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@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.

@Alad: Thanks. I can certainly fix the permissions. Did you try using the Kokkos package instead of Trilinos? It seems that file locations differ, so Trilinos is not a direct replacement for Kokkos

The linking error mentioned by @carlosal1015 also stops slepc from building:

Checking PETSc installation...
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Checking link with code:

#include "petscsnes.h"
int main() {
PetscErrorCode ierr; Vec v; Mat m; KSP k;
ierr = PetscInitializeNoArguments();
ierr = VecCreate(PETSC_COMM_WORLD,&v);
ierr = MatCreate(PETSC_COMM_WORLD,&m);
ierr = KSPCreate(PETSC_COMM_WORLD,&k);
(void)ierr;
return 0;
}

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Running command:
cd /tmp/slepc-_acdm5dt;/usr/bin/make checklink LINKFLAGS=""
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Output:
/usr/bin/mpicxx -o checklink.o -c -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/home/custompkgs/hpc/petsc/src=/usr/src/debug/petsc  -std=gnu++17 -fPIC  -I/opt/petsc/linux-c-opt/include -I/usr/include/hypre -I/usr/include/suitesparse -I/usr/include -I/usr/include/superlu_dist -I/usr/include/superlu -I/usr/include/kokkos    checklink.c
/usr/bin/mpicxx -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now          -Wl,-z,pack-relative-relocs  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/home/custompkgs/hpc/petsc/src=/usr/src/debug/petsc  -o checklink checklink.o  -Wl,-rpath,/opt/petsc/linux-c-opt/lib -L/opt/petsc/linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -lpetsc /usr/lib/libHYPRE.so -lspqr -lumfpack -lklu -lcholmod -lamd -lsuperlu_dist -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu -lfftw3_mpi -lfftw3 /usr/lib/libkokkoscore.so -llapack -lblas -lzfp -lzoltan -lptesmumps -lptscotchparmetisv3 -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -lnetcdf -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -ltriangle -lgsl -lgslcblas -lm -lz -ljpeg -lyaml -lX11 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `triangulate(char*, triangulateio*, triangulateio*, triangulateio*)'
collect2: error: ld returned 1 exit status
make: *** [makefile:2: checklink] Error 1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

ERROR: Unable to link with PETSc

Also the permissions on /etc/profile.d/petsc.sh are wrong on my machine:

% ls -ahl /etc/profile.d/petsc.sh
-rwxrwx--x 1 root root 99 28. Aug 00:45 /etc/profile.d/petsc.sh

Using chmod 644 instead of chmod +x avoids this issue -- any files in /etc/profile.d are sourced, not executed directly.

Getting an error with trilinos installed:

TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:89)
*********************************************************************************************
           UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
  Unable to find kokkos in default locations!
  Perhaps you can specify with --with-kokkos-dir=<directory>
  If you do not want kokkos, then give --with-kokkos=0
  You might also consider using --download-kokkos instead
*********************************************************************************************

==> ERROR: A failure occurred in build().
    Aborting...
==> Removing installed dependencies...

Going by configure.log the test searches for /usr/include/Kokkos_Macros.hpp when the trilinos package installs it to /usr/include/kokkos/Kokkos_Macros.hpp. The fix is to use

if [ -f "/usr/lib/libkokkoscore.so" ]; then
  CONFOPTS="${CONFOPTS} --with-kokkos=1 --with-kokkos-lib=/usr/lib/libkokkoscore.so --with-kokkos-include=/usr/include/kokkos"
fi

in test_optdepends.sh.

I noticed that if I installed before triangle and later petsc, this test failed. But if only install petsc in a clean environmnent only with base-devel, no error arises.

$ source /etc/profile.d/petsc.sh
$ cp -R /opt/petsc/linux-c-opt/share/petsc/examples .
$ cd examples/src/dm/dt/dualspace/impls/lagrange/tests/
$ make ex1
/usr/bin/mpicxx -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now          -Wl,-z,pack-relative-relocs  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS  -I/opt/petsc/linux-c-opt/include -I/usr/include/suitesparse -I/usr/include -I/usr/include/superlu     -Wl,-export-dynamic ex1.c   -Wl,-rpath,/opt/petsc/linux-c-opt/lib -L/opt/petsc/linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/15.1.1 -lpetsc -lspqr -lumfpack -lklu -lcholmod -lamd -lsuperlu -lfftw3_mpi -lfftw3 -llapack -lblas -lzfp -lnetcdf -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -ltriangle -lgsl -lgslcblas -lm -lz -ljpeg -lyaml -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath  -o ex1
/usr/sbin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `triangulate(char*, triangulateio*, triangulateio*, triangulateio*)'
collect2: error: ld returned 1 exit status
make: *** [/opt/petsc/linux-c-opt/lib/petsc/conf/rules:217: ex1] Error 1

After namcap petsc-3.23.5-1-x86_64.pkg.tar.zst, we have

petsc W: Referenced python module 'scipy.sparse' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/PetscBinaryIO.py'])
petsc W: Referenced python module 'lxml.objectify' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/xml2flamegraph.py'])
petsc W: Referenced python module 'configure' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/conf/reconfigure-linux-c-opt.py'])
petsc W: Referenced python module 'pandas' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petsc_tas_analysis.py', 'opt/petsc/linux-c-opt/share/petsc/bin/dmnetwork_view.py'])
petsc W: Referenced python module 'scipy.io' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/PetscBinaryIO.py'])
petsc W: Referenced python module 'h5py' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petsc_gen_xdmf.py'])
petsc W: Referenced python module 'matplotlib' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/share/petsc/bin/dmnetwork_view.py'])orials/ex100.py'])
petsc W: Referenced python module 'pyvista' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc4py/lib/_pytypes/viewer/petscpyvista.py'])
petsc W: Referenced python module 'matplotlib.pyplot' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petsc_tas_analysis.py', 'opt/petsc/linux-c-opt/lib/petsc/bin/PetscBinaryIOTrajectory.py', 'opt/petsc/linux-c-opt/share/petsc/bin/dmnetwork_view.py'])
petsc W: Referenced python module 'matplotlib.collections.LineCollection' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/share/petsc/bin/dmnetwork_view.py'])
petsc W: Referenced python module 'scipy.sparse.csr_matrix' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/PetscBinaryIO.py'])
petsc W: Referenced python module 'matplotlib.collections.CircleCollection' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/share/petsc/bin/dmnetwork_view.py'])
petsc W: Referenced python module 'distutils.version.LooseVersion' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petscnagupgrade.py'])
petsc W: Referenced python module 'requests' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/saws/SAWs.py'])
petsc W: Referenced python module 'urllib2.urlopen' is an uninstalled dependency (needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petscnagupgrade.py'])
petsc E: Dependency python-packaging detected and not included (python modules ['packaging.version.Version'] needed in files ['opt/petsc/linux-c-opt/lib/petsc/bin/petscnagupgrade.py'])

From these scripts in opt/petsc/linux-c-opt/lib/petsc/bin/, I think that if the import statement is in a try: ... except, then the referenced python module should be an optional dependency in PKGBUILD. So (python-scipy, python-lxml, python-pandas python-matplotlib python-requests) are optional and (python-h5py-openmpi python-pyvista) are dependencies.

@MartinDiehl I’ve tested both and it’s only works with enable_cxx. It’s not about importing petsc4py, It’s about importing PETSc from petsc4py.

@medaminezghal: when compiling with --enable-cxx=1 I get a warning that this is meant for development only. As far as I see, petsc4py 3.23.0 also works without it.

@MartinDiehl The only changes is using --enable-cxx=1 to make sure that python packages linking works fine and I move --with-bison=1 to test_optdepends.sh file to make scotch dependency works. Note that petsc use c to compile and its python implementation need C++ that why I add --enable-cxx=1

@MartinDiehl This is an updating test_optdepends.sh file:

#!/bin/bash

# Test if external packages for PETSC are installed

CONFOPTS=""

## External downloads
#for external_pkg in hypre; do
  #CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
#done

# Kokkos
if [ -f "/usr/lib/libkokkoscore.so" ]; then
  CONFOPTS="${CONFOPTS} --with-kokkos=1"
fi

# HYPRE
if [ -f "/usr/lib/libHYPRE.so" ]; then
  CONFOPTS="${CONFOPTS} --with-hypre-lib=/usr/lib/libHYPRE.so --with-hypre-include=/usr/include/hypre"
fi

# (Par)METIS
if [ -f "/usr/include/metis.h" ]; then
  CONFOPTS="${CONFOPTS} --with-metis=1"
  if [ -f "/usr/include/parmetis.h" ]; then
    CONFOPTS="${CONFOPTS} --with-parmetis=1"
  fi
fi

# MUMPS
if [ -f "/usr/lib/libmumps_common.so" ]; then
  CONFOPTS="${CONFOPTS} --with-mumps=1"
fi

# PaStiX https://gitlab.com/petsc/petsc/-/issues/1259
#if [ -f "/usr/lib/pkgconfig/pastic.pc" ]; then
#  CONFOPTS="${CONFOPTS} --with-pastix=1"
#fi

# ScaLAPACK
if [ -f "/usr/lib/pkgconfig/scalapack.pc" ]; then
  CONFOPTS="${CONFOPTS} --with-scalapack=1"
fi

# Scotch
if [ -f /usr/include/scotch.h ]; then
  SCOTCH_LIBS="libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so"
  # Include bzip2 if scotch was build with bzip2 support
  if [ -f /usr/include/bzlib.h ];then
    SCOTCH_LIBS="${SCOTCH_LIBS},libbz2.so"
  fi
  SCOTCH_LIBS="[${SCOTCH_LIBS}]"
  CONFOPTS="${CONFOPTS} --with-ptscotch=1 --with-bison=1"
fi

# SuperLU_DIST
if [ -f "/usr/lib/pkgconfig/superlu_dist.pc" ]; then
  CONFOPTS="${CONFOPTS} --with-superlu_dist-lib=-lsuperlu_dist --with-superlu_dist-include=/usr/include/superlu_dist"
fi

# Triangle
if [ -f "/usr/lib/libtriangle.so" ]; then
  CONFOPTS="${CONFOPTS} --with-triangle=1"
fi

# Zoltan
if [ -f "/usr/lib/libzoltan.so" ]; then
  CONFOPTS="${CONFOPTS} --with-zoltan=1"
fi

echo "${CONFOPTS}"