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Package Details: petsc 3.22.3-1

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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:	0.96
First Submitted:	2018-02-24 11:36 (UTC)
Last Updated:	2025-02-05 08:49 (UTC)

Dependencies (29)

fftw-openmpi
gsl (gsl-git^AUR)
hdf5-openmpi
lapack (aocl-libflame-aocc^AUR, lapack-git^AUR, atlas-lapack^AUR, blas-aocl-gcc^AUR, blas-aocl-aocc^AUR, blas-mkl^AUR, aocl-libflame^AUR, openblas-lapack^AUR, blas-openblas)
libjpeg-turbo (mozjpeg-git^AUR, libjpeg-turbo-git^AUR, mozjpeg^AUR)
libyaml (libyaml-git^AUR)
netcdf-openmpi
openmpi (openmpi-git^AUR)
python-mpi4py (python-mpi4py-intel^AUR)
python-numpy (python-numpy-git^AUR, python-numpy1^AUR, python-numpy-mkl-bin^AUR, python-numpy-mkl-tbb^AUR, python-numpy-mkl^AUR)
suitesparse
superlu
zfp
zlib (zlib-ng-compat-git^AUR, zlib-git^AUR, zlib-ng-compat)
cmake (cmake-git^AUR, cmake3^AUR) (make)
cython (cython-git^AUR) (make)
gcc (gcc-git^AUR, gccrs-git^AUR, gcc11^AUR, gcc-snapshot^AUR) (make)
gcc-fortran (gcc-fortran-git^AUR, gcc11-fortran^AUR, gcc-fortran-snapshot^AUR) (make)
python-setuptools (make)
hypre^AUR (optional) – support for HYPRE
kokkos^AUR (trilinos^AUR) (optional) – support Kokkos
metis^AUR (metis-git^AUR) (optional) – support for METIS
mumps^AUR (mumps-cmake^AUR, mumps-par^AUR, mumps-seq^AUR) (optional) – support for MUMPS
parmetis^AUR (parmetis-git^AUR) (optional) – support for ParMETIS
scalapack^AUR (optional) – support for ScaLAPACK
scotch^AUR (scotch-git^AUR) (optional) – support for Scotch
superlu_dist^AUR (optional) – support for SuperLU_DIST
triangle^AUR (optional) – support for Triangle
zoltan^AUR (trilinos^AUR) (optional) – support for zoltan

Required by (26)

Sources (2)

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

1 2 3 4 5 6 .. 11 Next › Last »

medaminezghal commented on 2025-04-15 10:09 (UTC)

@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

medaminezghal commented on 2025-04-15 10:06 (UTC)

@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}"

medaminezghal commented on 2025-04-15 10:05 (UTC)

@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
}

MartinDiehl commented on 2025-04-04 11:00 (UTC)

@ilovekiruna: Did you recompile PETSc?

ilovekiruna commented on 2025-04-04 10:57 (UTC)

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.

medaminezghal commented on 2025-02-05 14:04 (UTC)

@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.

MartinDiehl commented on 2025-01-03 13:54 (UTC)

@medaminezghal

thanks. Good to see that you fixed it. I can't reproduce the error here and will try on other setups later.

medaminezghal commented on 2025-01-03 07:35 (UTC)

@MartinDiehl I found a fix


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

Just add the -lstdc++ to the LDFLAGS

medaminezghal commented on 2025-01-02 17:53 (UTC)

@MartinDiehl I’ve already done the rebuild for all packages in my system to python 3.13 but this module has an issue when I import it. I found it by accident when I try to install donfinx. For that, I tried to test an example using the library in python and found this error.

MartinDiehl commented on 2025-01-02 16:12 (UTC)

@medaminezghal: maybe you need to rebuild for Python 3.13