Hi Kenneth, Loris Bennett <[email protected]> writes:
> Hi Kenneth, > > Kenneth Hoste <[email protected]> writes: > >> Hi Loris, >> >> On 12/09/2022 13:12, Loris Bennett wrote: >>> Hi Kenneth, >>> Kenneth Hoste <[email protected]> writes: >>> >>>> Dear EasyBuilders, >>>> >>>> We're happy to announce the release of EasyBuild v4.6.1 [1]. >>>> >>>> An independent jury of experts thoroughly evaluated this release, and >>>> reached >>>> the unanimous conclusion that this is the best EasyBuild release to date! >>> I am sure it is the best release ever, but I currently can't install it >>> on CentOS 7 :-( >>> I get the error >>> ModuleNotFoundError: No module named 'Crypto' >> >> >> Where/when/how are you hitting this exactly? EasyBuild doesn't require a >> Crypto >> module itself at all... > > During the sanity check: > > == 2022-09-12 13:04:29,701 build_log.py:169 ERROR EasyBuild crashed with an > error (at > easybuild/software/EasyBuild/4.6.0/lib/python3.6/site-packages/easybuild/base/exceptions.py:124 > in __init__): Sanity check failed: sanity check command eb --version exited > with code 1 (output: Traceback (most recent call last): > File "/usr/lib/python3.6/site-packages/keyring/backends/file.py", line > 199, in priority > __import__('Crypto.Cipher.AES') > ModuleNotFoundError: No module named 'Crypto' > > Maybe this is related to the issues I have had with the Github > integration. I installed 'python36-keyring' on 9th August, which was > after I had updated to EasyBuild 4.6.0, so maybe this is causing the > problem. I uninstalled the package python36-keyring and was able to update EasyBuild. Cheers, Loris > Cheers, > > Loris > >>> Via EPEL I can install >>> python36-pycryptodomex >>> but this installs it modules in the namespace 'Cryptodome', rather than >>> 'Crypto'. >>> I can probably just symlink 'Cryptodome' to 'Crypto', but is there a less >>> hacky option? >> >> I think we need some more information on how you're triggering this, and >> where >> the problem comes from. >> >> At first sight, it may be a sign of a broken Python installation, or of a >> dependency picked up by EasyBuild. >> >> >> regards, >> >> Kenneth >> >>> Cheers, >>> Loris >>> >>>> As usual, there's a lot of attempts to distract you from this, including >>>> soaring >>>> gas prices, granting rest to The Queen, and a Belgian 22-year old brat >>>> winning >>>> the Vuelta (w00! \o/). What will they think of next... >>>> >>>> The executive summary for this release: >>>> >>>> - various minor bug fixes for EasyBuild framework; >>>> - various bug fixes and enhancements to existing easyconfigs and >>>> easyblocks; >>>> - easyconfigs for various recent software versions: GATE v9.2, Graphviz >>>> v5.0.0, LAMMPS v23Jun2022, OpenFOAM v2206, ... >>>> - support for installing 37 new software applications and libraries; >>>> >>>> >>>> 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 [2] which includes links to the respective pull requests for >>>> more >>>> detailed information. >>>> >>>> (this information is also available at >>>> https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.6.1>>> >>>> ## 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 at [4]. >>>> >>>> >>>> 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 [5]. >>>> Two particularly easy options include: >>>> >>>> * eb --install-latest-eb-release >>>> >>>> * eb --from-pr 16240 # use easyconfig from PR #16240 [6] >>>> >>>> >>>> Enjoy! >>>> >>>> >>>> regards, >>>> >>>> Kenneth & Miguel >>>> >>>> >>>> [1] https://pypi.org/project/easybuild/4.6.1>>> [2] >>>> https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-6-1-september-12th-2022>>> >>>> [3] >>>> https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip>>> >>>> [4] >>>> https://docs.easybuild.io/en/latest/version-specific/Supported_software.html>>> >>>> [5] >>>> https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation>>> >>>> [6] https://github.com/easybuilders/easybuild-easyconfigs/pull/16240>>> >> -- Dr. Loris Bennett (Herr/Mr) ZEDAT, Freie Universität Berlin Email [email protected]
