Releases · easybuilders/easybuild

07 Sep 09:11

boegel

easybuild-v4.4.2

6ee42bf

EasyBuild v4.4.2

EasyBuild v4.4.2 is mostly a bugfix and update release, but also includes several minor enhancements.

Highlights for this release are listed below. More details are available in the release notes which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with (***))

add --filter-ecs configuration option to filter out easyconfigs from set of easyconfigs to install;
also define $BLAS_SHARED_LIBS & co in build environment (analogous to $BLAS_STATIC_LIBS);
add get_cuda_cc_template_value method to EasyConfig class;
pick up $MODULES_CMD to facilitate using Environment Modules 4.x as modules tool;
add 4 new software-specific easyblocks for CRISPR-DAV, jaxlib, ORCA, RepeatModeler;
update software-specific easyblocks for ABAQUS, Amber, BerkeleyGW, Clang, CP2K, ESMF, FreeFEM, GROMACS, LAMMPS, numexpr, numpy, Molpro, OpenFOAM, TensorFlow, VTune, WIEN2k;
enable make check and sanity check commands for OpenMPI;
(***) make sure AOCC commands like clang/flang pick up GCCcore as GCC toolchain;
(***) create CMakeConfig files for tbb >= 2020;
(***) generate and install pkg-config files for OpenSSL wrapper;
added easyconfig for foss/2021.07 (candidate for foss/2021b) and iomkl/2021a toolchains;
(***) add various extensions to recent R v4.x easyconfigs;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

(***) don’t add directory that doesn't include any files to $PATH or $LD_LIBRARY_PATH;
make sure git clone with a tag argument actually downloads a tag;
honor --ignore-test-failure in PythonPackage easyblock;
reset runtest to None in CMakePythonPackage easyblock;
let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly;
use ${BLAS,LAPACK}_SHARED_LIBS in GROMACS easyblock for FlexiBLAS-based toolchains;
(***) add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX);
(***) use correct GTK+ version for OpenCV based on dependencies;
(***) set $I_MPI_ROOT correctly for 2021.x in impi easyblock (only requires --module-only to fix);
(***) keep symlinks in cuDNN installations;
(***) fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost;
(***) add missing Bio-Search-hmmer dependency for prokka;
(***) patch MaxBin2 Perl script to use provided Perl dependency;
(***) avoid MPICXX dependency in SimpleElastics ITK;
(***) add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault);
(***) enable EGL in recent libepoxy easyconfigs;
(***) update tensorflow-probability easyconfigs to include --release flag in installopts;
(***) fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2;
update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check;
(***) create libtinfo symlinks in easyconfigs for ncurses with system toolchain;

Other changes

simplify Boost easyblock;
remove deprecated options from PythonPackage easyblock;
use custom ORCA easyblock in easyconfigs for ORCA v4.x;
rename NINJA to TWL-NINJA to avoid nameclash;
rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda toolchains, to ensure that get_software_root('CUDA') used in easyblocks works;

Supported software

Support for installing 79 new software packages has been added, including (but not limited to):

AlphaFold
AUTO-07p
biogeme
CellRank
Coin
CRISPR-DAV
DistributedStream
freebayes
GIMP (#13216)
GOATOOLS
GTK2 + GTK3
hipSYCL
jax
Kalign
Maude
Mish-Cuda
OSPRay
pandapower
pangolin
PYPOWER
pysamstats
QCxMS
RepeatModeler
SoQt
SpectrA
SyRI
UShER
Vampire
VisPy
Yices

This brings the total number of supported software packages to 2,467!

An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

AOCC 3.1.0
ASE 3.22.0
Biopython 1.79
Boost 1.76.0
Clang 12.0.1
CUDA 11.4.1
cuDNN 8.2.2.26
DIAMOND 2.0.11
ESMF 8.1.1
GCC(core) 11.2.0
GDRCopy 2.3
GenomeTools 1.6.2
GPAW 21.6.0
GROMACS 2021.3
Horovod 0.22.1
ImageMagick 7.1.0
IMOD 4.11.5
IPython 7.26.0
Java 16
likwid 5.2.0
LLVM 12.0.1
matplotlib 3.4.2
Mesa 21.1.7
Metal 2020-05-05
MPICH 3.4.2
NCCL 2.10.3
NCO 5.0.1
nodejs 14.17.6
NVHPC 21.7
OpenBLAS 0.3.17
OpenFOAM 9 + OpenFOAM v2106
OpenMM 7.5.1
OpenMolcas 21.06
ParaView 5.9.1
Perl 5.34.0
PETSc 3.15.1
petsc4py 3.15.0
PLUMED 2.7.2
PMIx 4.1.0
PostgreSQL 13.3
PyQt5 5.15.4
Python 3.9.6
R-bundle-Bioconductor 3.13
ReFrame 3.8.0
Rust 1.54.0
Scalasca 2.6
SLEPc 3.15.1
slepc4py 3.15.1
Spack 0.16.2
StringTie 2.1.7
TensorFlow 2.6.0,
UCX 1.11.0 + UCX-CUDA 1.11.0
WIEN2k 21.1
WPS 4.2
WRF 4.3
X11 20210802
xarray 0.19.0

These changes result from various contributions, made by 23 different contributors:

29 merged pull requests for EasyBuild framework
50 merged pull requests for easyblocks
459 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.4.2, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 13918 # use easyconfig from PR #13918

Assets 2

06 Jul 13:07

boegel

easybuild-v4.4.1

c56fcb8

EasyBuild v4.4.1

EasyBuild v4.4.1 is primarily a bugfix and update release, but also includes several minor enhancements.

Highlights for this release are listed below. More details are available in the release notes which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with (***))

add per-step timing information in standard output of eb command;
add new hook that triggers right before writing generated module file (module_write_hook);
add ignore-test-failure configuration option to ignore failing test step;
enhance ConfigureMake generic easyblock to add support for building multiple build targets;
5 new custom easyblocks, for AOMP, FreeFEM, NCCL (built from source), torchvision, and UCX plugins;
update custom easyblock for Boost to always build single and multi threaded versions;
(***) enhance sitecustomize.py in Python easyblock to support overriding core Python packages, and allowing overriding in virtualenv;
(***) updates & enhancements for various custom easyblocks, incl. Amber, Clang, FFTW, Hypre, intel-compiler, Java, OpenSSL wrapper, Perl, Python, XALT, Xmipp;
(***) additional extensions for recent R easyconfigs;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

add comment with test report in right location when combining --from-pr and --include-easyblocks-from-pr;
fix crash when copying modules that were imported in easyconfig file (like import os);
(***) fix location for modules installed with intel-compilers toolchain in HierarchicalMNS;
don’t make changes to software installation directory when using --sanity-check-only;
honour specified easyblock for extensions;
change Bundle easyblock to also collect altroot and altversion in the module step so they are set when running --module-only;
(***) bug fixes for various custom easyblocks, incl. GCC, intel-compilers, NVHPC, TensorFlow, VEP;
(***) set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper;
(***) add patch for GCC 10.2.0 to fix internal compiler error on aarch64;
(***) add missing rgdal dependency to R-INLA;
(***) add patch to fix uniq operation in TensorFlow 2.4.1;
(***) add patch for recent GCCcore versions to fix compatibility with CUDA 11;
(***) avoid using PMIx from system instead of PMIx dependency specified via --with-pmix for OpenMPI 4.x;
(***) add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc;

Other changes

deprecate EasyBuild bootstrap script;
rework the dependency handling of OpenMPI to use explicit configure options to disable features if required dependency is not provided;
- side effect of this is that you need to add --with-ucx yourself if you want to build OpenMPI on top of a system provided UCX!
(***) switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b;
cleanup of easyconfigs for (bundles) of Python packages: remove default PYPI_SOURCE source URLs + use PythonBundle rather than Bundle easyblock;

Supported software

Support for installing 39 new software packages has been added, including (but not limited to):

AOMP
dSFMT
FreeFEM
futhark
GenomeWorks
hipify-clang
microctools
Nektar++
OpenMM-PLUMED
phototonic
PyFoam
RECON
UCX-CUDA
Vala

This brings the total number of supported software packages to 2,388!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

Amber 20.11
Bonito 0.4.0
DOLFIN 2019.1.0.post0
ELPA 2021.05.001
FDS 6.7.6
GCC 8.4.0 + 9.4.0
GDAL 3.3.0
Go 1.16.5
GSL 2.7
h5py 3.2.1
Horovod 0.22.0
Hypre 2.21.0
IPython 7.25.0
LDC 1.26.0
libxc 5.1.5
medaka 1.4.3
MUMPS 5.4.0
NCCL 2.9.9
netCDF 4.8.0
Nim 1.4.8
nodejs 14.17.0
numba 0.53.1
NVHPC 21.5
Octave 6.2.0
petsc4py 3.12.0
PySCF 1.7.6
PyTorch 1.9.0
R 4.0.5 + R 4.1.0
ReFrame 3.6.2
Ruby 3.0.1
Score-P 7.0
Subread 2.0.2
SuiteSparse 5.10.1
sympy 1.8
TensorFlow 2.5.0
VMD 1.9.4a51
Z3 4.8.11

These changes result from various contributions, made by 23 different contributors:

27 merged pull requests for EasyBuild framework
41 merged pull requests for easyblocks
268 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.4.1, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 13344 # use easyconfig from PR #13344

Assets 2

02 Jun 12:56

boegel

easybuild-v4.4.0

be77b4e

EasyBuild v4.4.0

EasyBuild v4.4.0 is primarily a feature release, but also includes several bug fixes & minor enhancements.

Highlights for this release are listed below. More details are available in the release notes which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

[enhancements that (may) warrant updating existing installations are marked with (***)]

performance improvements for easyconfig parsing and eb startup;
support for downloading easyconfigs from multiple PRs with --from-pr;
support for re-running the sanity check for existing installations (without making modifications to the installation), via "eb --sanity-check-only";
toolchain definition for Fujitsu toolchain for use on Fugaku;
allow checking whether specific libraries are (not) linked into installed binaries/libraries in sanity check (see various ways to specify banned/required libraries);
update_build_option function to update specific build options after initializing the EasyBuild configuration;
run post-install commands specified for a specific extension;
add support for skipping the installation of extension via "eb --skip-extensions";
software-specific easyblocks for FlexiBLAS and dm-reverb;
custom easyblock to install OpenSSL wrapper for OpenSSL installed in OS, with fallback to build and install OpenSSL from source if not available in OS;
enable sanity_pip_check by default for Python easyconfigs if pip >= 9.0 will be installed;
add IceLake detection to OpenBLAS 0.3.12 and 0.3.15;

Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***)]

re-enable write permissions when installing with read-only-installdir;
avoid metadata greedy behavior when probing for external module metadata (mostly relevant for integration with Cray Programming Environment);
also run sanity check for extensions when using --module-only (you can use --skip-extensions to skip sanity checking of extensions when using --module-only);
fix use of --module-only on existing installations without write permissions;
use unload/load in ModuleGeneratorLua.swap_module, since swap is not supported by Lmod;
update HierarchicalMNS to also return ‘Toolchain/<name>/<version>’ as $MODULEPATH extension for cpe* Cray toolchains;
enhance sched_getaffinity function to avoid early crash when counting available cores on systems with more than 1024 cores;
(***) enhance Python easyblock: add option to install pip with core Python, tweak defaults, create unversioned pip symlink;
make custom easyblocks for GROMACS ad Tkinter work with --module-only;
make sure that self.python_cmd is set before using it in PythonPackage.sanity_check_step to make PythonBundle easyblock comaptible with --module-only;
(***) add patch to fix GCC 10.2.0 rejecting valid code on PPC;
(***) update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes;
(***) fix test failure in TensorFlow 2.4.1 on recent CUDA drivers;
(***) add patch to fix hardcoded num_cores in DMCfun extension included with R 4.0.x;
(***) fix typo in Delly easyconfig to actually do parallel build;
(***) fix potential memory leak in OpenBLAS 0.3.12;
(***) add patches for PyTorch 1.7.1 avoiding failures on POWER and A100;
fix source URLs for recent Boost and Boost.Python versions;

Other changes

tweak foss toolchain definition to switch from OpenBLAS to FlexiBLAS in foss/2021a;
don’t skip sanity check for --module-only --rebuild (sanity check is still skipped with --module-only --force);
consistently use pip to install Python packages in recent Python easyconfigs;
deprecate adding a non-existing path to $MODULEPATH via ModulesTool.use;
drop support for running EasyBuild with Python 2.6;

Supported software

Easyconfigs for 2021a version of custom toolchains:

foss/2021a:
- GCC 10.3.0 + binutils 2.36.1
- OpenMPI 4.1.1
- FlexiBLAS 3.0.4 with OpenBLAS 0.3.15 as backend
- ScaLAPACK 2.1.0
- FFTW 3.3.9
intel/2021a:
- GCC 10.3.0 + binutils 2.36.1 as base
- intel-compilers 2021.2.0
- impi 2021.2.0
- imkl 2021.2.0

Support for installing 58 new software packages has been added, including (but not limited to):

BirdNET
cell2location
cryoDRGN
FlexiBLAS
fsom
gemmi
georges
hifiasm
intervaltree
LDC
librosa
loompy
mongolite
NewHybrids
pagmo
pyfaidx
pyfasta
pygmo
R-INLA
rMATS-turbo
SeqLib
smithwaterman
SSW
TagDust
TALON
TranscriptClean
xESMF

This brings the total number of supported software packages to 2,349!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

ABINIT 9.4.1
BLIS 0.8.1
Bonito 0.3.8
ccache 4.2.1
CLHEP 2.4.4.0
CMake 3.20.1
CUDA(core) 11.3.0
CuPy 8.5.0
Eigen 3.3.9
FFTW 3.3.9
GATK 4.2.0.0
GCC 10.3.0 + 11.1.0
GDRCopy 2.2
GLPK 5.0
GROMACS 2021.2
GTDB-Tk 1.5.0
HMMER 3.3.2
Horovod 0.21.3
intel-compilers + impi + imkl 2021.2.0
Julia 1.6.1
libfabric 1.12.1
libRmath 4.0.0
LLVM 11.1.0
Mesa 21.1.1
metaWRAP 1.3
Nim 1.4.6
NWChem 7.0.2
OpenBLAS 0.3.15
openCARP 6.0
OpenMM 7.5.0
OpenMPI 4.1.1
Pandoc 2.13
Perl 5.32.1
PMIx 3.2.3
Primer3 2.5.0
PyTorch 1.8.1
Python 3.9.5
Qt5 5.15.2
Rmath 4.0.4
Rust 1.52.1
SciPy-bundle 2021.05
snakemake 6.1.0
UCX 1.10.0
Valgrind 3.17.0
X11 20210518
YAXT 0.9.0

These changes result from various contributions, made by 19 different contributors:

59 merged pull requests for EasyBuild framework
47 merged pull requests for easyblocks
349 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.4.0, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 13012 # use easyconfig from PR #13012

Assets 2

09 Apr 09:06

boegel

easybuild-v4.3.4

d9e1582

EasyBuild v4.3.4

EasyBuild v4.3.4 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 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 (***)]

sort output of eb --search in natural order (respecting numbers);
enhance eb command to ensure that easybuild.main can be imported before settling on python* command to use;
deprecate --accept-eula configuration option, renamed to --accept-eula-for;
fix problem with downloading large files when running EasyBuild with a recent Python 3 version, by passing file-like object to write_file in download_file so that the data is read is chunks;
(***) set $R_LIBS_SITE rather than $R_LIBS when installing R packages;
make WRF and WPS easyblocks aware of (pre)configopts;
remove PYPI_SOURCE source URL from easyconfigs using PythonPackage or PythonBundle;
(***) enhance BWA and g2clib easyblocks to pass down compiler flags;
(***) avoid 0.0.0 install version for various Python apps, including carputils, deepdiff, EMU, maze, Open-Cube-Core, pytest, Spyder, suave;
(***) bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0;
(***) update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages;
(***) bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error;
(***) fix numpy tests for recent SciPy-bundle easyconfig on POWER;
(***) add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI;
(***) revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0;
(***) use -D_USE_METIS_5p1 in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0;
(***) rename opencv_contrib and update to OpenCV v3.4.1 with contrib versionsuffix;

Highlighted enhancements

[enhancements that (may) warrant updating existing installations are marked with (***)]

avoid running expensive module use and module unuse commands when using Lmod as modules tool, update $MODULEPATH directly instead;
also accept regular expression value for --accept-eula-for;
update validate_github_token function to accept GitHub token in new format;
enhance cuDNN and CUDA easyblocks to support aarch64;
use PYPI_SOURCE as the default for source_urls of PythonPackage;
enhance PythonPackage easyblock to catch faulty version (0.0.0) for installed Python packages;
updated easyblocks for AOCC, CP2K, GROMACS, LAPACK, OpenCV, PETSc, PyTorch, VMD, VTune;
(***) add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a;
(***) add extensions to R-bundle-Bioconductor 3.12: motifmatchr (#12390), OUTRIDER + FRASER;
(***) add DMCfun + linkcomm + rnetcarto extensions to R v4.0.3;

Use "eb --rebuild --skip" to install the missing extensions for R and R-bundle-Bioconductor.

Supported software

Additional easyconfig file for existing goblf toolchain: goblf/2020b

Support for installing 41 new software packages has been added, including:

BEEF
CDAT
DL_POLY_4
ESMPy
GPyOpt
LncLOOM
LPJmL
MetaEuk
Myokit
PyOD
Ratatosk
scikit-cuda
Seeder
YACS

This brings the total number of supported software packages to 2,288!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

AOCC 3.0.0
BUSCO 5.0.0
CP2K 8.1
CellRanger 6.0.0
Clang 11.0.1
dask 2021.2.0
Extrae 3.8.0
GROMACS 2021
Hypre 2.20.0
Kent_tools 411
LAPACK 3.9.1
libxc 5.1.3
MUMPS 5.3.5
NVHPC 21.2
OpenCV 4.5.1
PETSc 3.14.4
PLUMED 2.7.0
PyCUDA 2020.1
PyOpenCL 2021.1.2
PyTorch-Geometric 1.6.3
pocl 1.6
preCICE 2.2.0
pymatgen 2022.0.4
R 4.0.4
RDFlib 5.0.0
ReFrame 3.5.1
Ruby 2.7.2
SIMPLE 3.0.0
SUNDIALS 5.7.0
Seurat 4.0.1
Spark 3.1.1
tensorboardX 2.1
VTK 9.0.1

These changes result from various contributions, made by 21 different contributors:

29 merged pull requests for EasyBuild framework
26 merged pull requests for easyblocks
220 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.3.4, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 12554 # use easyconfig from PR #12554

Assets 2

23 Feb 19:54

boegel

easybuild-v4.3.3

b7c4f5b

EasyBuild v4.3.3

EasyBuild v4.3.3 is primarily a bugfix/update release, but also includes several interesting enhancements.

Highlights for this release are listed below, more details are available in the release notes, which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes that 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.

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
ftlib
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 here.

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.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 12255 (use easyconfig from PR #12255)

Assets 2

10 Dec 21:15

boegel

easybuild-v4.3.2

c4e81c0

EasyBuild v4.3.2

EasyBuild v4.3.2 is primarily a bugfix/update release,
but also includes several interesting enhancements.

Highlights for this release are listed below.
More details are available in the release notes, which includes links to the respective pull requests for more detailed information.

Prominent bug fixes

(bug fixes that warrant reinstalling easyconfigs are marked with (***))

fix combination of --copy-ec and --from-pr options;
fix regression in apply_regex_substitutions: also accept list of paths to patch;
also inject -rpath options for all entries in $LIBRARY_PATH in RPATH wrappers;
only configure Python with --enable-optimizations when compiling with (recent) GCC compiler (to fix hanging installations of Python and Tkinter);
stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests;
fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK;
always define $FCCPP in QuantumESPRESSO easyblock (not just when using Intel compilers);
fix CPASSERT test faults on RHEL8 in CP2K easyblock;
set $UCX_TLS in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file;
fix source_urls in Geant4 easyconfigs;
add patch for TensorFlow 2.3.1 to fix installation on Arm64;
(***) add patch for GCCcore 10.2 to fix __has_include regression (required for building Libint);
(***) set $JUPYTER_PATH to make Jupyter find the ipywidgets extension in recent IPython easyconfigs;
(***) in-place update to magma 2.5.4 for PyTorch (to fix known bug in magma 2.5.2 which causes e.g. wrong results (NaNs) in PyTorch);
(***) add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check;
(***) add missing gnuplot dependency in OpenFOAM easyconfigs (just re-generating OpenFOAM module files via --module-only is sufficient);
(***) add patch to fix possible memory leak in OpenBLAS 0.3.3+;
renamed software to match official name or fix name clashes: Ray-assembler + Ray-project, RStudio-Server, SUMO, XCFun;

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with (***))

add (experimental) support for specifying easyconfig files via an "easystack" file;
- see https://easybuild.readthedocs.io/en/latest/Easystack-files.html for more information;
significantly speed up parsing of easyconfig files by only extracting comments from an easyconfig file when they’re actually needed;
add support for toolchain options like 'extra_cxxflags' to specify extra compiler options;
add support for '%(module_name)s' template value;
add support for skipping unit tests (test step) via --skip-test-step;
add support for building Clang and GCC with support for OpenMP offloading to GPUs;
update TensorFlow easyblock for upcoming TensorFlow 2.4;
enhance PyTorch easyblock to ensure it finds MKL;
(***) enable NVPTX offload support in GCCcore 10.2.0 easyconfig;
(***) add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
(***) add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs;

Use "eb --rebuild --skip" to install the missing extensions for R, Bioconductor, or Perl.

Supported software

Easyconfig files for the updated common toolchains are included:

foss/2020b
fosscuda/2020b
intel/2020b
intelcuda/2020b

In addition, easyconfigs for the new 'gobff' toolchain are included: gobff/2020.11, gobff/2020.06-amd.

The gobff toolchain includes the following components:

GCC + binutils
OpenMPI
BLIS + libFLAME (BLAS/LAPACK libraries)
ScaLAPACK
FFTW

The -amd variant uses the AMD forks of the upstream BLIS and libFLAME libraries.

Support for installing 41 new software packages has been added, including:

carputils
code-server
CRISPResso2
fgbio
IPM
LLDB
meshalyzer
meshtool
Metagenome-Atlas
MLxtend
MRChem
nanocompore
OpenSees
PEST++
pyFAI
pymca
scikit-bio
SpaceRanger
SWAT+
WCT

This brings the total number of supported software packages to 2,175!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

Boost 1.74.0
CUDA 11.1.1
CellRanger 5.0.0.eb
CheckM 1.1.3
Clang 11.0.0
cuDNN 8.0.4.30
FDS 6.7.5
FFmpeg 4.3.1
GROMACS 2020.4
Geant4 10.6.2
GlobalArrays 5.8
HDF5 1.10.7
h5py 3.1.0
magma 2.5.4
matplotlib 3.3.3
NCCL 2.8.3
netCDF-Fortran 4.5.3
OpenMolcas 20.10
packmol 20.2.2
Qt5 5.14.2
RAxML-NG 1.0.1
SCOTCH 6.1.0
SciPy-bundle 2020.11 (incl. numpy 1.19.4, scipy 1.5.4, 1.1.4, ...)
StringTie 2.1.4
SuperLU 5.2.2
scikit-learn 0.23.2
snakemake 5.26.1

These changes result from various contributions, made by 27 different contributors:

33 merged pull requests for EasyBuild framework
39 merged pull requests for easyblocks
187 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.3.2, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 11853 # use easyconfig from PR #11853

Assets 2

29 Oct 21:04

boegel

easybuild-v4.3.1

90858b9

EasyBuild v4.3.1

EasyBuild v4.3.1 is primarily a bugfix/update release,
but also includes some minor enhancements.

All details are available in the release notes, with links to the respective pull requests.

Prominent bug fixes

(bug fixes that warrant reinstalling easyconfigs are marked with (***))

fix compatibility of EasyBuild with Python 3.9;
fix various issues when using "sources" to specify extension sources;
(***) add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS 0.3.3 through 0.3.9;
(***) fix source for SQLite 3.31.1;
=> incorrect source URL and filename caused SQLite 3.29.0 to be installed instead;
(***) configure OpenMPI 4.x (foss/2020a) with --without-verbs when using UCX;
=> this fixes a warning message that occurs when using OpenMPI on systems with Infiniband, see also https://www.open-mpi.org/faq/?category=all#ofa-device-error;
(***) add patch for OpenMPI 3.1.4 (foss/2019b) adding device parameters for ConnectX-6;
=> fixes warning about missing device parameters on systems with recent Infiniband cards;
(***) enhance OpenFOAM easyblock to add symlinks for libraries to ensure MPI versions have preference over dummy versions;
=> fixes broken tools (like snappyHexMesh) in OpenFOAM installation if EasyBuild was configured to use RPATH linking (via --rpath);
(***) patch out bug in collective primitive in TensorFlow 2.2.0;
(***) remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (so pip can find SIP);
(***) remove GLog and GFlags dependencies from PyTorch easyconfigs (known to cause problems on POWER);
(***) fix dependency on Bowtie of v0.x in seq2HLA easyconfigs;
(***) add protobuf-python as a dependency for PyTorch 1.6 (required by caffe2.python module);
(***) add ncurses runtime dependency to Clang easyconfigs;
(***) fix PyVCF easyconfig, only supports Python 2;
(***) remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0;
make OpenBLAS installation procedure respect the parallelism set by EasyBuild;
fix checksum in NAMD 2.12 easyconfigs + add source URL;
rename jupyterhub to JupyterHub;

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with (***))

publish test reports to easybuild-easyblocks pull request when --include-easyblocks-from-pr is used without --from-pr;
add support for including easyblocks from multiple PRs at once via --include-easyblocks-from-pr;
update TensorFlow easyblock to:
- put Bazel build files in build directory;
- avoid unnecessary runtime patching;
- add XLA build support;
- leverage installed OpenSSL/BoringSSL when cURL is used as a dependency;
make easyblock for installing CMake aware of --sysroot EasyBuild configuration setting;
update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0);
(***) use more EasyBuild installed dependencies for TensorFlow 2.2.0;
(***) add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a);
(***) add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
=> use "eb --rebuild --skip" to install the missing extensions;
(***) make libtirpc easier to use as replacement of rpc in glibc (for RHEL8);
(***) build LibTIFF with -fPIC;

Supported software

Support for installing 75 new software packages has been added, including:

CFDEMcoupling
COMSOL
DIRAC
FRUIT (Fortran Unit Test Framework)
GDRCopy
mauveAligner
MyCC
Nek5000
NVHPC (NVIDIA HPC SDK) + support using it as a toolchain
OPERA-MS
PyOpenCL
QtPy
SeqKit

This brings the total number of supported software packages to 2,134!
An up-to-date list of supported software is available here.

Easyconfigs for fosscuda/2020a and intelcuda/2020a toolchains have been added.

Various software updates have been added, including:

ABINIT 9.2.1
Bazel 3.6.0
CUDA 11.0.2
GROMACS 2020.3
GTK+ 3.24.23
HMMER 3.3.1
Horovod 0.20.3
IPython 7.18.1
LLVM 11.0.0
medaka 1.1.3
Mesa 20.2.1
PSI4 1.3.2
PyQt5 5.15.1
PyRETIS 2.5.0
Python 3.8.6
ReFrame 3.2
Spyder 4.1.5
Taiyaki 5.1.0
TINKER 8.8.1
TensorFlow 2.3.1 (with foss/2019b, fosscuda/2019b, foss/2020a)
TRIQS 3.0.0
UCX 1.9.0
X11 20201008

These changes result from various contributions, made by 25 different contributors:

21 merged pull requests for EasyBuild framework
32 merged pull requests for easyblocks
287 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.3.1, there are several options.
Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 11590 # use easyconfig from PR #11590

Assets 2

13 Sep 10:09

boegel

easybuild-v4.3.0

ea76fe8

EasyBuild v4.3.0

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-0-september-13th-2020)

Assets 2

08 Jul 14:06

boegel

easybuild-v4.2.2

20d819b

EasyBuild v4.2.2

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-2-july-8th-2020

Assets 2

20 May 19:38

boegel

easybuild-v4.2.1

44a1779

EasyBuild v4.2.1

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-1-may-20th-2020

Assets 2

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