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. 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]
