
via --http-header-fields-urlpat configuration option;
- use https://sources/easybuild.io as fallback source URL;
- support for installing & using intel-compiler toolchain (versions >=
2021.x, oneAPI);
- support for running TensorFlow CPU and GPU tests;
- improved Bazel easyblock: added support for running tests, enable
static linking, use build dir rather than tmpdir, verbose output;
- updated impi easyblock for impi 2021.x (oneAPI);
- updated OpenFOAM easyblock for changes in v2012;
- run motorBike tutorial case as sanity check for recent (community)
OpenFOAM versions;
- (***) updated Clang easyblock to add support for building extra tools
+ leveraging hwloc and Z3 as optional dependencies;
- (***) enable NVPTX offload for GCCcore 9.3.0;
- (***) update Java/1.8 wrapper to Java 1.8.0_281;
- (***) move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore;
- (***) also build shared library in recent HDF easyconfigs + add
support for HDF4 to GDAL v3.0.2 and v3.0.4;
- (***) enable gipaw in QuantumESPRESSO 6.6 easyconfig;
- (***) add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs;
- (***) add additional extensions to Perl 5.30+, R 4.0.0, R 4.0.3,
R-bundle-Bioconductor 3.11;
=> use "eb --rebuild --skip" to install the missing extensions for R,
Bioconductor, Perl, or TensorFlow (see [3]);
## Supported software
Easyconfig file for the new 'iibff' toolchain: iibff/2020b
The iibff toolchain includes the following components:
Intel compilers (on top of GCC + binutils)
Intel MPI
BLIS + libFLAME (BLAS/LAPACK libraries)
ScaLAPACK
FFTW
Additional easyconfig files for existing toolchains:
gobff/2020b, goblf/2018b, gomkl/2020b, iimkl/2018a, iomkl/2019b,
iomkl/2020b
Support for installing 72 new software packages has been added, including:
AOCC
bgen
CuPy
cuTENSOR
decona
fftlib
FIRESTARTER
GPyTorch
GraPhlAn
intel-compilers (oneAPI)
Kaleido
limix
NanopolishComp
PHANOTATE
PIPITS
preCICE
PySAT
Raysect
samblaster
SeisSol
SuperLU_DIST
YANK
=> This brings the total number of supported software packages to 2,248!
An up-to-date list of supported software is available at [4].
Various software updates have been added, including (but not limited to):
AmberTools 20
ASE 3.21.1
AUGUSTUS 3.4.0
Bazel 3.7.2
BLAST+ 2.11.0
Bonito 0.3.5
CGAL 5.2
CUDAcore 11.2.1
DendroPy 4.5.2
FusionCatcher 1.30
GPAW 21.1.0
GROMACS 2020.5
HMMER 3.3.2,
Horovod 0.21.1
impi 2021.1.1
IQ-TREE 2.1.2
JUBE 2.4.1
medaka 1.2.0
MPICH 3.3.2
NVHPC 20.11
nvtop 1.1.0
OpenCoarrays 2.9.2
OpenFOAM v2012
OpenMPI 4.1.0
PLUMED 2.6.2
PyMC3 3.11.0
PyTorch 1.7.1
QuantumESPRESSO 6.7
R 4.0.3
R-bundle-Bioconductor 3.12
ReFrame 3.4.1
Salmon 1.4.0
SEPP 4.4.0
SuiteSparse 5.8.1
TensorFlow 1.15.5 + 2.4.1
Wannier90 3.1.0
These changes result from various contributions, made by 26 different
contributors:
* 33 merged pull requests for EasyBuild framework
* 49 merged pull requests for easyblocks
* 327 merged pull requests for easyconfigs
Thanks to everyone who contributed to this release in one way or another!
To upgrade to EasyBuild v4.3.3, there are several options [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 12255 # use easyconfig from PR #12255 [6]
Enjoy!
regards,
Kenneth & Miguel
[1] https://pypi.org/project/easybuild/4.3.3
[2]
https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-3-3-feb-23rd-2021
[3]
https://easybuild.readthedocs.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip
[4]
https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html
[5]
https://easybuild.readthedocs.io/en/latest/Installation.html#updating-an-existing-easybuild-installation
[6] https://github.com/easybuilders/easybuild-easyconfigs/pull/12255/files
(*) The list of potential software packages you could have in mind here
is endless!
