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4.5.5

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](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)

4.5.4

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](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)

4.5.3

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](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)

4.5.2

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](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)

4.5.1

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-1-december-13th-2021) 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](https://access.redhat.com/security/cve/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/Installing_extensions_in_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](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) for R-bundle-Bioconductor 3.13;

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


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

- AlphaFold 2.1.1
- 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](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 14545` use easyconfig from [PR 14545](https://github.com/easybuilders/easybuild-easyconfigs/pull/14545)

4.5.0

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-0-october-29th-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 `(***)`)

- 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/Installing_extensions_in_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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-0-october-29th-2021) for more details;

- `(***)` in-place updates for components of `foss/2021b` and `intel/2021b` common toolchains;
* see [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-5-0-october-29th-2021) 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


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](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 14248` use easyconfig from [PR 14248](https://github.com/easybuilders/easybuild-easyconfigs/pull/14248)

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