Easybuild

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)

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)

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)

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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-4-1-july-6th-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 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


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](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 13344` use easyconfig from [PR 13344](https://github.com/easybuilders/easybuild-easyconfigs/pull/13344)

**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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-4-0-june-2nd-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 `(***)`]

- 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.python_cmd is set before using it in `PythonPackage.sanity_check_step` to make `PythonBundle` easyblock 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

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](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 13012` use easyconfig from [PR 13012](https://github.com/easybuilders/easybuild-easyconfigs/pull/13012/files)

**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](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-3-4-apr-9th-2021) 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 $R_LIBS_SITE 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 $R_LIBS_SITE 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 MPI_Info_f2c issue with OpenMPI;

- `(***)` revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0;

- `(***)` use -D_USE_METIS_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`](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-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
* DL_POLY_4
* 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](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

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](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 12554` use easyconfig from [PR 12554](https://github.com/easybuilders/easybuild-easyconfigs/pull/12554/files)