Easybuild

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-6-1-september-12th-2022) 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
* how_are_we_stranded_here
* 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


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](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 16240` use easyconfig from [PR 16240](https://github.com/easybuilders/easybuild-easyconfigs/pull/16240)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-6-0-july-8th-2022) 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](https://docs.easybuild.io/en/latest/Common-toolchains.html#overview-of-common-toolchains));

- `(***)` additional extensions for R v4.2.0 (see [`--skip`](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

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](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 15832` use easyconfig from [PR 15832](https://github.com/easybuilders/easybuild-easyconfigs/pull/15832)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-5-june-8th-2022) 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](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

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](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 15635` use easyconfig from [PR 15635](https://github.com/easybuilders/easybuild-easyconfigs/pull/15635)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-4-march-31st-2022) 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`](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


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:

* [19 merged pull requests for EasyBuild framework](https://github.com/easybuilders/easybuild-framework/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.4)
* [24 merged pull requests for easyblocks](https://github.com/easybuilders/easybuild-easyblocks/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.4)
* [163 merged pull requests for easyconfigs](https://github.com/easybuilders/easybuild-easyconfigs/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.4)

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


To upgrade to EasyBuild v4.5.4, 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 15214` use easyconfig from [PR 15214](https://github.com/easybuilders/easybuild-easyconfigs/pull/15214)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-3-february-11th-2022) 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 rsync_from_ncbi.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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

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:

* [13 merged pull requests for EasyBuild framework](https://github.com/easybuilders/easybuild-framework/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.3)
* [10 merged pull requests for easyblocks](https://github.com/easybuilders/easybuild-easyblocks/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.3)
* [156 merged pull requests for easyconfigs](https://github.com/easybuilders/easybuild-easyconfigs/pulls?q=is%3Apr+is%3Amerged+sort%3Aupdated-desc+milestone%3A4.5.3)


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


To upgrade to EasyBuild v4.5.3, 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 14979` use easyconfig from [PR 14979](https://github.com/easybuilders/easybuild-easyconfigs/pull/14979)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-2-january-24th-2022) 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](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) for R-bundle-Bioconductor 3.14;

- `(***)` [additional extensions](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) for R v4.1.2;

- `(***)` update Java 1.8 wrapper to 1.8.0_311 for x86_64;

- `(***)` 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


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](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 14830` use easyconfig from [PR 14830](https://github.com/easybuilders/easybuild-easyconfigs/pull/14830)