Arch Linux User Repository

@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 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}"

@MartinDiehl This is a working PKGBUILD file for petsc 3.23.0:

# Maintainer: Martin Diehl <aur@martin-diehl.net>
# Contributor: Andreas Bilke <abilke at cosy dot sbg dot ac dot at>
# Contributor: Myles English <myles at rockhead dot biz>
# Contributor: Lucas H. Gabrielli <heitzmann at gmail dot com>
pkgver=3.23.0
pkgrel=1
pkgname=petsc
pkgdesc="Portable, extensible toolkit for scientific computation"
arch=('i686' 'x86_64')
url="https://petsc.org"
license=('BSD-2-Clause')
options=(staticlibs)
# note: zlib is not really needed by PETSc, but netcdf requires an HDF5 version with zlib
depends=('openmpi' 'lapack' 'hdf5-openmpi' 'fftw-openmpi' 'superlu' 'suitesparse' 'libyaml' 'gsl' 'libjpeg-turbo' 'netcdf-openmpi' 'zfp' 'zlib'
         'python-numpy' 'python-mpi4py')
makedepends=('gcc' 'gcc-fortran' 'cmake' 'cython' 'python-setuptools')
provides=('petsc4py')
optdepends=(
  'hypre: support for HYPRE'
  'kokkos: support Kokkos'
  'metis: support for METIS'
  'mumps: support for MUMPS'
  'parmetis: support for ParMETIS'
  'scalapack: support for ScaLAPACK'
  'scotch: support for Scotch'
  'superlu_dist: support for SuperLU_DIST'
  'triangle: support for Triangle'
  'zoltan: support for zoltan'
  )

install=petsc.install
source=(http://web.cels.anl.gov/projects/petsc/download/release-snapshots/${pkgname}-${pkgver}.tar.gz
        test_optdepends.sh)
sha512sums=('e5cd7649451277ff5c9dedac4948be12cd1465261f872319a8f1c42842a51a817cb36f4a36f02ccb1d8c13e4cfb6fd4bb36c297f74b22129d288001769a6d66b'
            '809e956a60be3604db08d523faba0de26f97d63e9ceb174e06202ca6f742df917670821246349974662d8e98f7a166c107d2f1627a6aa256a4b69efd1576b891')

PETSC_ARCH=linux-c-opt
_install_dir=/opt/petsc/${PETSC_ARCH}

build() {
  cd ${pkgname}-${pkgver}
  export PETSC_DIR=${PWD}
  export PETSC_ARCH=${PETSC_ARCH}

  CONFOPTS="--enable-cxx=1 \
            --with-shared-libraries=1 \
            --with-petsc4py=1 \
            --with-mpi-f90module-visibility=0 \
            --with-cmake=0 \
            --with-mpi-dir=/usr \
            --with-zfp=1 \
            --with-netcdf=1 \
            --with-libjpeg=1 \
            --with-yaml=1 \
            --with-fftw=1 \
            --with-gsl=1 \
            --with-zlib=1 \
            --with-superlu-lib=-lsuperlu --with-superlu-include=/usr/include/superlu \
            --with-suitesparse=1 \
            --with-hdf5=1 --with-hdf5-fortran-bindings=1 \
            $(sh ${srcdir}/test_optdepends.sh)"

  echo './configure' ${CONFOPTS}
  echo 'CFLAGS='${CFLAGS}
  echo 'CXXFLAGS='${CXXFLAGS}
  echo 'FFLAGS='${FFLAGS}
  echo 'LDFLAGS='${LDFLAGS}
  echo 'MAKEFLAGS='${MAKEFLAGS}

  ./configure --prefix=${_install_dir} ${CONFOPTS} \
              "CFLAGS=$CFLAGS" \
              "CXXFLAGS=$CXXFLAGS" \
              "FFLAGS=$FFLAGS" \
              "LDFLAGS=$LDFLAGS" \
              "MAKEFLAGS=$MAKEFLAGS"

  make all
}

package() {
  cd ${pkgname}-${pkgver}
  export PETSC_DIR=${PWD}
  export PETSC_ARCH=${PETSC_ARCH}

  make DESTDIR=${pkgdir} install

  install -Dm 644 LICENSE ${pkgdir}/usr/share/licenses/$pkgname/LICENSE

  mkdir -p ${pkgdir}/etc/profile.d
  echo export PETSC_DIR=${_install_dir} > ${pkgdir}/etc/profile.d/petsc.sh
  echo export PYTHONPATH=${_install_dir}/lib:'${PYTHONPATH}' >> ${pkgdir}/etc/profile.d/petsc.sh
  chmod +x ${pkgdir}/etc/profile.d/petsc.sh

  # show where the shared libraries are
  install -dm 755 ${pkgdir}/etc/ld.so.conf.d/
  echo ${_install_dir}/lib > ${pkgdir}/etc/ld.so.conf.d/petsc.conf

  # install pkgconfig settings
  install -Dm 644 ${PETSC_ARCH}/lib/pkgconfig/PETSc.pc ${pkgdir}/usr/share/pkgconfig/PETSc.pc
}

@ilovekiruna: Did you recompile PETSc?

It looks like the latest package still depends on libsuperlu in version 6. However, in the extra repo, the latest package is version 7. Therefore an ldd on libpetsc ldd /opt/petsc/linux-c-opt/lib/libpetsc.so.3.22 gives libsuperlu.so.6 => not found.

@MartinDiehl Could you send me your /etc/makepkg.conf file in the email? Because even after the update the same problem happens again and I need the same fix. Maybe it is related to this file in my computer.