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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-4-2-september-7th-2021) which includes links to the respective pull requests for more detailed information.
Highlighted enhancements
(enhancements that (may) warrant updating existing installations are marked with `(***)`)
- add `--filter-ecs` configuration option to filter out easyconfigs from set of easyconfigs to install;
- also define `$BLAS_SHARED_LIBS` & co in build environment (analogous to `$BLAS_STATIC_LIBS`);
- add `get_cuda_cc_template_value` method to `EasyConfig` class;
- pick up `$MODULES_CMD` to facilitate using Environment Modules 4.x as modules tool;
- add 4 new software-specific easyblocks for CRISPR-DAV, jaxlib, ORCA, RepeatModeler;
- update software-specific easyblocks for ABAQUS, Amber, BerkeleyGW, Clang, CP2K, ESMF, FreeFEM, GROMACS, LAMMPS, numexpr, numpy, Molpro, OpenFOAM, TensorFlow, VTune, WIEN2k;
- enable make check and sanity check commands for OpenMPI;
- `(***)` make sure AOCC commands like clang/flang pick up GCCcore as GCC toolchain;
- `(***)` create CMakeConfig files for tbb >= 2020;
- `(***)` generate and install pkg-config files for OpenSSL wrapper;
- added easyconfig for `foss/2021.07` (candidate for `foss/2021b`) and `iomkl/2021a` toolchains;
- `(***)` add various extensions to recent R v4.x easyconfigs;
Prominent bug fixes & changes
(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)
- `(***)` don’t add directory that doesn't include any files to $PATH or $LD_LIBRARY_PATH;
- make sure git clone with a tag argument actually downloads a tag;
- honor `--ignore-test-failure` in `PythonPackage` easyblock;
- reset `runtest` to None in `CMakePythonPackage` easyblock;
- let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly;
- use `${BLAS,LAPACK}_SHARED_LIBS` in GROMACS easyblock for FlexiBLAS-based toolchains;
- `(***)` add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX);
- `(***)` use correct GTK+ version for OpenCV based on dependencies;
- `(***)` set `$I_MPI_ROOT` correctly for 2021.x in impi easyblock (only requires `--module-only` to fix);
- `(***)` keep symlinks in cuDNN installations;
- `(***)` fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost;
- `(***)` add missing Bio-Search-hmmer dependency for prokka;
- `(***)` patch MaxBin2 Perl script to use provided Perl dependency;
- `(***)` avoid MPICXX dependency in SimpleElastics ITK;
- `(***)` add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault);
- `(***)` enable EGL in recent libepoxy easyconfigs;
- `(***)` update tensorflow-probability easyconfigs to include --release flag in installopts;
- `(***)` fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2;
- update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check;
- `(***)` create libtinfo symlinks in easyconfigs for ncurses with system toolchain;
Other changes
- simplify Boost easyblock;
- remove deprecated options from PythonPackage easyblock;
- use custom ORCA easyblock in easyconfigs for ORCA v4.x;
- rename NINJA to TWL-NINJA to avoid nameclash;
- rename `CUDAcore` to `CUDA` for v11.3.1 and v11.4.1 after merging foss/fosscuda toolchains, to ensure that `get_software_root('CUDA')` used in easyblocks works;
Supported software
Support for installing 79 new software packages has been added, including (but not limited to):
- AlphaFold
- AUTO-07p
- biogeme
- CellRank
- Coin
- CRISPR-DAV
- DistributedStream
- freebayes
- GIMP (13216)
- GOATOOLS
- GTK2 + GTK3
- hipSYCL
- jax
- Kalign
- Maude
- Mish-Cuda
- OSPRay
- pandapower
- pangolin
- PYPOWER
- pysamstats
- QCxMS
- RepeatModeler
- SoQt
- SpectrA
- SyRI
- UShER
- Vampire
- VisPy
- Yices
This brings the total number of supported software packages to 2,467!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).
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](https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:
- `eb --install-latest-eb-release`
- `eb --from-pr 13918` use easyconfig from [PR 13918](https://github.com/easybuilders/easybuild-easyconfigs/pull/13918)