petsc-pkgbuild/PKGBUILD

# This package tries to compile PETSc with a working branch
# of the git sources (either main or release) and its
# documentation. It prevents the use of non-free software
# and finds most optional dependencies. The petsc package
# from AUR is still recommended if you don't care about the
# documentation, freedom or extra compatibility. If you find
# any similarities to the petsc-git package it's because I was
# the owner and maintainer of that package until I decided to
# host this one.
# Maintainer: eDgar <edgar |at] openmail cc>
# Contributor: Martin Diehl <aur@martin-diehl.net>
# Contributor: Lucas H. Gabrielli <heitzmann@gmail.com> (creator)

_base=petsc
pkgname=("${_base}"-free+opts "${_base}"-doc-bin)
pkgver=3.20.5.910.gec4bd5ab864
pkgrel=1
_mainver="${pkgver:0:6}"
pkgdesc="Portable, extensible toolkit for scientific computation"
arch=('i686' 'x86_64')
url="https://gitlab.com/petsc/${_base}"
license=('BSD')
# DAMASK requires PETSc's static libraries
options=(staticlibs)
depends=('openmpi' 'lapack' 'fftw' 'zlib' 'cython'
         'python-mpi4py' "python-numpy" "eigen>=3" "blas-openblas")
# Force version to force recompilation of HYPRE
hypre=$(pacman -Qs hypre | head -n 1 | cut -f2 -d' ')
makedepends=('gcc' 'gcc-fortran' 'cmake' 'sowing' "pkgconf"
             'git' 'cython' 'chrpath' "hypre=${hypre}")
source=("git+${url}.git#branch=main"
        "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-with-docs-3.19.5.tar.gz"
        # "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-with-docs-${_mainver}.tar.gz"
        test_optdepends.sh
        0001-sowing-minversion1_1_26.patch)
sha512sums=('SKIP'
            'b00026074349f3995312b407044def7a104f62e9ba68e1b571e7f09ddb8aa56aa64bea5e5f9e5546d4d6866c37278d8b40334af2697bd0f837ca3981229d700a'
            '49bf2d313582a51d5ce866a9b5a640266a8132e817d2f5266c70f3b77ef3c49eac12a2a3bdcf773c8b030a3f7a47d5f4d7c082ff3f49a05bd8d18847453a1c0a'
            '3c156d1c465c10ba0a3c79b829f98ecc05e48b8f002a3a382f86ac834faaa34108d522f04757af38257f4a4e1292d8d8b79c9c039ecb9ea25444d902a384907f')
install=petsc.install

_config=linux-c-opt
_install_dir="/usr"

#  From UPC: Building And Using Static And Shared "C"
#  Libraries.html
# #+begin_QUOTE
# we need that all jump calls ("goto", in assembly speak)
# and subroutine calls will use relative addresses, and not
# absolute addresses. Thus, we need to use ... ~-fPIC~ or
# ~-fpic~
# #+end_QUOTE
#
#  From makepkg.conf
# -march (or -mcpu) builds exclusively for an architecture
# -mtune optimizes for an architecture, but builds for
#  whole processor family
#
# -O3 optimises
#
# -D-FORTIFY-SOURCE=2
# | https://stackoverflow.com/a/16604146
# |- man 7 feature_test_macros
# checks to be performed to detect some buffer overflow
# errors when employing various string and memory
# manipulation functions ... some  conforming programs
# might fail
#
# -fcf-protection
# | Info pages for gcc (gnu compiler collection)
# intended to protect against such threats as
# Return-oriented Programming (ROP), and similarly
# call/jmp-oriented programming (COP/JOP)
#
# -pipe
# | Info pages for gcc (controlling the kind of output)
# Use pipes rather than temporary files for communication
# between the various stages of compilation
#
# -fno-plt
# | Info pages for gcc (code generation conventions)
# leads to more efficient code by eliminating PLT stubs and
# exposing GOT loads to optimizations
#
# -fopenmp
# | Info pages for gcc (controlling c dialect)
# Enable handling of OpenMP directives

safe_flags="-Wp,-D-FORTIFY-SOURCE=2,-D_GLIBCXX_ASSERTIONS"
safe_flags+=" -fcf-protection -fno-plt"
safe_flags+=" -fstack-clash-protection -Wformat"
safe_flags+=" -Werror=format-security"
generic_flags="-march=native -mtune=native"
generic_flags+=" -pipe -fno-plt -fPIC -fopenmp"
generic_flags+="${safe_flags}"
opt_flags="${generic_flags} -O3"
generic_flags="${generic_flags} -O2"

export LANG=C
# Try to mute warnings from missing CUDA
# https://github.com/open-mpi/ompi/issues/4405
export OMPI_MCA_opal_cuda_support=0
# (muting may not work:
# https://github.com/open-mpi/ompi/issues/10049)
export OMPI_MCA_opal_warn_on_missing_libcuda=0
# export OMPI_MCA_mpi_oversubscribe=0
unset PETSC_DIR
export PETSC_ARCH=${_config}

prepare() {
  cd "${srcdir}"/"${_base}"
  # patch -Np1 -i "${srcdir}"/hypre_global_error.error_flag-0.patch
  patch -Np1 -i "${srcdir}"/0001-sowing-minversion1_1_26.patch
}

pkgver() {
  cd "${srcdir}"/"${_base}"
  git describe --tags --match '*.*' | tr '-' '.' | sed 's-^v--'
}

build() {
  CONFOPTS=(
    --silent --enable-silent-rules
    --ignoreWarnings=1
    --prefix="${_install_dir}"
    --COPTFLAGS="${opt_flags}"
    --CXXOPTFLAGS="${opt_flags}"
    --FOPTFLAGS="${opt_flags}"
    --CFLAGS="${generic_flags}"
    --CXXFLAGS="$generic_flags"
    --CPPFLAGS="$generic_flags"
    --FCFLAGS="$generic_flags"
    --F90FLAGS="$generic_flags"
    --FFLAGS="$generic_flags"
    --MAKEFLAGS=${MAKEFLAGS}
    --LDFLAGS=${LDFLAGS}
    --with-environment-variables=1
    --with-cxx-dialect=auto
    --with-mpi=1
    --with-pic=1
    --with-shared-libraries=1
    --with-zlib=1
    --with-petsc4py=1
    --with-mpi-f90module-visibility=0
    --with-cuda=0
    # Disabled for DAMASK
    # --with-scalar-type=complex
    " $(sh ${srcdir}/test_optdepends.sh)")
    # --with-single-library=1

  cd "${srcdir}"/"${_base}"
  export PETSC_DIR="${srcdir}"/"${_base}"
  python ./configure ${CONFOPTS[@]}
  make -s ${MAKEFLAGS} all
  make DESTDIR=${srcdir}/tmp install
}

check() {
  cd "${srcdir}"/"${_base}"

  if [ -z "$(ldconfig -p | grep libcuda.so.1)" ]; then
    export OMPI_MCA_opal_warn_on_missing_libcuda=0
  fi
  export OMPI_MCA_plm_rsh_agent=sh
  PYTHONPATH=${srcdir}/tmp/${_install_dir}/lib:${PYTHONPATH} make check ||
    printf "Tests failed\n"
}

package_petsc-free+opts() {
  optdepends=(
    "boost: Free peer-reviewed portable C++ source libraries"
    "cgns: Recording and recovering computer data"
    "eigen: Lightweight C++ template library for vector and matrix math"
    "fftw: Fast-Fourier Transform"
    "gdb: Debugging"
    "hdf5: large files"
    "hwloc: Portable Hardware Locality (abstraction of hierarchical architectures)"
    "med>=4.0: Data Modelization and Exchanges (meshes)"
    "metis: Partitioning library (for meshes)"
    "mumps: Sparse solver library"
    "netcdf-openmpi: Management of array-data"
    "openblas: Linear algebra libraries"
    "opencl: GPU computing"
    "opencl-headers: for opencl (GPU computing)"
    "opencl-clhpp: for opencl C++ compatibility (GPU computing)"
    "openmp: Parallel distributed tasks"
    "libpng"
    "scalapack: Parallel memory linear algebra"
    "scotch: Partitioning with sparse matrices"
    "suitesparse: Sparse matrix library"
    "superlu: Subroutines for sparsse linear systems"
    "tetgen: For meshing (tetrahedral mesh and 3D Delaunay triangulator)"
    "libyaml: configuration files")
  provides=(${_base}="${_mainver}"
            petsc4py="${_mainver}"
            ${_base}="${pkgver}-${pkgrel}"
            petsc4py="${pkgver}-${pkgrel}")
  conflicts=(${_base} ${_base}-git)

  # # From OpenCV (hack destination of petsc4py)
  # _pythonpath=`python -c "from sysconfig import get_path; print(get_path('platlib'))"`
  # sed -i "s%\(installLibPath = \)os.path.join(self.installDir, 'lib')%\1'${_pythonpath}'%"
  unset PETSC_DIR
  _build_dir="${srcdir}"/"${_base}"

  make -C "${_build_dir}" \
       ${MAKEFLAGS} DESTDIR="${pkgdir}" install

  export PETSC_DIR=${_install_dir}

  # install licence (even though there is no such word as licenses)
  install -Dm 644 ${_build_dir}/LICENSE \
          "${pkgdir}"/"${_install_dir}"/share/licenses/"${pkgname}"/LICENSE

  mkdir -p "${pkgdir}"/etc/profile.d
  echo "export PETSC_DIR=${_install_dir}" > \
       "${pkgdir}"/etc/profile.d/${_base}.sh
  echo "export OMPI_MCA_opal_cuda_support=0 OMPI_MCA_opal_warn_on_missing_libcuda=0" >> \
       "${pkgdir}"/etc/profile.d/${_base}.sh
  # echo "export PYTHONPATH=\$PYTHONPATH:/${_install_dir}/${_base}/${_config}/lib" \
  #      >> "${pkgdir}"/etc/profile.d/${_base}.sh
  chmod +x "${pkgdir}"/etc/profile.d/${_base}.sh

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

  # install pkgconfig settings
  install -Dm 644 "${_build_dir}/${_config}"/lib/pkgconfig/PETSc.pc \
          "${pkgdir}"/"${_install_dir}"/share/pkgconfig/PETSc.pc

  # cd "${srcdir}"/"${_base}"/src/binding/petsc4py
  # CFLAGS="$(echo "${CFLAGS}" | sed 's%-D[^[:space:]]*%%g')" python setup.py install --root="${pkgdir}" --optimize=1 --skip-build
  # cd -
  _pythonpath="${pkgdir}"/`python -c "from sysconfig import get_path; print(get_path('platlib'))"`
  install -dm 755 ${_pythonpath}
  ln -s "${_install_dir}"/lib/petsc4py ${_pythonpath}
}

package_petsc-doc-bin () {
  depends=()
  optdepends=()
  provides=(${_base}-doc)
  conflicts=()
  pkgdesc="Documentation for PETSc"
  # Two options: compile the documentation or get it from
  # the web. Downloading is easier.
  [[ -d ${pkgdir}/${_install_dir}/share/doc ]] && \
    rm -fr "${pkgdir}"/"${_install_dir}"/share/doc
  mkdir -p "${pkgdir}"/"${_install_dir}"/share/doc
  cp -r "${srcdir}/${_base}-"*"/docs" \
     "${pkgdir}"/"${_install_dir}"/share/doc/${_base}
}