| 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-2-Clause |
| Provides: | petsc4py |
| Submitter: | heitzmann |
| Maintainer: | MartinDiehl |
| Last Packager: | MartinDiehl |
| Votes: | 20 |
| Popularity: | 0.024163 |
| First Submitted: | 2018-02-24 11:36 (UTC) |
| Last Updated: | 2025-10-04 08:37 (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.
I suggest add openssh as checkdependency.
I'm getting a different error (also during check). It compiles okay but fails during testing.
==> Starting check()...
Running check examples to verify correct installation
Using PETSC_DIR=/home/jr/.cache/yay/petsc/src/petsc-3.18.0 and PETSC_ARCH=arch-linux-c-opt
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ example src/snes/tutorials/ex19 run successfully with suitesparse
Possible error running C/C++ Python src/ksp/ksp/tutorials/ex100 with 1 MPI process
See https://petsc.org/release/faq/
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: method zeroEntries()
[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-nox (no value)
[0]PETSC ERROR: Option left: name:-nox_warning (no value)
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.18.0, Sep 30, 2022
[0]PETSC ERROR: ./ex100 on a named jr-xps13 by jr Wed Oct 5 22:43:05 2022
[0]PETSC ERROR: Configure options --prefix=/opt/petsc/linux-c-opt --with-shared-libraries=1 --with-petsc4py=1 --with-mpi-f90module-visibility=0 --with-cc=/usr/bin/mpicc --with-cxx=/usr/bin/mpicxx --with-fc=/usr/bin/mpifort --with-fftw=1 --with-metis=1 --with-suitesparse=1 --COPTFLAGS=-O3 -march=native --CXXOPTFLAGS=-O3 -march=native --FOPTFLAGS=-O3 -march=native
[0]PETSC ERROR: #1 MatZeroEntries_Python() at src/libpetsc4py/libpetsc4py.c:5497
[0]PETSC ERROR: #2 MatSetUp() at /home/jr/.cache/yay/petsc/src/petsc-3.18.0/src/mat/interface/matrix.c:933
[0]PETSC ERROR: #3 RunTest() at ex100.c:25
[0]PETSC ERROR: #4 main() at ex100.c:83
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -nox
[0]PETSC ERROR: -nox_warning
[0]PETSC ERROR: -test
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
with errorcode 83.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
Error while running make check
make[1]: *** [makefile:149: check] Error 1
make: *** [GNUmakefile:17: check] Error 2
==> ERROR: A failure occurred in check().
Aborting...
@fsimonis I tried to add it, but for me it gives
The option -Wp,-D_FORTIFY_SOURCE should probably be -Wp,-D-FORTIFY-SOURCE
Could you see if the same happens if you add --CFLAGS=${CFLAGS} to configure.
Hi and thanks for maintaining the package! Could you pass the C/CXX/LD flags defined in /etc/makepkg.conf to the PETSc configuration? PETSc always tells me that it ignores the envs.
Hi dear @MartinDiehl, I submit a bug report for python-mpi4py because something is wrong in petsc4py because of mpi4py.
Now that I see, mpi4py is an optional dependency.
Edited 2022-06-13:
Adding this changed solved the issue from my side, the same applies for mumps, petsc, petsc-complex or any PKGBUILD that have check() function and depends of openmpi. E.g.
==> Starting check()...
Running check examples to verify correct installation
Using PETSC_DIR=/tmp/makepkg/petsc/src/petsc-3.17.2 and PETSC_ARCH=arch-linux-c-opt
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ Python example src/ksp/ksp/tutorials/ex100 run successfully with 1 MPI process
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
==> Starting check()...
Running check examples to verify correct installation
Using PETSC_DIR=/tmp/makepkg/petsc-complex/src/petsc-3.17.2 and PETSC_ARCH=arch-linux-c-opt
C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
C/C++ Python example src/ksp/ksp/tutorials/ex100 run successfully with 1 MPI process
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
I have an error during check:
PKGBUILD: line 73: [: too many arguments
I think the line:
if [ -z $(ldconfig -p | grep libcuda.so.1) ]; then
should be
if [ -z "$(ldconfig -p | grep libcuda.so.1)" ]; then
@a.kudelin
I've inherited the PKGBUILD and don't know the exact reasons for installation into /opt However, PETSc installation is a little bit special. It relies on PETSC_DIR (and optionally PETSC_ARCH). Installing it into /usr might have unwanted effects, for example the PETSC_DIR/PETSC_ARCH mechanism to handle multiple versions might not work anymore.
If you have a modified PKGBUILD to change the installation path and/or test_optdepends.sh to include http://viennacl.sourceforge.net/ I will give it a try.
Hello,
Is there a reason for the package to be installed in /opt instead of /usr?
Also I suggest to enable OpenCL.
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.