easybuild

https://github.com/easybuilders/easybuild - EasyBuild v5.0.0

EasyBuild v5.0.0 is a major release, which includes various backwards-incompatible changes.

Overview of changes

A high-level overview of changes in EasyBuild v5.0.0 is available in the EasyBuild documentation . The pages and sections to which the entries in the high-level overview link will be updated in the next couple of days with more information, so stay tuned...

A detailed list of all changes with links to the pull requests in which these changes were implemented is available in the release notes.

This release includes support for 148 new software packages!

Installation

There are several ways of installing EasyBuild v5.0.0, including:

Via pip install (or other standard Python tools), see also here
Via eb --install-latest-eb-release, which downloads the easyconfig file for EasyBuild v5.0.0 from the develop branch of the easybuild-easyconfigs repository .

Note that installing EasyBuild v5.0.0 with EasyBuild v4.x using "eb --from-pr" will not work shortly after the release of EasyBuild v5.0.0, because the develop branch of the easybuild-easyconfigs repository will be updated, and recent EasyBuild versions don't allow "cross-version" installations via --from-pr .

Contributions

This release includes contributions made by 25 different contributors:

245 merged pull requests for EasyBuild framework;
341 merged pull requests for easyblocks;
778 merged pull requests for easyconfigs;

That's 1,364 merged pull requests in total!

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

Best release ever?

While this release includes breaking changes + changes to the default configuration of EasyBuild, the EasyBuild maintainers are confident that this version of EasyBuild is stable and ready for production, since it has been thoroughly tested.

If you find any unexpected problems or bugs, please report them (via Slack, GitHub, mailing list, etc.) so we can publish a (quick) bugfix release, should that be required.

So for once: let's take some time to conclude whether this really is the best EasyBuild release ever. We're pretty sure it is, but do make your own assessment after taking it for a spin...

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Published by boegel 11 months ago

https://github.com/easybuilders/easybuild - EasyBuild v4.9.4

EasyBuild v4.9.4 is primarily a bugfix & update release, but it also includes various enhancements.

The main motivation for this quick release is a bug in the custom easyblock for GCC that led to a crash in EasyBuild unless the cuda-compute-capabilities configuration option was specified; see https://github.com/easybuilders/easybuild-easyblocks/pull/3449 for more details.

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 & updates

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

(***) enhance custom easyblock for NCCL: add licence to NCCL installation;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6;
take into account alternate sysroot for /bin/bash used by run_cmd;
fix crash in GCC easyblock when cuda-compute-capabilities EasyBuild configuration option is not set;

Supported software

Support for installing 14 new software packages has been added, including (but not limited to):

Biotite
cramino
ESM3
MOKIT
PyBullet
xskillscor

This brings the total number of supported software packages to 3,670 (excluding extensions)! An up-to-date list of supported software is available here.

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

BiG-SCAPE-1.1.9
GATE 9.4
HarfBuzz 9.0.0
LDC 1.39.0
NanoPlot 1.43.0
pocl 6.0
RHEIA 1.1.11,
SNAP-ESA 10.0.0
VirtualGL 3.1.1

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

6 merged pull requests for EasyBuild framework;
8 merged pull requests for easyblocks;
71 merged pull requests for easyconfigs;

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

To upgrade to EasyBuild v4.9.4, there are several options.

Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 21465 # use easyconfig from PR #21465

- Shell
Published by boegel over 1 year ago

https://github.com/easybuilders/easybuild - EasyBuild v4.9.3

EasyBuild v4.9.3 is primarily a bugfix & update release, but it also includes various enhancements.

The executive summary for this release:

Easyconfigs for the foss/2024a and intel/2024a common toolchains;
Support for installing 107 (!) new software applications, tools, and libraries, including HERRO, MAGIC, pyMBE, Sagemath, Single-cell-python-bundle, Visit;
Easyconfigs for various recent software versions, including AlphaPulldown 2.0.0b4, Clang + LLVM 18.1.8, CUDA 12.5.0 + 12.6.0, FFmpeg 7.0.2, GCC 14.2.0, jax 0.4.25, ORCA 6.0.0, OpenFOAM 12 + v2406, R 4.4.1, SciPy-bundle 2024.05, WRF 4.5.1, and many more;
Bug fixes/enhanchements/changes to easyblocks/easyconfigs that require reinstallation (more info below, marked with (***));

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 & updates

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

add support for --extra-source-urls to fetch sources from additional URLs;
use Intel's oneAPI Fortran compiler by default for version 2024.0.0 and newer;
enhancements to generic easyblocks: Cargo, JuliaPackage, PythonBundle, PythonPackage, RPackage, RubyGem;
(***) enhance custom easyblock for GCC to use with-arch option for nvptx with 13.1+;
additional updates & enhancements to custom easyblocks for Bazel, binutils, Boost, ESMF, Extrae, Geant4, MCR, impi, LAMMPS, OpenFOAM, ORCA, psmpi, PETSc, PyTorch, QuantumESPRESSO, Tensorflow, Tkinter;
(***) add additional extensions to R-bundle-CRAN easyconfigs;
(***) add Qt support to VTK 9.3.0;
(***) also build & install the plugins with OpenFOAM v2406;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

(***) patch ctypes for Python installations when filtering LD_LIBRARY_PATH + fix path to ldconfig when using alternate sysroot ;
merge of the ConfigureMake and CMakeMake versions of the easyblock for QuantumESPRESSO;
bug fixes in generic easyblocks: Cargo, CargoPythonPackage, PythonBundle, PythonPackage;
bug fixes in custom easyblocks for ANSYS, EasyBuild, Extrae, impi, OCaml, OpenFOAM, OpenMPI, OpenSSL_wrapper, PALM, Python, WPS;
(***) add patch to fix implicit function declaration in OpenMPI 4.1.4;
(***) disable auto-vectorizer (-ftree-vectorize) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11;
(***) add patch for HDF5 v1.14.3 to suppress fp exceptions;
(***) fix easyconfigs for recent versions of QuantumESPRESSO;
(***) add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection;
fix download URLs for old Intel software (2018-2023) by using IRC_NAS instead of irc_nas;

Supported software

Support for installing 107 (!) new software packages has been added, including (but not limited to):

absl-py
BayesOpt
CORSIKA
dictys
EGA-QuickView
fish
Flax
GPflow
HERRO
LRBinner
MAGIC
MBX
nifty
OpenForceField-Toolkit
PEcAn
pyMBE
Sagemath
SharedMeatAxe
Single-cell-python-bundle
torch-em
Visit
Zoltan

This brings the total number of supported software packages to 3,656 (excluding extensions)! An up-to-date list of supported software is available here.

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

AlphaPulldown 2.0.0b4
AmberTools 26.3
Arrow 16.1.0
Biopython 1.84
CUDA 12.5.0 + 12.6.0
CellOracle 0.18.0
Clang 18.1.8
cutadapt 4.9
dorado 0.7.3
Extrae 4.2.0
FFmpeg 7.0.2
GCC 14.2.0
GDAL 3.9.0
GLM 1.0.1
GPAW 24.6.0
genomepy 0.16.1
Highway 1.2.0
IQ-TREE 2.3.5
jax 0.4.25
LLVM 18.1.8
MPICH 4.2.1
MariaDB 11.6.0
Mesa 24.1.3
matplotlib 3.9.2
NanoCaller 3.6.0
ORCA 6.0.0
OpenFOAM 12 + v2406
Optax 0.2.2
Perl-bundle-CPAN 5.38.2
Pillow-SIMD 10.4.0
PostgreSQL 16.4
PyAEDT 0.9.9
PyWavelets 1.7.0
Pygments 2.18.0
Python-bundle-PyPI 2024.06
pyGenomeTracks 3.9
QuantumESPRESSO 7.3.1
R-bundle-CRAN 2024.06
R 4.4.1
RDKit 2024.03.3,
ReFrame 4.6.2
Rust 1.79.0
SciPy-bundle 2024.05
SeqKit 2.8.2
SingleM 0.16.0
SuiteSparse 7.7.0
TELEMAC-MASCARET 8p5r0
UCX-CUDA 1.16.0
WRF 4.5.1
X11 20240607
XGBoost 2.1.1
xarray 2024.5.0

These changes result from various contributions, made by 33 different contributors:

31 merged pull requests for EasyBuild framework;
52 merged pull requests for easyblocks;
367 merged pull requests for easyconfigs;

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

To upgrade to EasyBuild v4.9.3, there are several options.

Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 21412 # use easyconfig from PR #21412

- Shell
Published by boegel over 1 year ago

https://github.com/easybuilders/easybuild - EasyBuild v4.9.2

EasyBuild v4.9.2 is primarily a bugfix & update release, but it also includes various enhancements.

The executive summary for this release:

EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;
Bug fix for --from-commit, so easyconfigs for dependencies are found if they're available in the commit;
4 new sofware-specific easyblocks: AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;
Support for installing 82 new software applications, tools, and libraries;
Easyconfigs for various recent software versions, including BLIS 1.0, Clang 17.0.6, GCC 13.3.0 + 14.1.0, IOR 4.0.0, OCaml 5.1.1, OpenMPI 5.0.3, PyTorch-bundle 2.1.2, Python 3.12.3, TensorFlow 2.15.1, and many more;
Bug fixes/changes to easyblocks/easyconfigs that require reinstallation (more info below, marked with (***));

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 & updates

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

implement EasyBuild API version checks to avoid mixing major versions across the EasyBuild components;
4 software-specific easyblock for AEDT, MetalWalls, optiSLang, QuantumESPRESSO with CMake;
enhancement to PythonPackage generic easyblock;
add a sanity check for OpenFOAM's wmake to make sure it finds the compiler commands;
refactor GAMESS-US easyblock to directly write install.info;
additional updates & enhancements to custom easyblocks for ABAQUS, Clang, CUDA, FFTW, Java, Mesa, OpenMPI, OpenSSL, torchvision, UCX-Plugins;
(***) additional extensions for R-bundle-CRAN v2023.12;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

symlink downloaded repo at specified commit when using --from-commit so easyconfigs for dependencies are found;
bug fixes for CargoPythonBundle generic easyblock;
bug fixes in custom easyblocks for intel-compilers and Python;
(***) add patch to fix CVE-2024-27322 in R v3.6.x, v4.0.x, v4.1.x, v4.2.x, v4.3.x;
(***) fix detection of CC/CXX compilers for wmake in OpenFOAM v2306 + v2312;
(***) change arrow-R dependency of R-bundle-Bioconductor v3.18 to v14.0.1;
(***) add dependencies required for GUI in Cellpose 2.2.2 easyconfigs;
(***) add missing dependencies for funannotate;
(***) make sure mummerplot can use gnuplot if available for recent MUMmer;
remove easyconfigs for CellBender v0.3.1, since this version has been redacted due to a serious bug (see here);

Supported software

Support for installing 82 new software packages has been added, including (but not limited to):

AEDT
AMGX
Cassiopeia
CheckM2
Compass
CVX
EasyMocap
FDMNES
HiGHS
HOMER
LangChain
libabigail
LIBSVM-MATLAB
Lightning
MetalWalls
ml-collections
MOFA2
orthAgogue
planarity
PRRTE
PSM2
PyHMMER
PyVista
SCReadCounts
TF-COMB
TorchIO
VAMPIRE-ASM
WGDgc

This brings the total number of supported software packages to 3,552 (excluding extensions)! An up-to-date list of supported software is available here.

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

AFNI 24.0.02
alevin-fry 0.9.0
BCFtools 1.19
BLIS 1.0
BWA 0.7.18
Boost 1.85.0
CGAL 5.6.1
CellRank 2.0.2
Clang 17.0.6
dask 2024.5.1
deal.II 9.5.2
dorado 0.5.3
ESPResSo 4.2.2
FMM3D 1.0.4
GAMESS-US 20220930-R2 + 20230930-R2
GCC 13.3.0 + 14.1.0
GOATOOLS 1.4.5
GTDB-Tk 2.4.0
gemmi 0.6.5
gmsh 4.12.2,
HDDM 0.9.9
HTSlib 1.19.1
HyPhy 2.5.60
h5py 3.11.0
IOR 4.0.0
Jupyter-bundle 20240522 (incl. JupyterHub 4.1.5, JupyterLab 4.2.0, JupyterNotebook 7.2.0, ...)
Kalign 3.4.0
kallisto 0.50.1
MATSim 15.0
MetaMorpheus 1.0.5
MuJoCo 3.1.4
mold 2.31.0
NanoPlot 1.42.0
nglview 3.1.2
nvtop 3.1.0
OCaml 5.1.1
OpenMPI 5.0.3
PhyML 3.3.20220408
PyTorch-bundle 2.1.2
Python 3.12.3
petsc4py 3.20.3
polars 0.20.2
py3Dmol 2.1.0
pyiron 0.5.1
ROOT 6.30.06
Rust 1.78.0
SAMtools 1.19.2
SentencePiece 0.2.0
Seurat 5.1.0
SimNIBS 4.0.1
Spack 0.21.2
Squidpy 1.4.1
SymEngine 0.11.2
scikit-learn 1.4.2
TensorFlow 2.15.1
Transformers 4.39.3
tokenizers 0.15.2
UCX 1.16.0
Valgrind 3.23.0
VisPy 0.14.1
zlib-ng 2.1.6

These changes result from various contributions, made by 29 different contributors:

16 merged pull requests for EasyBuild framework
27 merged pull requests for easyblocks
326 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.2, there are several options.

Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 20801 # use easyconfig from PR #20801

- Shell
Published by boegel over 1 year ago

https://github.com/easybuilders/easybuild - EasyBuild v4.9.1

EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements.

Executive summary

Support for --from-commit and --include-easyblocks-from-commit;
1 new sofware-specific easyblocks for DualSPHysics;
Support for installing 101 (!) new software applications, tools, and libraries;
Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more;
Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below);

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 & updates

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

new software-specific easyblock for DualSPHysics;
enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage;
updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k;
(***) significant improvements to QuantumESPRESSO easyblock, incl. running the test suite;
enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems;
(***) add extensions to R-bundle-CRAN v2023.12 (use --rebuild --skip);
(***) add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency;
(***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use --rebuild --skip);

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

bug fixes for generic easyblocks: Cargo, CMakeMake,
bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision;
(***) fix link order in PETSc easyblock for SCOTCH >= 7.x;
(***) do not rename GCC's include-fixed directory by default + add script to regenerate it; Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0, see easyblocks PR #3254 for more info.
(***) add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component; We recommend re-installing OpenMPI 4.1.x to pick up this fix.
(***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support;
(***) add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin;
add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs;
(***) move setuptools_scm extension from hatchling to Python easyconfig; We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.5-GCCcore-13.2.0 using eb --rebuid --skip (or the reinstall these modules).
add patches for PyTorch v2.1.2 to fix test failures;
add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+;
(***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency;

Supported software

Support for installing 101 (!) new software packages has been added, including (but not limited to):

AMICA
Circlator
Clarabel.rs
DeepLoc
devbio-napari
EpiSCORE
ExtremeLy
GenomeComb
GRASP-suite
IDG
IonQuant
libspectre
MLflow
MSFragger
noise
PAGAN2
phyluce
python-casacore
QuPath
RHEIA
SemiBin
Sentence-Transformers
SQLAlchemy
Vamb
zUMIs

This brings the total number of supported software packages to 3,470 (excluding extensions)! An up-to-date list of supported software is available here.

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

anvio 8
arrow-R 14.0.0.2
BerkeleyGW 3.1.0 + 4.0
Cartopy 0.22.0
Clang-Python-bindings 16.0.6
CUDA 12.3.2 + 12.4.0
CuPy 13.0.0
CVXPY 1.4.2
DeepLabCut 2.3.6
EggLib 3.3.0
ESMF 8.4.2
FDS 6.8.0
Flask 3.0.0
FLINT 3.1.1
GATK 4.5.0.0
GLFW 3.4
GROMACS 2024.1
Gurobi 11.0.0
HeFFTe 2.4.0
LAMMPS 2Aug2023_update2
likwid 5.3.0
matplotlib 3.8.2
medaka 1.11.3
MOABB 1.0.0
MONAI 1.3.0
NCCL 2.20.5
NGSpeciesID 0.3.0
NLTK 3.8.1
NVHPC 24.1
OCaml 4.14.0
ONNX 1.15.0
OpenFOAM v2306 + v2312
OpenSSL/3 (wrapper)
PAPI 7.1.0
ParaView 5.12.0
PETSc 3.20.3
plotly.py 5.18.0
PyQt5 5.15.10
PyTables 3.9.2
pytest-rerunfailures 14.0
python-irodsclient 2.0.0,
PyTorch-Lightning 2.2.1
Qt5 5.15.13
Qt6 6.6.3
QuantumESPRESSO 7.3
R 4.3.3
R-bundle-Bioconductor 3.18
rMATS-turbo 4.2.0
Ruby 3.3.0
Rust 1.76.0
scikit-learn 1.4.0
Score-P 8.4,
SLEPc 3.20.1
timm 0.9.7
VEP 111
WIEN2k 23.2
wrf-python 1.3.4.1
YODA 1.9.9

These changes result from various contributions, made by 34 different contributors:

28 merged pull requests for EasyBuild framework
43 merged pull requests for easyblocks
575 (!) merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.1, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 20299 # use easyconfig from PR #20299

- Shell
Published by boegel almost 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.9.0

EasyBuild v4.9.0 is primarily a feature release, mainly because it includes the 2023b version of the common toolchains (foss + intel), but it also includes various bug fixes, and much more.

The executive summary for this release:

improved support for using recent version of Environment Modules as modules tool;
new generic CargoPythonBundle easyblock;
3 new custom easyblocks: for flook, HPCC, and PALM;
easyconfigs for foss/2023b and intel/2023b;
Easyconfigs for various recent software versions, including GROMACS 2023.3, NWChem 7.2.2, Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, SciPy-bundle 2023.11, Spark 3.5.0, VTK 9.3.0, ...;
Support for installing 77 new software applications and libraries;

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 & updates

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

add generic CargoPythonBundle easyblock;
3 new software-specific easyblocks for flook, HPCC, PALM;
update easyblocks for intel-compilers, impi, imkl to support latest versions;
update numpy easyblock for v1.26+;
updates and enhancements to custom easyblocks for Ferret, SuiteSparse;
add easyconfigs for foss/2023b and intel/2023b (see also common toolchains overview);

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

fix support for Environment Modules as modules tool to pass unit tests with v4.2+;
adapt module function check for Environment Modules v4+;
disable LLVM build downloads from CI in Rust;
update SuiteSparse easyblock to only install SuiteSparse libraries with make install;
fix specifying path to SuiteSparse header files and libraries in numpy, Trilinos, PETSc easyblocks;
add support for allowing version mismatch + consider versionsuffix when creating .modulerc in ModuleRC easyblock;
fix det_pylibdir provided by PythonPackage easyblock for Python 3.12+;
bug fixes for custom easyblocks for Clang, CUDA, numpy, NWChem, PETSc, PyTorch, Rust, SuiteSparse, TensorFlow, Trilinos
add patch to fix regression in GCC 12.x on AVX512 systems (***);
add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (***);
add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23;
fix OpenBLAS 0.3.20+ on newer Intel CPUs;
add patch to fix [cz]asums in OpenBLAS 0.3.24 (***);
add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (***);
change toolchain in json-fortran easyconfigs to GCC, since it includes Fortran modules (***);
use GCC toolchain in kim-api, since it includes Fortran modules (***);
allow ITK legacy code and Python wrappers in ITK v5.2.1 (***);

Supported software

Support for installing 77 new software packages has been added, including (but not limited to):

BRiAl
CellBender
DIA-NN
EUKulele
FACE
GFF3-toolkit
HPCC
iperf
LoopTools
MitoHiFi
PFFT
PySINDy
R-bundle-CRAN
scikit-lego
SEACells
solo
Triton
waLBerla

This brings the total number of supported software packages to 3,369 (excluding extensions)! An up-to-date list of supported software is available here.

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

Arrow 14.0.1
Boost 1.83.0
CellRanger 7.2.0
CUDA 12.3.0
f90wrap 0.2.11
FPM 1.15.1
GPyTorch 1.10
GROMACS 2023.3
ITK 5.3.0,
LinBox 1.7.0
magma 2.7.2,
Molden 7.3
NWChem 7.2.2
phonopy 2.20.0
PostgreSQL 16.1,
Python-bundle-PyPI 2023.10
PyTorch 2.1.2
R 4.3.2
SciPy-bundle 2023.11
Seurat 4.4.0
Spark 3.5.0
SuiteSparse 7.1.0
UCX-CUDA 1.15.0
VTK 9.3.0
XGBoost 2.0.2

These changes result from various contributions, made by 34 different contributors:

21 merged pull requests for EasyBuild framework
26 merged pull requests for easyblocks
276 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.9.0, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 19464 # use easyconfig from PR #19464

- Shell
Published by boegel about 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.8.2

EasyBuild v4.8.2 is primarily a bugfix and update release, but it also includes various enhancements.

The executive summary for this release:

Various small enhancements and bug fixes in EasyBuild framework, easyblocks, and easyconfigs;
Easyconfigs for various recent software versions, including Cantera 3.0.0, mold 2.3.1, Perl-bundle-CPAN 5.38.0, PyTorch 2.0.1, ...;
Support for installing 48 new software applications and libraries, incl. PyTensor, Qt6, SNAP-ESA;

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 & updates

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

add dependency_names method to EasyConfig class to get set of names of (direct) dependencies;
use more test programs in sanity check step of OpenMPI easyblock;
updates and enhancements to various generic easyblocks, including CMake, Conda, ConfigureMake;
updates and enhancements to custom easyblocks for imkl, numpy, Perl, PyTorch, WRF, wxPython;
add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7;
(***) don't disable building of third and fourth derivates in libxc 6.1.0;
(***) also build Python bindings for ITK 5.2.1 with foss/2022a;
(***) add extensions to recent versions of R and R-bundle-Bioconductor, use "eb --skip --rebuild" to install the missing extensions;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

reset tempfile.tempdir to None to avoid that tmpdir path gets progressively deeper with each easystack item;
only use -DCMAKE_SKIP_RPATH=ON for CMake < 3.5.0;
fix --sanity-check-only and --module-only for UCX plugins;
enhance TensorFlow easyblock to avoid use of -mcpu=native for XNNPACK component when building on aarch64;
fix the blas/lapack name passed to meson when building recent scipy versions (>= 1.9.0) on top of Intel MKL;
(***) add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and GCCcore/12.3.0;
(***) add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs;
rename ACT to Artemis;
rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions;
add patch for recent OpenBLAS versions (0.3.23, 0.3.24) to fix flaky and hanging tests;
(***) add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3;
(***) fix invalid pointer access in UCX 1.11-1.14;
(***) statically link Boost 1.75 in Cufflinks v20190706 installed with GCC/11.2.0, so Boost can be changed to build dependency;
add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20;
(***) add missing dependencies for MONAI to support extras required by MONAI-Label;
(***) disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain;

Supported software

Support for installing 48 new software packages has been added, including (but not limited to):

ALL
bases2fastq
biobakery-workflows
CLEAR
EveryBeam
imutils
Jmol
MACS3
MUSCLE3
ProBiS
PyPy
PyTensor
Qt6
ResistanceGA
scCODA
SNAP-ESA
starparser
XBeach

This brings the total number of supported software packages to 3,292 (excluding extensions)! An up-to-date list of supported software is available here.

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

Amber 22.4
BLAST+ 2.14.1
Cantera 3.0.0
CapnProto 1.0.1
CGAL 5.6
CUDA-Samples 12.1.1
CuPy 12.1.0
FastANI 1.34
GDAL 3.7.1
GMP 6.3.0
GPAW 23.9.1
HMMER 3.4
IsoSeq 4.0.0
libpng 1.6.40
libxc 6.2.2
MEGAN 6.25.3
Mesa 23.1.9
mold 2.3.1
OpenBLAS 0.3.24
OpenCV 4.8.1
OpenMPI 4.1.6
OrthoFinder 2.5.5
ParaView 5.11.2
Perl-bundle-CPAN 5.38.0
pyEGA3 5.0.2
Python 3.11.5
PyTorch 2.0.1
PyTorch-bundle 1.13.1
RagTag 2.1.0
RAxML-NG 1.2.0,
RDFlib 7.0.0
ReFrame 4.3.3
Rust 1.73.0
scikit-learn 1.3.1
TensorRT 8.6.1
UCX 1.15.0
X11 20231019
xtb 6.6.0

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

15 merged pull requests for EasyBuild framework
20 merged pull requests for easyblocks
267 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.2, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 19105 # use easyconfig from PR #19105

- Shell
Published by boegel over 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.8.1

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 prerunshellcmdhook 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 which includes links to the respective pull requests for more detailed information.

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;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling 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 here.

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. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 18761 # use easyconfig from PR #18761

- Shell
Published by boegel over 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.8.0

EasyBuild v4.8.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

The executive summary for this release:

Easyconfigs for the 2023a update of the foss + intel common toolchains;
2 new easyblocks: a generic PerlBundle easyblock, and a custom easyblock for Rust;
Easyconfigs for various recent software versions, including elastix 5.0.0, GROMACS 2023.1, PyTorch 1.13.1, VTK 9.2.6, ...;
Support for installing 76 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.

Highlighted enhancements & updates

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

add PerlBundle generic easyblock for installing a bundle of Perl modules;
add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if --rpath is used;
add support for install_cmds in Binary easyblock;
update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes;
(***) add extra packages to recent R easyconfigs;
(***) add extra packages to recent R-bundle-Bioconductor easyconfigs;
(***) enable building static libs and check for libexslt.* in libxslt;

Prominent bug fixes & changes

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

fix regex for extracting glibc version from output of 'ldd --version' in Gentoo Linux;
stop running tests with Python 2.7 since it is no longer supported in GitHub Actions;
patch CMake's UnixPaths.cmake script if --sysroot is set;
use upstream patch for symbol compatibility in XZ 5.2.5;
(***) change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a);
(***) use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2;
(***) stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2;
(***) fix exec permissions for all binaries & scripts of LRNAscaffolder 20190530;
(***) update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies;
(***) fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17);
(***) fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b);
(***) bump OpenSSL 1.1 wrapper fallback to 1.1.1u;

Supported software

Support for installing 76 new software packages has been added, including (but not limited to):

alleleIntegrator
BayesPrism
Circuitscape
DALI
DaliLite
ecFlow
FragPipe
GLIMPSE
KerasTuner
mannkendall
MONAI-Label
NanoStat
pastml
Perl-bundle-CPAN
PyBioLib
PyWBGT
Sniffles
Tapenade
timm
wrapt
xclip

This brings the total number of supported software packages to 3,161 (excluding extensions)! An up-to-date list of supported software is available here.

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

alleleCount 4.2.1
BayesTraits 3.0.2
Bowtie2 2.5.1
Cellpose 2.2.2
CUDA 12.1.1 + 12.2.0
CVXOPT 1.3.1
deepTools 3.5.2
DMTCP 3.0.0
dorado 0.3.0 + 0.3.1
duplex-tools 0.3.3
fastp 0.23.4
FreeSurfer 7.4.0
GATK 4.4.0.0
GCC 11.4.0
Geant4 11.1.2
GROMACS 2023.1
Horovod 0.25.0
Julia 1.9.0
LibLZF 3.6
MAGeCK 0.5.9.5
MaxQuant 2.4.2.0
MMseqs2 14-7e284
MuJoCo 2.2.2
ncbi-vdb 3.0.5
ont-fast5-api 4.1.1
openpyxl 3.1.2
ParaView 5.11.1
Perl 5.36.1
PSI4 1.7
Pysam 0.21.0
Python 3.11.3
PyTorch 1.13.1
Rust 1.70.0
seqtk 1.4
SUNDIALS 6.5.1
TransDecoder 5.5.0
Transformers 4.29.2 + 4.30.2
VTK 9.2.6
xarray 2023.4.2
zlib-ng 2.0.7

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

9 merged pull requests for EasyBuild framework
13 merged pull requests for easyblocks
301 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.8.0, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 18282 # use easyconfig from PR #18282

- Shell
Published by boegel over 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.7.2

EasyBuild v4.7.2 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

Various small enhancements and bug fixes to EasyBuild framework, easyblocks, and easyconfigs;
Easyconfigs for various recent software versions, including AlphaFold 2.3.4, CP2K 2022.1, GCC 12.3.0 + 13.1.0, R-bundle-Bioconductor 3.16, ...;
Support for installing 89 new software applications and libraries;

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 & updates

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

extend (experimental) support for generating container images with Apptainer;
2 new generic easyblocks for installing Rust crates with cargo: Cargo and CargoPythonPackage;
(***) enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0;
(***) add additional extensions to recent R and R-bundle-Bioconductor easyconfigs;
(***) switch bamtofastq + Longshot to Cargo easyblock;
(***) add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file;
(***) add missing FastTreeMP binary for FastTree;
(***) bump versions in Java wrappers to latest builds that include ppc64le;

Prominent bug fixes & changes

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

fix --check-github as gist url now includes username;
(***) force building torchvision with CUDA support if CUDA is included as dependency by setting $FORCE_CUDA;
(***) use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0;
(***) add missing OpenJPEG dependency for recent GDAL versions;
(***) upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues;
(***) add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6;
(***) FLINT needs BLAS so move it up from GCC level;
add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test;
exclude flaky testoptim + add patch to fix testquantization for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent;
add make 4.3 as build dependency for recent OpenBLAS versions;
add alternative checksum for MONAI 1.0.1;
add historical repo paths to install command for old versions of texlive;

Supported software

Support for installing 89 new software packages has been added, including (but not limited to):

AGeNT
Annocript
BoltzTraP2
Casanovo
CellOracle
ColabFold
DiCE-ML
ESPResSo
FunGAP
GLI
HTSplotter
IsoSeq
LoRDEC
OptaDOS
PGPLOT
pod5-file-format
pytesseract
Python-bundle
PyTorch-bundle
Raven
Scalene
SoPlex
sysbench
TOPAS
turbinesFoam

This brings the total number of supported software packages to 3,085 (excluding extensions)! An up-to-date list of supported software is available here.

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

AlphaFold 2.3.4
Arrow 11.0.0
Clang 15.0.5
CP2K 9.1 + 2022.1
GCC 12.3.0 + 13.1.0
intel/2023.03 (incl. intel-compilers 22023.1.0, impi 2021.9.0, imkl 2023.1.0)
OpenMM 8.0.0
picard 3.0.0
R-bundle-Bioconductor 3.16
ReFrame 4.2.0
UCC-CUDA 1.1.0

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

14 merged pull requests for EasyBuild framework
15 merged pull requests for easyblocks
316 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.2, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 17986 # use easyconfig from PR #17986

- Shell
Published by boegel over 2 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.7.1

EasyBuild v4.7.1 is primarily a bugfix and update release, but it also includes various minor enhancements.

The executive summary for this release:

Various small enhancements and bug fixes to EasyBuild framework, easyblocks, and easyconfigs;
Easyconfigs for various recent software versions: AlphaFold 2.3.0, HDF5 1.14.0, networkx 3.0, TensorFlow v2.11.0, Trilinos 13.4.1, ...;
Additional easyconfigs using the latest 2022b toolchains, incl. SciPy-bundle 2023.02 with gfbf/2022b (subtoolchain of foss/2022b);
Support for installing 99 new software applications and libraries;

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 support for %(start_dir)s easyconfig template;
add pre/post extension hook that is triggered before/after individual extension installations;
enforce absolute paths as start dir of extensions;
updates and enhancements for various generic easyblocks: GoPackage, MesonNinja, PythonPackage;
updates and enhancements for various software-specific easyblocks: EasyBuildMeta, ELPA, Maple, Mathematica, NAMD, pybind11, Python, QScintilla, scipy, TensorFlow, Trilinos;
(***) add additional extensions to Python 3.10.8 (required for scipy test suite) (see --skip);
(***) add extensions to Perl 5.32.1 (see --skip);
(***) add additional extensions to R 4.2.1 (see --skip);
(***) add additional extensions to Bioconductor 3.15 (see --skip);
(***) enhance OpenFold 1.0.1 for standalone usage;
(***) add SDL2 dependency for FFmpeg 5.0.1 to build ffplay;
(***) add ffnvcodec build dependency to all recent FFmpeg easyconfigs;
(***) set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs;
(***) add missing zstd dep to Boost;

Prominent bug fixes & changes

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

restore initial environment before processing each easystack item (support for easystack files is still experimental);
various fixes and improvements for the EasyBuild framework test suite;
(***) fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions;
(***) fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets;
(***) fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x;
bug fixes for various generic easyblocks: CMakeMake, CMakePythonPackage, PythonPackage, PythonBundle;
bug fixes for various software-specific easyblocks: FlexiBLAS, netCDF, NVHPC, PyTorch;
(***) add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug;
(***) add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b;
(***) replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs;
(***) update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (see --skip);
(***) replace src include path with installation dir for HDF5;
(***) use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API;
(***) add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2;
(***) fix postinstallcmds in shovill easyconfigs;
(***) add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1
(***) add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs;
(***) enable -fPIC in GEOS 3.11.1 (required by GDAL);
add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes);
rename some software names in existing easyconfigs, or archive these easyconfigs, to avoid case-insensitive name clashes;

Supported software

Support for installing 99 (!) new software packages has been added, including (but not limited to):

CatLearn
Cellpose
chemprop
cuSPARSELt
DensPart
dorado
fastjet
finder
genomepy
grid
Health-GPS
HiCMatrix
Inferelator
kineto
LASSO-Python
netMHCII
PfamScan
plot1cell
PyTorch-Ignite
rapidNJ
scArches
scib
smfishHmrf
Strainberry
VirSorter2
YODA

This brings the total number of supported software packages to 2,995 (excluding extensions)! An up-to-date list of supported software is available here.

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

AlphaFold 2.3.0
AUGUSTUS 3.5.0
BCFtools 1.17
Biopython 1.81
Boost 1.81.0
CFITSIO 4.2.0
CUDA 12.1.0
DIAMOND 2.1.0,
epiScanpy 0.4.0
FFmpeg 5.1.2
GDAL 3.6.2
GPyTorch 1.9.1
h5py 3.8.0
HTSlib 1.17
Hypre 2.27.0
intel/2022.12 (incl. intel-compilers 2023.0.0, impi 2021.8.0, imkl 2023.0.0)
jax 0.4.4
MaSuRCA 4.1.0
MATLAB 2022b
MDAnalysis 2.4.2
mpi4py 3.1.4
NetLogo 6.3.0
networkx 3.0
numba 0.56.4
NVHPC 23.1
OpenMPI 4.1.5
PLUMED 2.8.1
pyGenomeTracks 3.8
PySCF 2.1.1
Python 3.11.2
R 4.2.2
ReFrame 4.0.5
ROOT 6.22.08
SAMtools 1.17,
scikit-learn 1.2.1
SciPy-bundle 2023.02,
SPAdes 3.15.5
TensorFlow 2.11.0
Trilinos 13.4.1
Xerces-C++ 3.2.4

These changes result from various contributions, made by 30 different contributors:

36 merged pull requests for EasyBuild framework
34 merged pull requests for easyblocks
386 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.1, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 17568 # use easyconfig from PR #17568

- Shell
Published by boegel almost 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.7.0

EasyBuild v4.7.0 is primarily a feature release, but it also includes various minor bug fixes and 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 (***))

also run unit tests with Python 3.11;
add support for checksums specified in external checksums.json file;
take into account custom configuration options specified in easystack files - see also docs;
add support for using --output-format=md (MarkDown);
add support for postinstallmsgs;
add gfbf as subtoolchain of foss;
make iimkl toolchain aware of intel-compilers;
add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage + JuliaBundle;
updates and enhancements for various generic easyblocks, incl. ConfigureMake, PythonPackage;
(***) updates and enhancements for various software-specific easyblocks: BerkeleyGW, Clang, Clang-AOMP, ESMF, libxml2, LLVM, OpenCV, OpenMPI, PETSc, QScintill, TensorFlow, Xmipp;

Prominent bug fixes & changes

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

print deprecation warning with running EasyBuild with Python 2;
various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format;
vendor distutils.version.LooseVersion as easybuild.tools.LooseVersion (since distutils is deprecated in Python 3.10, to be removed in Python 3.12);
auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0;
use -march=x86-64 -mtune=generic instead of -xSSE2 when using Intel oneAPI compilers;
drop support for easystack files using 'software' top-level key;
make PythonPackage easyblock compatible with --sanity-check-only by loading module early during sanity check step;
(***) update HDF5 easyblock to use --enable-threadsafe configure option to make C API thread safe;
(***) bug fixes for various software-specific easyblocks: ANSYS, Clang, MRtrix, PyTorch;

Supported software

New version of common toolchains: foss/2022b, intel/2022b

Support for installing 107 new software packages has been added, including (but not limited to):

Alfred
bamFilters
CAT-BAT
CloudCompare
COBRApy
CUDA-Samples
DeepLabCut
DRAGMAP
ESM-2
HighFive
IJulia
KaHIP
LHAPDF
Magics
MEMOTE
MONAI
MOOSE
MultilevelEstimators
napari
nf-core-mag
OmegaFold
pyccel
PyDamage
pyWannier90
scvi-tools
SELFIES
SISSO++
spaCy
Squidpy
TBA
trimesh
UCX-ROCm

This brings the total number of supported software packages to 2,904 (excluding extensions)! An up-to-date list of supported software is available here.

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

AOCC 4.0.0
CDO 2.1.1
CubeGUI/CubeLib/CubeWriter 4.8
CUDA 11.8.0 + 12.0.0
deepdiff 5.8.1
FLANN 1.9.1
GATK 4.3.0.0
GDCM 3.0.20
Ghostscript 10.0.0
GRASS 8.2.0
JasPer 4.0.0
libspatialite 5.0.1
LLVM 15.0.5
Mesa 22.2.4
mold 1.7.1
MRChem 1.1.1
ncbi-vdb 3.0.0
nglview 3.0.3
nodejs 18.12.1
Octave 7.1.0
OpenFOAM 10
OpenFold 1.0.1
OpenMolcas 22.10
OpenStackClient 6.0.0
PAPI 7.0.0,
PETSc 3.17.4
pyproj 3.4.0
Python 3.10.8
PyTorch 1.12.1
PyTorch-Geometric 2.1.0
QGIS 3.28.1
Qt5 5.15.7
QtPy 2.2.1
ReFrame 3.12.0
scanpy 1.9.1
Score-P 8.0
SignalP 6.0g
SLEPc 3.17.2
SNAP 2.0.1
SpaceRanger 2.0.0
SuperLU_DIST 8.1.0
tensorboardX 2.5.1
TensorFlow 2.8.4
tesseract 5.3.0
Valgrind 3.20.0
Vim 9.0.0950
VTK 9.2.2
wandb 0.13.6
WebKitGTK+ 2.37.1
WPS/WRF 4.4
wxPython 4.2.0
X11 20221110
Xmipp 3.22.07

These changes result from various contributions, made by 29 different contributors:

42 merged pull requests for EasyBuild framework
36 merged pull requests for easyblocks
469 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.7.0, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 17065 # use easyconfig from PR #17065

- Shell
Published by boegel about 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.6.2

EasyBuild v4.6.2 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 which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

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

enable running of LAPACK tests for recent OpenBLAS easyconfigs;
2 new software-specific easyblocks: CUDA compatibility libraries (CUDAcompat) + mamba;
updates and enhancements for various software-specific easyblocks: OpenFOAM, ESMF, netCDF, numexpr;
enhance EasyBuildMeta easyblock: auto-enable installing with pip;

Prominent bug fixes & changes

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

(***) add patch to GCC 11.x + 12.x to fix vectorizer bug;
(***) add patch to fix failing LAPACK tests due to use of -ftree-vectorize;
correctly count the number of failing tests (not failing test suites) in PyTorch builds;
(***) add patches to fix incompatibilites between ASE and other packages in 2022a toolchain;
(***) fix execution permissions for bin/ngm* for NextGenMap v0.5.5;
(***) add bzip2 and libxml2 as dependencies for netCDF 4.9.0;
(***) add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0;
make --inject-checksums inject dictionary value for checksums which maps filename to SHA256 checksum;
fix trying to generate RPATH wrappers for Clang;
update easyconfigs to use SYSTEM template constant instead of True in dependencies;

Supported software

New version of intel toolchain: intel/2022.09

Support for installing 25 new software packages has been added, including (but not limited to):

AMAPVox
buildingspy
CDBtools
f90wrap
Miller
NVSHMEM
paladin
PyMOL
python-irodsclient
ruffus
TELEMAC-MASCARET
x13as

This brings the total number of supported software packages to 2,798 (excluding extensions)! An up-to-date list of supported software is available here.

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

ASE 3.22.1
biogeme 3.2.10
Delly 1.1.5
ESMF 8.3.0
FDS 6.7.9
Go 1.18.3
GPAW 22.8.0
IPython 8.5.0
Julia 1.8.2
LIBSVM 3.30
netcdf4-python 1.6.1
Nipype 1.8.5,
OpenCV 4.6.0
OpenMM 7.7.0
Perl 5.36.0
PyTorch 1.12.0
PyTorch-Lightning 1.7.7
RDFlib 6.2.0
SAMtools 1.16.1
scikit-learn 1.1.2
Score-P 7.1
SuiteSparse 5.13.0
SUNDIALS 6.3.0
sympy 1.11.1
torchvision 0.13.1
TRIQS 3.1.1
UCX 1.13.1
VEP 107
Wayland 1.21.0
wxWidgets 3.2.1

These changes result from various contributions, made by 24 different contributors:

17 merged pull requests for EasyBuild framework
20 merged pull requests for easyblocks
159 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.2, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 16465 # use easyconfig from PR #16465

- Shell
Published by boegel over 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.6.1

EasyBuild v4.6.1 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 which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

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

run python in the same process as eb wrapper script by using exec (which improves startup performance of eb command);
reduce the number of command line options for cmake command in CMakeMake generic easyblock;
enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when return_output_ec=True is used;
updates and enhancements for various software-specific easyblocks: GROMACS, LAMMPS, libQGLViewer, NVHPC, PyTorch;
(***) add extra symlinks and sanity checks for libtinfo in ncurses;
speed up OpenMPI 4.1.4 configure by not running autogen.pl --force, but only running required Autotools commands;

Prominent bug fixes & changes

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

use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (rather than assuming that CMake is loaded as a build dependency);
don’t enable building of ld.gold when installing binutils on a RISC-V system + don’t configure GCC to use gold as default linker on a RISC-V system;
make Amber easyblock aware of FlexiBLAS;
tweak Amber(Tools) easyblock to run tests from top-level directory, and enable running of tests for AmberTools v20 + v21;
work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong;
various fixes for installing PyTorch on POWER systems;
(***) replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn’t use odd minor versions of HDF5 which are not stable releases;
(***) use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option);
(***) add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs;
(***) add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9;
simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency;
(***) add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 and 2021;
(***) fix checksum for Stacks v2.62 (due to silent re-release without version bump);
(***) consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs;
(***) update Java/11 to 11.0.16 and Java/17 to 17.0.4;

Supported software

Support for installing 37 new software packages has been added, including (but not limited to):

BigDFT
colossalai
Dakota
FastFold
howarewestrandedhere
libmad
MetaMorpheus
muMerge
olaFlow
OpenFAST
OpenFold
pyGenomeTracks
RheoTool
Satsuma2
UCC-CUDA
VESTA

This brings the total number of supported software packages to 2,773 (excluding extensions)! An up-to-date list of supported software is available here.

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

AmberTools 22.3
BCFtools 1.15.1
binutils 2.39
BLAST+ 2.13.0
CDO 2.0.5
CoordgenLibs 3.0.1,
Elk 8.5.2,
FFmpeg 4.4.2 + 5.0.1
FreeSurfer 7.3.2
GATE 9.2
GCC(core) 12.2.0
GDB 12.1
gnuplot 5.4.4
Graphviz 5.0.0
HDF5 1.12.2
HTSlib 1.15.1
Hypre 2.25.0,
jax 0.3.14,
LAMMPS 23Jun2022
Libint 2.7.2
maeparser 1.3.0
matplotlib 3.5.2
MATSim 14.0
medaka 1.6.0
Megalodon 2.5.0
MetaEuk 6,
MUMPS 5.5.1
netCDF-Fortran 4.6.0
ont-remora 1.0.0
OpenFOAM v2206
ParaView 5.10.1
Perl 5.36.0
Pyomo 6.4.2
PyStan 3.5.0
PyYAML 6.0
scikit-bio 0.5.7
scikit-learn 1.1.2
SCOTCH 7.0.1
spglib-python 2.0.0
SUMO 1.14.1
Valgrind 3.19.0
ViennaRNA 2.5.1
wxPython 4.1.1
zfp 1.0.0

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

16 merged pull requests for EasyBuild framework
20 merged pull requests for easyblocks
266 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.1, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 16240 # use easyconfig from PR #16240

- Shell
Published by boegel over 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.6.0

EasyBuild v4.6.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

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 support for OneAPI compilers using toolchain option 'oneapi';
add support for setting environment variables via 'pushenv' with modextravars;
fall back to sequential extension install if parallel install is not implemented;
one new software-specific custom easyblock for STAR-CCM+;
updates and enhancements for various software-specific easyblocks: FFTW, Libint, OpenSSL, Siesta, TensorFlow, WPS;
add support for allowing some PyTorch tests to fail + print warning if one or more tests fail;
easyconfigs for foss/2022a and intel/2022a common toolchains (see also here);
(***) additional extensions for R v4.2.0 (see --skip);
(***) add patch for GCCcore 11.3.0 to support using -fuse-ld=mold;

Prominent bug fixes & changes

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

tweak 'eb' wrapper script to correctly handle errors when python command being considered fails to run;
tweak is_patch_for function to make it more robust;
tweak apply_patch function to not create .orig files (by default) when applying patch files;
make sure that CMakeMakeCp generic easyblock uses correct build dir;
make VEP easyblock compatible with --sanity-check-only;
only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension;
switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1;
(***) avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs;
(***) correct configopts in deal.II v9.1.1 easyconfig;

Supported software

Support for installing 24 new software packages has been added, including (but not limited to):

fio
G-PhoCS
Gibbs2
Minipolish
NetPyNE
SISSO
sklearn-pandas
SWIPE
topaz
uncertainty-calibration

This brings the total number of supported software packages to 2,736 (excluding extensions)! An up-to-date list of supported software is available here.

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

AlphaFold 2.2.2
Arrow 8.0.0
CellRanger 7.0.0
deal.II 9.3.3
FSL 6.0.5.1
GDAL 3.5.0
geopandas 0.11.0
GEOS 3.10.3
h5py 3.7.0
HDF5 1.13.1
ImageMagick 7.1.0-37
jemalloc 5.3.0
Leptonica 1.82.0
libRmath 4.2.0
libxc 5.2.3
MaSuRCA 4.0.9
mold 1.3.0
netCDF 4.9.0
NEURON 7.8.2
NLopt 2.7.1
nvtop 2.0.2
PLUMED 2.8.0,
PRISMS-PF 2.2
PROJ 9.0.0
PyTorch 1.11.0
Qt5 5.15.5
QuantumESPRESSO 7.1
R 4.2.1
Ray-project 1.13.0
ReFrame 3.11.2
SpectrA 1.0.1
TensorFlow 2.7.1
UCX-CUDA 1.12.1
WPS 3.9.1

These changes result from various contributions, made by 24 different contributors:

17 merged pull requests for EasyBuild framework
17 merged pull requests for easyblocks
149 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.6.0, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 15832 # use easyconfig from PR #15832

- Shell
Published by boegel over 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.5

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 which includes links to the respective pull requests for more detailed information.

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 + R v4.1.2 (see --skip);
(***) 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 here.

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. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 15635 # use easyconfig from PR #15635

- Shell
Published by boegel over 3 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.4

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 which includes links to the respective pull requests for more detailed information.

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 (see --skip;
(***) 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 here.

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:

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

To upgrade to EasyBuild v4.5.4, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 15214 # use easyconfig from PR #15214

- Shell
Published by boegel almost 4 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.3

EasyBuild v4.5.3 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 which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

avoid crash in get_os_version on modern SLES-based OSs;
fix get_os_name and get_os_version to avoid reporting UNKNOWN in output of eb --show-system-info;
switch to using pip3 for installing EasyBuild in container recipes generated by EasyBuild;
(***) add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1;
(***) add patch to fix Kraken2 ncbi ftp/https check in rsyncfromncbi.pl for versions 2.0.9-2.1.1;
(***) consistently apply patch for mapDamage 2.2.1 to use external seqtk;
fix download URL in UDUNITS v2.2.28 easyconfigs;
add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 and R 4.1.2 easyconfigs;

Highlighted enhancements & changes

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

new software-specific easyblock for reticulate R package;
updates and enhancements for various software-specific easyblocks: CUDA, HDF5, NAMD;
(***) set CUDA target architecture(s) for GROMACS based CUDA compute capabilities listed in EasyBuild configuration;
(***) also install Python bindings for SHTns 3.5.1;

Supported software

Support for installing 25 new software packages has been added, including (but not limited to):

Arcade-Learning-Environment
Bambi
CASTEP
deepmedic
histolab
MuJoCo + mujoco-py
OpenCensus-python
PyEVTK
pyradiomics
PyTorch-Lightning
Redis
SoXt
SURVIVOR
xtensor

This brings the total number of supported software packages to 2,647 (excluding extensions)! An up-to-date list of supported software is available here.

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

AOCC 3.2.0
Bowtie 1.3.1
Clang 13.0.1
ConnectomeWorkbench 1.5.0
CUDA 11.5.1 + 11.6.0
dask 2022.1.0
deepTools 3.5.0
FDS 6.7.7
GATE 9.1
Geant4 11.0.0
Graphviz 2.50.0
GROMACS 2021.5
JupyterLab 3.2.8
MEGA 11.0.10
methylpy 1.2.9
minimap2 2.24
ncbi-vdb 2.11.2
OpenCV 4.5.5
pyFAI 0.20.0
Racon 1.5.0
RAxML 8.2.12
ReFrame 3.10.1
ROOT 6.24.06
scikit-image 0.19.1
SeqKit 2.1.0
Siesta 4.1.5
SqueezeMeta 1.5.0
torchvision 0.11.3

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

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

To upgrade to EasyBuild v4.5.3, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 14979 # use easyconfig from PR #14979

- Shell
Published by boegel about 4 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.2

EasyBuild v4.5.2 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 which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

fix compatibility with Python 3.10;
minor fixes for IntelBase generic easyblocks and various software-specific easyblocks: CP2K, GATE, Perl, Siesta, WRF;
(***) add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ...;
(***) fix broken patch file for recent GPAW versions;
(***) add missing PCRE dependency for pullseq;
(***) enforce using internal Boost for bcl2fastq2 with a GCC 10.x toolchain;
(***) add patches to fix CVE-2021-23437 for Pillow and Pillow-SIMD;

Highlighted enhancements & changes

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

enhance get_cpu_architecture and get_cpu_family to be aware of RISC-V;
deprecate use of (actual) patch files that don’t have a filename ending with .patch;
add support for enabling sanity checks for specific components in the Bundle easyblock;
use all available cores for running Perl test suite;
updates and enhancements for various software-specific easyblocks: AOCC, CUDA, Bazel, Gurobi, intel-compilers, itac, LibInt, Mathematica, NAMD, SuiteSparse, WPS;
bundle LAPACKE with FlexiBLAS 3.0.4;
(***) additional extensions for R-bundle-Bioconductor 3.14;
(***) additional extensions for R v4.1.2;
(***) update Java 1.8 wrapper to 1.8.0311 for x8664;
(***) bump nbconvert extension in recent IPython easyconfigs to version 6.4.0;
update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain;

Supported software

Support for installing 48 new software packages has been added, including (but not limited to):

ANGEL
Calcam
DyMat
ExaML
FMPy
hivtrace
MetaPhlAn
mold
OpenFace
PhyloPhlAn
PuLP
PyTorch3D
SCopeLoomR
SHTns
TALYS
xxHash

This brings the total number of supported software packages to 2,622 (excluding extensions)! An up-to-date list of supported software is available here.

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

intel/2022.00 toolchain
antiSMASH 5.2.0
BLAST+ 2.12.0
CP2K 8.2
Extrae 3.8.3
gmsh 4.9.0
h5py 3.6.0
IQ-TREE 2.1.3
Java/15 + Java/17
libxsmm 1.17
MultiQC 1.11
numba 0.54.1
NVHPC 21.11,
openCARP 8.2
OpenCV 3.4.1
OpenFOAM v2112
Pillow + Pillow-SIMD 8.3.2
PLUMED 2.7.3
Raysect 0.7.1
scanpy 1.8.2
SqueezeMeta 1.0.0
statsmodels 0.13.1

These changes result from various contributions, made by 30 different contributors:

16 merged pull requests for EasyBuild framework
23 merged pull requests for easyblocks
199 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.2, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 14830 # use easyconfig from PR #14830

- Shell
Published by boegel about 4 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.1

EasyBuild v4.5.1 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 which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***))

don't try to ensure absolute path for path part of --repositorypath EasyBuild configuration option;
only remove lock if it was created in the same EasyBuild session (not if it existed already);
(***) minor fixes for various software-specific easyblocks: CP2K, MUMmer, netcdf4-python, ORCA, OpenFOAM, OpenMPI, PETSc, SLEPc;
(***) add patch for libfabric v1.12.1 to fix unknown link width 0x10 warning;
add patch for GCCcore 9.1-9.3 and 10.1-11.1 to fix compatibility with recent kernel headers;
(***) add patch to fix CVE-2021-43527 in NSS;
pass tests on A* GPUs by setting NVIDIA_TF32_OVERRIDE=0 in jax 0.2.19;
(***) add patch to fix broken (hanging) Mash binaries;
seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs;
rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme;
comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0;
consistently use 'Grace' software name + sync homepage/source_urls;

Highlighted enhancements

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

enhancements for experimental feature --parallel-extensions-install:
- also determine which extensions can be skipped in parallel;
- fall back to sequential installation for extensions with unknown dependencies;
- see also https://docs.easybuild.io/en/latest/Installingextensionsin_parallel.html;
allow oversubscription in sanity check for OpenMPI-based toolchains;
new software-specific easyblock for Clang-AOMP;
enhanced Rpm generic easyblock;
updates and enhancements for various software-specific easyblocks: Eigen, GROMACS, Inspector, jaxlib, SAMtools, tbb;
(***) additional extensions for R-bundle-Bioconductor 3.13;
(***) additional extensions for R v4.1.x;

Supported software

Support for installing 71 new software packages has been added, including (but not limited to):

BabelStream
bamtofastq
bcbio-gff
Clang-AOMP
CMSeq
dRep
DUBStepR
elprep
epiScanpy
FMM3D
HIP
InChI
LERC
libtree
Megalodon
nnU-Net
PPanGGOLiN
ProFit
PySide2
ROCm
Shasta
SimNIBS
SMV (Smokeview)
ThemisPy
TOBIAS
zlib-ng
Zopfli

This brings the total number of supported software packages to 2,575 (excluding extensions)! An up-to-date list of supported software is available here.

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

AlphaFold 2.1.1
Arrow 6.0.0
Boost 1.77.0
Eigen 3.4.0
ESMF 8.2.0
Flye 2.9
Horovod 0.23.0
ITK 5.2.1
jax 0.2.24
NCO 5.0.3
OpenMPI 4.1.2
pangolin 3.1.16
PyTorch 1.10.0
R 4.1.2
R-bundle-Bioconductor 3.14
scikit-learn 1.0.1
torchvision 0.11.1
Trycycler 0.5.2
Unicycler 0.4.9
UShER 0.5.0
WPS 4.3.1
Yambo 5.0.4

These changes result from various contributions, made by 24 different contributors:

15 merged pull requests for EasyBuild framework
19 merged pull requests for easyblocks
244 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.1, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 14545 # use easyconfig from PR #14545

- Shell
Published by boegel about 4 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.5.0

EasyBuild v4.5.0 is primarily a feature release, but it also includes various minor bug fixes and updates.

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 (***))

support for showing progress bars when installing easyconfigs;
- enabled by default if the Rich Python package (https://pypi.org/project/rich) is installed;
- see https://docs.easybuild.io/en/latest/Progress_bars.html for more information;
add initial/experimental support for installing extensions in parallel;
- currently only supported for R extensions;
- see https://docs.easybuild.io/en/latest/Installingextensionsin_parallel.html for more information;
add support for checking required/optional EasyBuild dependencies via eb --check-eb-deps;
add support for --insecure-download configuration option;
one new software-specific custom easyblock for imkl-FFTW;
enhance GCC easyblock to add support for AMD GPU offloading;
enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend;
enhance imkl easyblock to add support for installing with NVHPC;
(***) detect problem with compiling CPU detection code in configure output in GROMACS easyblock;
- only relevant for specific GROMACS versions that were installed using CMake 3.15.3;
easyconfigs for foss/2021b and intel/2021b common toolchains;
- see also https://docs.easybuild.io/en/latest/Common-toolchains.html#overview-of-common-toolchains;

Prominent bug fixes & changes

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

deprecate old toolchain versions (pre-2019a common toolchains);
- see also https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains;
refactor EasyBlock to decouple collecting of information on extension source/patch files from downloading them;
change copy_file function to raise an error when trying to copy non-existing file;
fix library paths to add to $LDFLAGS for intel-compilers toolchain component;
restore RPATH wrappers for OpenMPI sanity check;
(***) don’t use --config=mkl configuration option when installing TensorFlow 2.4+;
- this fixes some performance related issues for TensorFlow installations, see release notes for more details;
(***) in-place updates for components of foss/2021b and intel/2021b common toolchains;
- see release notes for more details;
(***) add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0;
(***) add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection;

Supported software

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

ARTS
bashplotlib
CIRI-long
ESL-Bundle
FreeTDS
imkl-FFTW
libSBML
longread_umi
MixMHC2pred
OpenSceneGraph
pycoQC
radeontop
RInChI
scGeneFit
TOML-Fortran
vawk
VMTK

This brings the total number of supported software packages to 2,506 (excluding extensions)!

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

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

AlphaFold 2.0.1
artic-ncov2019 2021.06.24
BerkeleyGW 3.0.1
CP2K 8.2
CUDA 11.4.2
Dalton 2020.0
ELSI 2.7.1
FFTW 3.3.10
jax 0.2.20
ibxc 5.1.6
MEME 5.4.1
OpenBLAS 0.3.18
OSU-Micro-Benchmarks 5.8
PyTorch-Geometric 2.0.1
Qiskit 0.31.0
QuantumESPRESSO 6.8
RDKit 2021.03.4
SAMtools 1.13
SciPy-bundle 2021.10
UCX + UCX-CUDA 1.11.2
Z3 4.8.12

These changes result from various contributions, made by 30 different contributors:

40 merged pull requests for EasyBuild framework
33 merged pull requests for easyblocks
225 merged pull requests for easyconfigs

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

To upgrade to EasyBuild v4.5.0, there are several options. Two particularly easy options include:

eb --install-latest-eb-release
eb --from-pr 14248 # use easyconfig from PR #14248

- Shell
Published by boegel over 4 years ago

https://github.com/easybuilders/easybuild - 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 $LDLIBRARYPATH;
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

- Shell
Published by boegel over 4 years ago

https://github.com/easybuilders/easybuild - 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

- Shell
Published by boegel over 4 years ago

https://github.com/easybuilders/easybuild - 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.pythoncmd is set before using it in `PythonPackage.sanitycheck_stepto makePythonBundleeasyblock 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

- Shell
Published by boegel over 4 years ago

https://github.com/easybuilders/easybuild - 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 $RLIBSSITE 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 $RLIBSSITE 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 MPIInfof2c issue with OpenMPI;
(***) revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0;
(***) use -DUSEMETIS_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 * DLPOLY4 * 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

- Shell
Published by boegel almost 5 years ago

https://github.com/easybuilders/easybuild - 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)

- Shell
Published by boegel almost 5 years ago

https://github.com/easybuilders/easybuild - 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

- Shell
Published by boegel about 5 years ago

https://github.com/easybuilders/easybuild - 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

- Shell
Published by boegel over 5 years ago

https://github.com/easybuilders/easybuild - 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)

- Shell
Published by boegel over 5 years ago

https://github.com/easybuilders/easybuild - 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

- Shell
Published by boegel over 5 years ago

https://github.com/easybuilders/easybuild - 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

- Shell
Published by boegel almost 6 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.2.0

EasyBuild v4.2.0 is primarily a feature/update release, but also includes various bug fixes.

Highlights of the changes in this release include:

(experimental) support for --try-update-deps, to upgrade dependencies based on available easyconfigs;
a locking mechanism to prevent two simultaneous installations of the same easyconfig file to the same installation path (see https://easybuild.readthedocs.io/en/latest/Locks.html for more information);
significant speedup for -D/--dry-run by avoiding useless 'module show' calls;
support for creating an index & using it to speed up searching for easyconfigs (see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html for more information);
additional GitHub integration features:
- support for targeting the easyblocks and framework repositories with eb --new-pr (via --pr-target-repo)
- support for including easyblocks from an (open) pull request via --include-easyblocks-from-pr
- for more information, https://easybuild.readthedocs.io/en/latest/IntegrationwithGitHub.html
probing of external modules for missing metadata that is not provided via an external module metadata file (mostly relevant for integration with the Cray Programming Environment);
leveraging the archspec Python library (if it is installed) to show the "code name" of the processor in your system in the output of "eb --show-system-info" and in test reports uploaded to PRs via --upload-test-report;
support for using templates like %(cudaver)s for the CUDA version (if it's included as direct dependency);
fix for UnicodeDecodeError that was raised when reading a patch file that contained non-ASCII characters (if EasyBuild was being run with Python 3);
fixed filtering of already installed extensions under --skip (mostly relevant for Python packages installed as bundles of extensions);
also support %(installdir)s and %(builddir)s templates for extensions;
take into account toolchain hierarchy when dumping easyconfig files, to avoid hardcoded subtoolchains in '*dependencies' easyconfig parameters (relevant when using --try-* options);
take into account dependencies marked as external modules when composing template values like %(pyver)s;
deprecate rmtree2 function provided by easybuild.tools.filetools (the remove_dir function should be used instead);
7 new software-specific easyblocks: BerkeleyGW, CMake, ELSI, LAMMPS, libdrm, Mesa, SEPP;
updates, enhancements & bug fixes for the CMakeMake, PythonPackage and PythonBundle generic easyblocks;
updates, enhancements & bug fixes in the software-specific easyblocks for Clang, Ferret, Hypre, impi, libxml2, MATLAB, numexpr, OpenBabel, OpenBLAS, OpenCV, OpenFOAM, ParMETIS, PETSc, Python, QuantumESPRESSO, Qt, ROOT, Siesta, tbb, TensorFlow, TensorRT, Trinity, VMD, XCrySDen;
added support for no less than 114 (!) new software packages, incl. ADIOS, ArviZ, Bonito, ELSI, FuSeq, GraphMap2, LAMMPS, MedPy, motionSegmentation, OpenAI-Gym, PyMC3, PyRe, PyTorch-Geometric, RAxML-NG, Shapely, STEAK, UQTk, Zip, ...;
updates for already supported software, incl. Arrow 0.16.0, BUSCO 4.0.5, Clang 10.0.0, ELPA 2019.11.001, Ferret 7.5.0, GCC(core) 9.3.0, GROMACS 2020, GTK+ 3.24.13, Hypre 2.18.2, IQ-TREE 1.6.12, Java 13(.0.2), LLVM 9.0.1 + 10.0.0, likwid 5.0.1, medaka 0.12.0, numba 0.47.0, Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, PETSc 3.12.4, PyTorch 1.4.0, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, Racon 1.4.10, ReFrame 2.21, SLEPc 3.12.2, SimpleElastix 1.1.0, SimpleITK 1.2.4, TensorFlow 1.15.2 + 2.0.1, Trinity 2.10.0, XGBoost 0.90, xarray 0.15.1, ...;
update Java/1.8 wrapper to Java/1.8.0_241;
enhanced Java/11 wrapper to support both x86_64 and POWER;
fixed source URL for ISL component in GCCcore easyconfigs;
checksum fixes in easyconfigs for R 3.6.0 and 3.6.2;
revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs;
fixed packaging issue that resulted in CVS easyconfigs to be missing from EasyBuild releases;
updated checksum/homepage in tbb easyconfigs after move to 'oneapi-src' repository;
various additional updates, enhancements & bug fixes;

This brings the total number of supported software packages to 1,912! An up-to-date list of supported software is available at https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html .

A detailed overview of all changes, which links to the respective pull requests, is available in the release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-0-april-14th-2020 .

These changes result from various contributions, made by 26 different contributors:

56 merged pull requests for EasyBuild framework
63 merged pull requests for easyblocks
381 merged pull requests for easyconfigs

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

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Published by boegel almost 6 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.1.2

This release fixes a problem where the GitHub token that EasyBuild uses for some of the GitHub integration features (like --from-pr, --new-pr, etc.) got included in plain text in the 'top-level' EasyBuild log file when the --debug configuration option is enabled, potentially leaving it exposed to be used by others.

We strongly encourage that you revoke the GitHub tokens you are using currently, via https://github.com/settings/tokens, and to replace them using a new token (using "eb --install-github-token --force").

More information is available in the security advisory that was published.

Detailed release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-1-2-march-16th-2020 .

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Published by boegel almost 6 years ago

https://github.com/easybuilders/easybuild - EasyBuild v4.1.1

This release is primarily a bug fix/update release, but it also includes a couple of minor enhancements.

Highlights of the changes in EasyBuild v4.1.1 include:

support for "eb --show-ec" to show the contents of the specified easyconfig file, and "eb --copy-ec" to copy an easyconfig file to a specified location;
a new --cuda-compute-capabilities configuration option, which can be used to specify with which CUDA compute capabilities GPU software should be built (for now this is only relevant for TensorFlow);
various fixes for permission issues that occurred when (re-)installing software with EasyBuild using multiple different users;
avoiding needless warnings that commonly arise in EasyBuild log files;
one new software-specific easyblock for the cryptography Python package;
various fixes for installing software on POWER systems;
making the TensorFlow easyblock print a clear warning when no custom CUDA compute capabilities are specified (either via the new --cuda-compute-capabilities configuration option, or via the TensorFlow-specific cuda_compute_capabilities easyconfig parameter);
- by default recent TensorFlow versions only build with the 3.5 and 7.0 CUDA compute capabilities, which implies potentially significant performance loss on systems using NVIDIA Tesla GPUs like P100;
updates, enhancements & bug fixes for the Bundle, CMakeMake, conda, PythonPackage and VersionIndependentPythonPackage generic easyblocks;
updates, enhancements & bug fixes for the software-specific easyblocks for Bazel, CUDA, ESMF, FSL, GCC, GROMACS, HDF5, iccifort, imkl, impi, MATLAB, MRtrix, NCL, netCDF, OpenFOAM, Python, SAMtools, SWIG, tbb, TensorFlow, WPS, and WRF;
fixed problem that occurred when installing EasyBuild with EasyBuild running on top of Python 3;
added support for 27 new software packages, incl. breseq, CrossMap, horton, LEMON, OpenSlide, pythran, Qualimap, ...;
updates for already supported software, incl. Beast 1.10.4, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, GDAL 3.0.2, GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, Julia 1.3.1, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, Salmon 1.0.0, SuiteSparse 5.6.0, TensorFlow 2.1.0 w/ fosscuda/2019b, WPS 4.1, WRF 4.1.3, ...;
added easyconfigs for intel/2020.00 toolchain;
added missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs;
updated Java/1.8 wrapper to Java/1.8.0231 (for x8664);
enable building of CMake in parallel;
actually use Java dependency when building/running Bazel (rather the JDK included with Bazel);
fix source URLs in various easyconfigs, incl. ant, libsodium, libxc, Mesa, QCA, xorg-macros, ...;
add missing extensions in easyconfigs for cyvcf2 and pyfits;
add alternate valid SHA256 checksums for kallisto 0.43.1 + MASS 7.3-51.4 & rda 1.0.2-2.1 extensions in R 3.6.0 easyconfigs;
make sure we use provided Clang dependency for building pocl;
- require that sanitypipcheck is enabled in easyconfigs for Python packages that are touched by pull requests;
use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters;
various additional updates, enhancements & bug fixes;

This brings the total number of supported software packages to 1,798! An up-to-date list of supported software is available at https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html .

A detailed overview of all changes, which links to the respective pull requests, is available in the release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html .

These changes result from various contributions, made by 22 different contributors:

27 merged pull requests for EasyBuild framework
47 merged pull requests for easyblocks
197 merged pull requests for easyconfigs

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

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Published by boegel about 6 years ago

https://github.com/easybuilders/easybuild - EasyBuild v2.1.0

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Published by boegel almost 11 years ago

https://github.com/easybuilders/easybuild - easybuild-v1.16.1

easybuild v1.16.1

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Published by JensTimmerman about 11 years ago