Package Details: petsc 3.21.0-2

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: 0.000100
First Submitted: 2018-02-24 11:36 (UTC)
Last Updated: 2024-04-03 06:01 (UTC)

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.

Latest Comments

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MartinDiehl commented on 2022-10-06 16:22 (UTC)

@lahwaacz: I'm just trying to understand what's going on and find a solution, not workarounds. If ssh is a dependency for openmpi, it has to be solved in the respective package. If all PETSc applications require it, it is a dependency. But checkdepends seems to be a quick fix that should not be in the official PKGBUILD

lahwaacz commented on 2022-10-06 15:33 (UTC)

@MartinDiehl petsc currently can't be built in a clean chroot without openssh in checkdepends. The solution for more problems is more workarounds, not delaying previous workarounds.

MartinDiehl commented on 2022-10-06 15:11 (UTC)

@lahwaacz and @carlosal1015: I think then it makes sense to apply the same fix as for MUMPS.

However, it seems that ssh is not the problem the only problem. At least on my setup, I cannot run MPI applications if WiFi and ethernet is disabled. I understand that MPI is meant to work over network, but it would be nice if one could use the same executable on a machine without ssh and a network connection.

lahwaacz commented on 2022-10-06 11:12 (UTC)

@MartinDiehl The openssh problem is reported in https://bugs.archlinux.org/task/75535 but carlosal1015's comment was about adding it to checkdepends, not depends. FWIW it's the same problem that you've recently fixed in https://aur.archlinux.org/cgit/aur.git/commit/?h=mumps&id=05532ed6645296c32c6e9c247024959aa4715bcc

MartinDiehl commented on 2022-10-06 10:43 (UTC)

@carlosal1015: I don't think that PETSc has a dependency on openssh. Maybe openMPI has (there are some ongoing discussions).

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.

carlosal1015 commented on 2022-10-05 21:04 (UTC)

I suggest add openssh as checkdependency.

jrohwer commented on 2022-10-05 20:47 (UTC)

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...

MartinDiehl commented on 2022-07-07 21:58 (UTC)

@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.

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