@gpettinello Have you rebuilt trilinos with openmpi version 5? See what ldd /usr/lib/libml.so
shows.
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Package Details: petsc 3.20.5-2
Package Actions
Git Clone URL: | https://aur.archlinux.org/petsc.git (read-only, click to copy) |
---|---|
Package Base: | petsc |
Description: | Portable, extensible toolkit for scientific computation |
Upstream URL: | https://petsc.org |
Keywords: | computing scientific |
Licenses: | BSD |
Provides: | petsc4py |
Submitter: | heitzmann |
Maintainer: | MartinDiehl |
Last Packager: | MartinDiehl |
Votes: | 19 |
Popularity: | 0.000185 |
First Submitted: | 2018-02-24 11:36 (UTC) |
Last Updated: | 2024-02-28 17:53 (UTC) |
Dependencies (30)
- fftw-openmpi
- gsl (gsl-gitAUR)
- hdf5-openmpi
- lapack (aocl-libflame-aoccAUR, aocl-libflameAUR, blas-mklAUR, lapack-gitAUR, openblas-lapackAUR, atlas-lapackAUR, blas-aocl-gccAUR, blas-aocl-aoccAUR, blas-openblas)
- libjpeg-turbo (mozjpeg-gitAUR, libjpeg-turbo-gitAUR, mozjpegAUR)
- libyaml (libyaml-gitAUR)
- netcdf-openmpi
- openmpi (openmpi-gitAUR)
- python-mpi4py (python-mpi4py-intelAUR)
- python-numpy (python-numpy-flameAUR, python-numpy-mkl-binAUR, python-numpy-gitAUR, python-numpy-mklAUR)
- suitesparse
- superlu
- zfp
- zlib (zlib-ng-compat-gitAUR, zlib-gitAUR, zlib-ng-compatAUR)
- cmake (cmake-gitAUR) (make)
- cython (cython-gitAUR, cython0) (make)
- gcc (gccrs-gitAUR, gcc11AUR, gcc-gitAUR) (make)
- gcc-fortran (gccrs-fortran-gitAUR, gcc11-fortranAUR, gcc-fortran-gitAUR) (make)
- hypreAUR (optional) – support for HYPRE
- kokkosAUR (trilinosAUR) (optional) – support Kokkos
- Show 10 more dependencies...
Required by (24)
- coolfluid-svn
- damask (make)
- damask-grid
- damask-grid (make)
- damask-mesh
- damask-mesh (make)
- deal-ii (optional)
- dolfin
- dolfin-hpc
- dolfinx
- dolfinx-git
- fenics-basix-git (check)
- freefem (optional)
- libmesh-petsc
- pism
- precice
- precice-git
- python-basix-git
- python-clawpack (optional)
- python-damask (make)
- Show 4 more...
Sources (2)
lahwaacz commented on 2024-02-25 11:52 (UTC)
gpettinello commented on 2024-02-25 11:46 (UTC)
Same problem to compile as written below about ml libraries. Only solution was to pecify --with-ml = 0 in test_optdepens.sh
lahwaacz commented on 2024-02-24 06:46 (UTC)
You can also remove export OMPI_MCA_plm_rsh_agent=sh
, since openmpi
has had a hard dependency on openssh
since 4.1.5-1 and it will be solved in a better way by https://gitlab.archlinux.org/archlinux/packaging/packages/prrte/-/merge_requests/2
lahwaacz commented on 2024-02-23 17:17 (UTC)
The tests should behave as before with openmpi 5.0.2-4 where the warnings were disabled (by default): https://gitlab.archlinux.org/archlinux/packaging/packages/openmpi/-/commit/ca64cda9e8dcf1460936132eb73e666741a5c38e
So you might want to remove the following from the PKGBUILD:
export OMPI_MCA_opal_warn_on_missing_libcuda=0
if [ -z "$(ldconfig -p | grep libamdhip64.so)" ] || [ -z "$(ldconfig -p | grep libucc.so)" ]; then
echo "skipping tests"
else
The petsc check target is still bad though, treating all warnings as errors is very naive...
MartinDiehl commented on 2024-02-23 10:13 (UTC)
@Alad: That was my mistake, installing CUDA should not be necessary. It's fixed now.
Alad commented on 2024-02-23 04:03 (UTC) (edited on 2024-02-23 04:20 (UTC) by Alad)
I managed to get past the dependency issues with trilinos
15 and a chroot build, but now tests ex19
and ex47
fail.
edit: I suppose this is due to the CUDA issue mentioned below. Installing cuda
into the chroot worked (arch-nspawn <chroot_dir> pacman -S cuda
).
MartinDiehl commented on 2024-02-22 21:56 (UTC)
@Alad: Did you recompile after updating openMPI to 5.x?
Alad commented on 2024-02-18 16:11 (UTC)
I have trilinos
installed but get the following error:
*********************************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
Unable to find ml in default locations!
Perhaps you can specify with --with-ml-dir=<directory>
If you do not want ml, then give --with-ml=0
You might also consider using --download-ml instead
*********************************************************************************************
MartinDiehl commented on 2024-02-10 10:42 (UTC)
Unfortunately, OpenMPI with CUDA shows warnings if CUDA is not available. This causes the failure of PETSc tests. See https://github.com/open-mpi/ompi/issues/12314 for the upstream bug report. For the moment, I recommend to simply disable the tests in PKGBUILD, I'll provide a sustainable solution soon.
Pinned Comments
MartinDiehl commented on 2022-10-06 10:26 (UTC)
@jrohwer
When building PETSc (more specifically, petsc4py), one test (ex100 from ksp) will fail if a previous (major) version is installed. I could not figure out why this happens. The solution would be to build in a clean root (which is a little bit complicated due to dependency on other AUR packages) or simply uninstall the old version before.
Any help to solve this issue is welcomed.