Name:           bout++

Version:        5.1.0

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

# https://github.com/boutproject/BOUT-dev/pull/2742

Patch:  0001-fmt10.patch

Patch:  0002-sphinx.patch

Patch:  test-timeout.patch

Patch:  0004-pvode-config.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}-zoidberg

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

%endif

%if %{with petsc} && %{with openmpi}

BuildRequires: petsc-openmpi-devel

BuildRequires: hdf5-openmpi-devel

%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 openmpi %{?mpi_list}

%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} -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=/usr \

      -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} \

      -DBOUT_TEST_TIMEOUT=900 \

%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

      # Store original values

      PYPA=${PYTHONPATH}

      LDPA=${LD_LIBRARY_PATH}

      # Add our stuff

      export PYTHONPATH=${PYTHONPATH}:$(pwd)/build_$mpi/tools/pylib/

      export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$(pwd)/build_$mpi/lib/

      %cmake_build

      # Restore

      export LD_LIBRARY_PATH=$LDPA

      export PYTHONPATH=$PYPA

%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 -E '/libbout|/libpvode|/libpvpre') ; 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 <

#%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

# s390x: https://bugzilla.redhat.com/show_bug.cgi?id=1998838

# s390x: https://bugzilla.redhat.com/show_bug.cgi?id=2259532

%if %{with test}

for mpi in %{mpi_list}

do

    fail=1

    if [ $mpi = mpich ] ; then

        %_mpich_load

	%ifarch s390x

	fail=0

	%endif

    else

        %_openmpi_load

    fi

    pushd build_$mpi

    export OMPI_MCA_rmaps_base_oversubscribe=yes

    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe

    # Workaround for https://bugzilla.redhat.com/show_bug.cgi?id=1997717

    export HDF5_USE_FILE_LOCKING=FALSE

    # Increase timeout for copr / s390x

    sed 's/ 3s / 30s /' tests/integrated/test-coordinates-initialization/runtest

    make %{?_smp_mflags} build-check

    SEGFAULT_SIGNALS="segv" make check-unit-tests || $(exit $fail)

    SEGFAULT_SIGNALS="segv" make check-mms-tests || $(exit $fail)

    SEGFAULT_SIGNALS="segv" make check-integrated-tests || $(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.5.1.0

%{_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.5.1.0

%{_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