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rpms / bout++

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Fedora:: davidsch
EPEL:: davidsch
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Name:           bout++
Version:        5.0.0
Release:        %autorelease
Summary:        Library for the BOUndary Turbulence simulation framework

# BOUT++ itself is LGPL, but we are linking with GPLed code, so the distributed library is GPL
License:        GPLv3+
URL:            https://boutproject.github.io/
Source0:        https://github.com/boutproject/BOUT-dev/releases/download/v%{version}/BOUT++-v%{version}.tar.gz

Patch:  https://github.com/boutproject/BOUT-dev/pull/2659.patch
Patch:  https://github.com/boutproject/BOUT-dev/pull/2661.patch
Patch:  https://github.com/boutproject/BOUT-dev/pull/2664.patch
# Removed confliting whitespace changes in PVODE
Patch:  https://github.com/boutproject/BOUT-dev/pull/2678.patch
Patch:  https://github.com/boutproject/BOUT-dev/commit/489270184ba9e03cb9996c614050cb92513424e6.patch#./petsc_318_compat.patch

# https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
ExcludeArch: %{ix86}

%if 0%{?fedora} >= 33
%bcond_without flexiblas
%else
%bcond_with flexiblas
%endif

# Disable tests and manual on epel < 8
%if 0%{?rhel} && 0%{?rhel} < 8
%bcond_with manual
%bcond_with test
%bcond_with sundials
%bcond_with petsc
%else
%bcond_without manual
%bcond_without test
%bcond_without sundials
%bcond_without petsc
%endif

# Enable both mpi every where
%bcond_without mpich
%bcond_without openmpi

%if 0%{?fedora} || ( 0%{?rhel} && 0%{?rhel} > 7 )
# Use system mpark
%bcond_without system_mpark
%else
%bcond_with system_mpark
%endif

#
#           DEPENDENCIES
#

BuildRequires:  m4
BuildRequires:  zlib-devel
BuildRequires:  cmake
BuildRequires:  gettext-devel
BuildRequires:  environment-modules
BuildRequires:  netcdf-devel
BuildRequires:  netcdf-cxx%{?fedora:4}-devel
BuildRequires:  hdf5-devel
BuildRequires:  fftw-devel
BuildRequires:  make
BuildRequires:  fmt-devel
BuildRequires:  chrpath
BuildRequires:  python%{python3_pkgversion}
BuildRequires:  python%{python3_pkgversion}-numpy
BuildRequires:  python%{python3_pkgversion}-Cython
BuildRequires:  python%{python3_pkgversion}-netcdf4
BuildRequires:  python%{python3_pkgversion}-scipy
BuildRequires:  python%{python3_pkgversion}-boututils
BuildRequires:  python%{python3_pkgversion}-boutdata
BuildRequires:  python%{python3_pkgversion}-tables
%if %{with flexiblas}
BuildRequires:  flexiblas-devel
%else
BuildRequires:  blas-devel
BuildRequires:  lapack-devel
%endif
BuildRequires:  gcc-c++
%if %{with system_mpark}
BuildRequires:  mpark-variant-devel
%endif
# cxx generation
BuildRequires:  python%{python3_pkgversion}-jinja2
# Documentation
%if %{with manual}
BuildRequires:  doxygen
BuildRequires:  python3-sphinx
%endif
%if %{with petsc} && %{with mpich}
BuildRequires: petsc-mpich-devel
BuildRequires: hdf5-mpich-devel
BuildRequires: python%{python3_pkgversion}-h5py-mpich
%endif
%if %{with petsc} && %{with openmpi}
BuildRequires: petsc-openmpi-devel
BuildRequires: hdf5-openmpi-devel
BuildRequires: python%{python3_pkgversion}-h5py-openmpi
%endif
%if %{with sundials} && %{with mpich}
BuildRequires: sundials-mpich-devel
# https://bugzilla.redhat.com/show_bug.cgi?id=1839131
BuildRequires: sundials-devel
%endif
%if %{with sundials} && %{with openmpi}
BuildRequires: sundials-openmpi-devel
# https://bugzilla.redhat.com/show_bug.cgi?id=1839131
BuildRequires: sundials-devel
%endif

#
#           DESCRIPTIONS
#


%if %{with mpich}
BuildRequires:  mpich-devel
%global mpi_list mpich
%endif
%if %{with openmpi}
BuildRequires:  openmpi-devel
%global mpi_list %{?mpi_list} openmpi
%endif

%description
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.



%if %{with mpich}
%package mpich
Summary: BOUT++ mpich libraries
Requires: %{name}-common = %{version}-%{release}
# Use bundled version, to reproduce upstream results
Provides: bundled(libpvode)
Recommends: environment-modules
Recommends: python%{python3_pkgversion}-boututils
Recommends: python%{python3_pkgversion}-boutdata
Recommends: python%{python3_pkgversion}-xbout

%package mpich-devel
Summary: BOUT++ mpich libraries
Requires:  %{name}-mpich = %{version}-%{release}
Recommends:  gcc-c++
Recommends:  make
Recommends:  mpich-devel
Recommends:  zlib-devel
Recommends:  gettext-devel
Recommends:  netcdf-devel
Recommends:  netcdf-cxx%{?fedora:4}-devel
Recommends:  hdf5-devel
Recommends:  fftw-devel
%if %{with flexiblas}
Recommends:  flexiblas-devel
%else
Recommends:  blas-devel
Recommends:  lapack-devel
%endif
%if %{with system_mpark}
Recommends:  mpark-variant-devel
%endif
%if %{with petsc}
Recommends:  petsc-mpich-devel
Recommends:  hdf5-mpich-devel
%endif
%if %{with sundials}
Recommends:  sundials-mpich-devel
# https://bugzilla.redhat.com/show_bug.cgi?id=1839131
Recommends:  sundials-devel
%endif


%description mpich-devel
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.

This BOUT++ library is build for mpich.

%description mpich
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.

This BOUT++ library is build for mpich.

%package -n python%{python3_pkgversion}-%{name}-mpich
Summary:  BOUT++ mpich library for python%{python3_pkgversion}
Requires: %{name}-mpich
Requires: python%{python3_pkgversion}-%{name}
BuildRequires: python%{python3_pkgversion}-devel
Requires: mpich
Requires: python%{python3_pkgversion}-mpich
Requires: python%{python3_pkgversion}-numpy
Requires: python%{python3_pkgversion}-boututils
Requires: python%{python3_pkgversion}-boutdata
Recommends: python%{python3_pkgversion}-xbout

%py_provides python%{python3_pkgversion}-%{name}-mpich
%description  -n python%{python3_pkgversion}-%{name}-mpich
This is the BOUT++ library python%{python3_pkgversion} with mpich.

%endif




%if %{with openmpi}
%package openmpi
Summary: BOUT++ openmpi libraries
# Use bundled version, to reproduce upstream results
Provides: bundled(libpvode)
Requires: %{name}-common = %{version}-%{release}
Recommends: environment-modules
Recommends: python%{python3_pkgversion}-boututils
Recommends: python%{python3_pkgversion}-boutdata
Recommends: python%{python3_pkgversion}-xbout

%package openmpi-devel
Summary: BOUT++ openmpi libraries
Requires: %{name}-openmpi = %{version}-%{release}
Recommends:  gcc-c++
Recommends:  make
Recommends:  openmpi-devel
Recommends:  zlib-devel
Recommends:  gettext-devel
Recommends:  netcdf-devel
Recommends:  netcdf-cxx%{?fedora:4}-devel
Recommends:  hdf5-devel
Recommends:  fftw-devel
%if %{with flexiblas}
Recommends:  flexiblas-devel
%else
Recommends:  blas-devel
Recommends:  lapack-devel
%endif
%if %{with system_mpark}
Recommends:  mpark-variant-devel
%endif
%if %{with petsc}
Recommends:  petsc-openmpi-devel
Recommends:  hdf5-openmpi-devel
%endif
%if %{with sundials}
Recommends:  sundials-openmpi-devel
# https://bugzilla.redhat.com/show_bug.cgi?id=1839131
Recommends:  sundials-devel
%endif



%description openmpi-devel
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.

This BOUT++ library is build for openmpi and provides the required
header files.

%description openmpi
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.

This BOUT++ library is build for openmpi.

%package -n python%{python3_pkgversion}-%{name}-openmpi
Summary:  BOUT++ openmpi library for python%{python3_pkgversion}
Requires: %{name}-openmpi
Requires: python%{python3_pkgversion}-%{name}
BuildRequires: python%{python3_pkgversion}-devel
Requires: openmpi
Requires: python%{python3_pkgversion}-openmpi
Requires: python%{python3_pkgversion}-numpy
Requires: python%{python3_pkgversion}-boututils
Requires: python%{python3_pkgversion}-boutdata
Recommends: python%{python3_pkgversion}-xbout

%py_provides python%{python3_pkgversion}-%{name}-openmpi

%description  -n python%{python3_pkgversion}-%{name}-openmpi
This is the BOUT++ library python%{python3_pkgversion} with openmpi.

%endif


%package common
Summary: Common files for BOUT++
%description common
MPI-independent files for BOUT++, namely localisation files.

%package -n python%{python3_pkgversion}-%{name}
Summary: BOUT++ python library
Requires: netcdf4-python%{python3_pkgversion}
Requires: python%{python3_pkgversion}-numpy
Recommends: python%{python3_pkgversion}-scipy
Recommends: python%{python3_pkgversion}-matplotlib
Recommends: python%{python3_pkgversion}-boututils
Recommends: python%{python3_pkgversion}-boutdata

BuildArch: noarch
%py_provides python%{python3_pkgversion}-%{name}

%description -n python%{python3_pkgversion}-%{name}
Python%{python3_pkgversion} library for pre and post processing of BOUT++ data




%if %{with manual}
%package -n %{name}-doc
Summary: BOUT++ Documentation
BuildArch: noarch

%description -n %{name}-doc
BOUT++ is a framework for writing fluid and plasma simulations in
curvilinear geometry. It is intended to be quite modular, with a
variety of numerical methods and time-integration solvers available.
BOUT++ is primarily designed and tested with reduced plasma fluid
models in mind, but it can evolve any number of equations, with
equations appearing in a readable form.

This package contains the documentation.
%endif

#
#           PREP
#

%prep
%autosetup -n BOUT++-v%{version}.dev10626+gd935fa1ea -p 1


# Switch to standard theme
# sphinx_book_theme is not packaged
sed -e 's/html_theme = "sphinx_book_theme"/html_theme = "sphinxdoc"/' -i manual/sphinx/conf.py

%if %{with system_mpark}
# use mpark provided by fedora
rm -rf externalpackages/mpark.variant/
mkdir -p externalpackages/mpark.variant/include/
%endif

rm -rf tools/pylib/boutdata
rm -rf tools/pylib/boututils

# Remove shebang
for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build )
do
    sed -i '/^#!\//d' $f
done


#
#           BUILD
#

%build

# MPI builds
export CC=mpicc
export CXX=mpicxx

for mpi in %{mpi_list}
do
  mkdir build_$mpi
done
for mpi in %{mpi_list}
do
  %global _vpath_builddir build_$mpi
  if [ $mpi = mpich ] ; then
      %_mpich_load
  elif [ $mpi = openmpi ] ; then
      %_openmpi_load
  else
      echo "unknown mpi" &> /dev/stderr
      exit 1
  fi

  %cmake \
      -DBOUT_USE_FFTW=ON \
      -DBOUT_USE_NETCDF=ON \
      -DBOUT_USE_SCOREP=OFF \
      -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
      -DBOUT_USE_LAPACK=ON \
      -DBOUT_USE_NLS=ON \
      -DBOUT_USE_SYSTEM_FMT=ON \
      -DBOUT_USE_UUID_SYSTEM_GENERATOR=ON \
      -DCMAKE_INSTALL_PREFIX=/ \
      -DCMAKE_INSTALL_LIBDIR=%{_libdir}/$mpi/lib \
      -DCMAKE_INSTALL_BINDIR=%{_libdir}/$mpi/bin \
      -DCMAKE_INSTALL_INCLUDEDIR=%{_includedir}/$mpi-%{_arch}/bout++/ \
      -DCMAKE_INSTALL_DATAROOTDIR=%{_datadir} \
      -DCMAKE_INSTALL_PYTHON_SITEARCH=${MPI_PYTHON3_SITEARCH} \
%if %{with manual}
      -DBOUT_BUILD_DOCS=ON \
%endif
%if %{with petsc}
      -DBOUT_USE_PETSC=ON \
%endif
%if %{with sundials}
      -DBOUT_USE_SUNDIALS=ON \
%endif

      %cmake_build

%if %{with manual}
      %global _vpath_builddir build_$mpi/manual
      %cmake_build
%endif

  if [ $mpi = mpich ] ; then
      %_mpich_unload
  elif [ $mpi = openmpi ] ; then
      %_openmpi_unload
  fi
done

#
#           INSTALL
#

%install

for mpi in %{mpi_list}
do
  %global _vpath_builddir build_$mpi
  if [ $mpi = mpich ] ; then
      %_mpich_load
  else
      %_openmpi_load
  fi
  %cmake_install

  for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep /libbout) ; do
    chrpath -r $MPI_LIB $f
  done

  rm -rf  ${RPM_BUILD_ROOT}/usr/share/bout++

  mkdir -p ${RPM_BUILD_ROOT}/usr/share/modulefiles/bout++
  cat > ${RPM_BUILD_ROOT}/usr/share/modulefiles/bout++/$MPI_COMPILER <<EOF
#%Module 1.0
#
#  BOUT++ module for use with 'environment-modules' package
#  Created by bout-add-mod-path v0.9
# Only allow one bout++ module to be loaded at a time
conflict bout++
# Require mpi
prereq mpi/$MPI_COMPILER

setenv    BOUT_TOP   $MPI_INCLUDE/bout++/
EOF

%if %{with manual}
      %global _vpath_builddir build_$mpi/manual
      %cmake_install
%endif

  if [ $mpi = mpich ] ; then
      %_mpich_unload
  else
      %_openmpi_unload
  fi
done


%find_lang libbout

#
#           CHECK
#

%check

# Ignore errors on some architectures
# armv7: https://bugzilla.redhat.com/show_bug.cgi?id=1998836
# s390x: https://bugzilla.redhat.com/show_bug.cgi?id=1998838
fail=1
%ifarch armv7hl s390x
fail=0
%endif


%if %{with test}
for mpi in %{mpi_list}
do
    if [ $mpi = mpich ] ; then
        %_mpich_load
    else
        %_openmpi_load
    fi
    pushd build_$mpi

    export OMPI_MCA_rmaps_base_oversubscribe=yes
    # Workaround for https://bugzilla.redhat.com/show_bug.cgi?id=1997717
    export HDF5_USE_FILE_LOCKING=FALSE
    # Increase timeout for copr / s390x
    export BOUT_TEST_TIMEOUT=15m
    sed 's/ 3s / 30s /' tests/integrated/test-coordinates-initialization/runtest

    make %{?_smp_mflags} build-check
    SEGFAULT_SIGNALS="segv" make check || $(exit $fail)

    popd
    if [ $mpi = mpich ] ; then
        %_mpich_unload
    else
        %_openmpi_unload
    fi
done
%endif

#
#           FILES SECTION
#

%if %{with mpich}
%files mpich
%{_libdir}/mpich/lib/libbout++.so.5.0.0
%{_libdir}/mpich/lib/*.so.1.0.0
%{_libdir}/mpich/bin/*
%doc README.md
%doc CITATION.bib
%doc CITATION.cff
%doc CHANGELOG.md
%doc CONTRIBUTING.md
%license LICENSE
%license LICENSE.GPL
/usr/share/modulefiles/bout++/mpich-*

%files mpich-devel
%{_includedir}/mpich-%{_arch}/bout++
%{_libdir}/mpich/lib/*.so
%{_libdir}/mpich/lib/cmake/*

%files -n python%{python3_pkgversion}-%{name}-mpich
%{python3_sitearch}/mpich/*
%endif


%if %{with openmpi}
%files openmpi
%{_libdir}/openmpi/lib/libbout++.so.5.0.0
%{_libdir}/openmpi/lib/*.so.1.0.0
%{_libdir}/openmpi/bin/*
%doc README.md
%doc CITATION.bib
%doc CITATION.cff
%doc CHANGELOG.md
%doc CONTRIBUTING.md
%license LICENSE
%license LICENSE.GPL
/usr/share/modulefiles/bout++/openmpi-*

%files openmpi-devel
%{_includedir}/openmpi-%{_arch}/bout++
%{_libdir}/openmpi/lib/*.so
%{_libdir}/openmpi/lib/cmake/*

%files -n python%{python3_pkgversion}-%{name}-openmpi
%{python3_sitearch}/openmpi/*
%endif

%files common -f libbout.lang
%dir /usr/share/modulefiles/bout++/

%files -n python%{python3_pkgversion}-%{name}
%doc README.md
%doc CITATION.bib
%doc CITATION.cff
%doc CHANGELOG.md
%doc CONTRIBUTING.md
%license LICENSE
%license LICENSE.GPL


%if %{with manual}
%files -n %{name}-doc
%doc  %{_defaultdocdir}/bout++/
%endif

#
#           CHANGELOG
#

%changelog
%autochangelog
rpms / bout++

Source Code

Files
