Releases · easybuilders/easybuild

14 Apr 18:40

boegel

easybuild-v4.2.0

e2c41c2

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/Integration_with_GitHub.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!

Assets 2

14 Apr 17:47

boegel

easybuild-v4.1.2

f3714ca

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 .

Assets 2

16 Jan 19:07

boegel

easybuild-v4.1.1

dec172d

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/1.8.0_231 (for x86_64);
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 sanity_pip_check 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: