# This is a serial build of NEURON

%global _description %{expand:

NEURON is a simulation environment for modeling individual neurons and networks

of neurons. It provides tools for conveniently building, managing, and using

models in a way that is numerically sound and computationally efficient. It is

particularly well-suited to problems that are closely linked to experimental

data, especially those that involve cells with complex anatomical and

biophysical properties.

Please install the %{name}-devel package to compile nmodl files, and please

install the MPI specific sub-packages for MPICH and OpenMPI builds.

}

%global tarname nrn

# fails somehow, disabled by default

%bcond_with metis

# Music support

%bcond_with music

%bcond_without mpich

%bcond_without openmpi

Name:       neuron

Version:    8.2.2

Release:    %autorelease

Summary:    A flexible and powerful simulator of neurons and networks

License:    GPLv3+

URL:        http://www.neuron.yale.edu/neuron/

Source0:    https://github.com/neuronsimulator/%{tarname}/archive/%{version}/%{name}-%{version}.tar.gz

# they bundle HPC coding conventions as a git submodule

%global conv_git_commit  5d4bcd2d410e67bdc1d23d3280c08ee5c9df943b

%global conv_short_commit %(c=%{conv_git_commit}; echo ${c:0:7})

Source1:    https://github.com/BlueBrain/hpc-coding-conventions/archive/%{conv_git_commit}/hpc-coding-conventions-%{conv_short_commit}.tar.gz

%global rxd_tests_commit 2a08564a45fac78f259d23203d737db924c224c8

%global rxd_short_commit %(c=%{rxd_tests_commit}; echo ${c:0:7})

Source2:    https://github.com/neuronsimulator/rxdtestdata/archive/%{rxd_tests_commit}/rxdtestdata-%{rxd_short_commit}.tar.gz

Patch0:     0001-Unbundle-Random123.patch

# libstdc++ bundled is from 1988: seems heavily modified. Headers from there

# are not present in the current version

# https://github.com/neuronsimulator/nrn/issues/145

# Use system copy of Catch

Patch1:     0002-Unbundle-catch.patch

# We install the python bits ourselves

Patch2:     0003-Disable-python-build-and-install.patch

# Set soversions for all shared objects

Patch3:     0004-Set-soversions-for-libs.patch

# Set the right path for libdir

# Upstreamable

Patch4:     0005-Correct-librxdmath-path-for-64bit.patch

# stop build scripts from generating version during build

Patch5:     0006-Do-not-generate-version-info-at-buildtime.patch

# Remove rpaths

Patch6:     0007-Remove-rpaths.patch

# do not download data git submodule

Patch7:     0008-Dont-download-testdata-submodule.patch

# place help file in correct location

Patch8:     0009-Add-help-file-as-package-data.patch

# tries to create /usr/x86_64 etc dirs

Patch9:     0010-Remove-unneeded-symlinks.patch

# remove build time flags from the nrnmech makefile---it should not use these

Patch10:    0011-Strip-build-flags-from-nrnmech_makefile.patch

# Random123 does not build on these, so neither can NEURON

# https://github.com/neuronsimulator/nrn/issues/114

ExcludeArch:    mips64r2 mips32r2

BuildRequires:  make

BuildRequires:  autoconf

BuildRequires:  automake

BuildRequires:  bison

BuildRequires:  bison-devel

BuildRequires:  cmake

BuildRequires:  catch-devel

# Needs to be packaged separately

# BuildRequires:  coreneuron-devel

BuildRequires:  flex

BuildRequires:  (flex-devel or libfl-devel)

BuildRequires:  gcc

BuildRequires:  gcc-c++

BuildRequires:  git-core

# the cmake build requires iv with cmake too

BuildRequires:  iv-devel >= 0.1

BuildRequires:  libX11-devel

BuildRequires:  libXext-devel

BuildRequires:  libtool

%if %{with metis}

BuildRequires:  metis-devel

%endif

BuildRequires:  ncurses-devel

BuildRequires:  readline-devel

BuildRequires:  Random123-devel

# Bundles sundials. WIP

# https://github.com/neuronsimulator/nrn/issues/113

# BuildRequires:  sundials-devel

Provides: bundled(sundials) = 2.0.1

%description %_description

%package devel

Summary:    Development files for %{name}

Requires: %{name}%{?_isa} = %{version}-%{release}

Requires:  ncurses-devel

Requires:  readline-devel

Requires:  gcc-c++

Requires:  libtool

Requires:  libX11-devel

Requires:  libXext-devel

Requires:  iv-devel

%description devel

Headers and development shared libraries for the %{name} package

%package doc

Summary:    Documentation for %{name}

BuildArch:  noarch

%description doc

Documentation for %{name}

%package -n python3-%{name}

Summary:   Python3 interface to %{name}

Requires:  %{name}%{?_isa} = %{version}-%{release}

BuildRequires:  python3-devel

BuildRequires:  python3-setuptools

BuildRequires:  python3-Cython

BuildRequires:  python3-pytest

%description -n python3-%{name} %_description

%if %{with mpich}

%package mpich

Summary:   %{name} built with MPICH support

BuildRequires:  mpich-devel

BuildRequires:  rpm-mpi-hooks

BuildRequires:  python3-mpi4py-mpich

Requires:       mpich

Requires:       python3-mpi4py-mpich

%description mpich %_description

%package mpich-devel

Summary:    Development files for %{name}

Requires: %{name}-mpich%{?_isa} = %{version}-%{release}

%description mpich-devel

Headers and development shared libraries for the %{name} package

%package -n python3-%{name}-mpich

Summary:    Python3 interface to %{name}-mpich

Requires:  %{name}-mpich%{?_isa} = %{version}-%{release}

%description -n python3-%{name}-mpich %_description

%endif

%if %{with openmpi}

%package openmpi

Summary:   %{name} built with OpenMPI support

BuildRequires:  openmpi-devel

BuildRequires:  rpm-mpi-hooks

BuildRequires:  python3-mpi4py-openmpi

Requires:       openmpi

Requires:       python3-mpi4py-openmpi

%description openmpi %_description

%package openmpi-devel

Summary:    Development files for %{name}

Requires: %{name}-openmpi%{?_isa} = %{version}-%{release}

%description openmpi-devel

Headers and development shared libraries for the %{name} package

%package -n python3-%{name}-openmpi

Summary:    Python3 interface to %{name}-openmpi

Requires:  %{name}-openmpi%{?_isa} = %{version}-%{release}

%description -n python3-%{name}-openmpi %_description

%endif

%prep

%autosetup -n %{tarname}-%{version} -S git

# Remove executable perms from source files

find src -type f -executable ! -name '*.sh' -exec chmod -x {} +

# remove shebangs: check again each release

pushd share/lib/auditscripts/

for f in *

do

sed -i -e "/^#!\/bin\/sh.*/ d" $f

done

popd

# Remove bundled Random123

rm -rf src/Random123

rm -rf src/readline

# extract coding convention tar

# can probably use setup macro etc.

pushd external/coding-conventions

cp %SOURCE1 .

tar -xvf hpc-coding-conventions*.tar.gz --strip-components=1

rm -f hpc-coding-conventions*.tar.gz

popd

# extract rxdtestdata tar

pushd test/rxd/testdata

cp %SOURCE2 .

tar -xvf rxdtestdata*.tar.gz --strip-components=1

rm -f rxdtestdata*.tar.gz

popd

# Create version file ourselves

# To create this, we run the git2version.sh script in a checked out copy of neuron

export TIMESTAMP=$(date +%Y-%m-%d)

cat > src/nrnoc/nrnversion.h << EOF

#define GIT_DATE "$TIMESTAMP"

#define GIT_BRANCH "master"

#define GIT_CHANGESET "f0ca745418e942ad4763bdc47459c409f0b11512"

#define GIT_DESCRIBE "8.0.2 (Fedora %{fedora})"

EOF

# Stop system from using hard coded flags

sed -i '/CompilerFlagsHelpers/ d' cmake/ReleaseDebugAutoFlags.cmake

# Setting SETUPTOOLS_USE_DISTUTILS=stdlib does not work on Python 3.12

# https://github.com/neuronsimulator/nrn/issues/2263

#

# We change each occurrence to SETUPTOOLS_USE_DISTUTILS=local (the default).

# The find-then-modify pattern keeps us from discarding mtimes on any sources

# that do not need modification.

find . -type f -name 'CMakeLists.txt' -exec gawk \

    '/export SETUPTOOLS_USE_DISTUTILS=stdlib/ { print FILENAME; nextfile }' \

    '{}' '+' |

  xargs -r -t sed -r -i 's/(export SETUPTOOLS_USE_DISTUTILS=)stdlib/\1local/'

%build

# Not yet to be used

# export SUNDIALS_SYSTEM_INSTALL="yes"

%global do_build %{expand:

echo

echo "*** BUILDING %{name}-%{version}$MPI_COMPILE_TYPE ***"

echo

%set_build_flags

    cmake \\\

        -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\

        -DCMAKE_INSTALL_INCLUDEDIR:PATH=$MPI_INCLUDE \\\

        -DCMAKE_INSTALL_LIBDIR:PATH=$MPI_LIB \\\

        -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\

        -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\

        -DCMAKE_SKIP_RPATH:BOOL=ON \\\

        -DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\

        -DBUILD_SHARED_LIBS:BOOL=ON \\\

        -DNRN_ENABLE_SHARED=ON \\\

        -DNRN_ENABLE_INTERVIEWS=ON \\\

        -DNRN_ENABLE_PYTHON=ON \\\

        -DNRN_ENABLE_PYTHON_DYNAMIC=OFF \\\

        -DNRN_ENABLE_THREADS=ON \\\

        -DNRN_ENABLE_MEMACS=ON \\\

        -DNRN_ENABLE_RX3D=ON \\\

        -DNRN_ENABLE_CORENEURON=OFF \\\

        -DNRN_ENABLE_TESTS=OFF \\\

        -DNRN_ENABLE_REL_RPATH=OFF \\\

        -DNRN_ENABLE_MODULE_INSTALL=ON \\\

        -DNRN_ENABLE_INTERNAL_READLINE=OFF \\\

        -DNRN_ENABLE_MPI=$MPI_YES \\\

        -DNEURON_CMAKE_FORMAT:BOOL=OFF \\\

        -DMPI_INCLUDE_PATH=$MPI_INCLUDE \\\

        -DMPI_LIBRARY=$MPI_LIBFILE \\\

%if "%{_lib}" == "lib64" \

        -DLIB_SUFFIX=64 -B $MY_CMAKE_BUILDDIR && \

%else                      \

        -DLIB_SUFFIX="" -B $MY_CMAKE_BUILDDIR && \

%endif

%__cmake --build $MY_CMAKE_BUILDDIR %{_smp_mflags} \

%if %{with music}

pushd $MY_CMAKE_BUILDDIR/src/neuronmusic

%__cmake --build %{_smp_mflags}

%{py3_build}

popd

%endif

}

# Serial version

export MPI_COMPILER=serial

export MPI_SUFFIX=""

export MPI_HOME=%{_prefix}

export MPI_BIN=%{_bindir}

export MPI_INCLUDE=%{_includedir}

export MPI_LIB="%{_libdir}"

export MPI_LIBFILE=""

export MPI_YES=OFF

# Python 3

export MPI_COMPILE_TYPE=""

export MPI_SITEARCH="%{python3_sitearch}"

export MY_CMAKE_BUILDDIR="%_vpath_builddir"

%{do_build}

# MPICH

%if %{with mpich}

%{_mpich_load}

export CC=mpicc

export CXX=mpicxx

export FC=mpif90

export F77=mpif77

export MPI_YES=ON

# Python 3

export MPI_COMPILE_TYPE="-mpich"

export MY_CMAKE_BUILDDIR="%_vpath_builddir""-mpich"

export MPI_LIBFILE="$MPI_LIB/libmpi.so"

%{do_build}

%{_mpich_unload}

%endif

# OpenMPI

%if %{with openmpi}

%{_openmpi_load}

export CC=mpicc

export CXX=mpicxx

export FC=mpif90

export F77=mpif77

export MPI_YES=ON

# Python 3

export MPI_COMPILE_TYPE="-openmpi"

export MY_CMAKE_BUILDDIR="%_vpath_builddir""-openmpi"

export MPI_LIBFILE="$MPI_LIB/libmpi.so"

%{do_build}

%{_openmpi_unload}

%endif

%install

# Install everything

%global do_install %{expand:

echo

echo "*** INSTALLING %{name}-%{version}$MPI_COMPILE_TYPE ***"

echo

DESTDIR=%{buildroot} %__cmake --install $MY_CMAKE_BUILDDIR

%if %{with music}

pushd $MY_CMAKE_BUILDDIR/src/neuronmusic

%{py3_install}

popd

%endif

# Python bits from the post install hook

# It requires the libraries before to be installed, not just built, so it must

# be done here. The only alternative is a different package that requires this,

# but this is simpler

RPM_LD_FLAGS="%{?__global_ldflags} -L$RPM_BUILD_ROOT/$MPI_LIB"

pushd $MY_CMAKE_BUILDDIR/src/nrnpython/

%{py3_build}

%{py3_install "--install-lib" "$MPI_PYTHON3_SITEARCH"}

popd

# set up second symlink for shared objects

pushd $RPM_BUILD_ROOT/$MPI_LIB/

    ln -sv ./libnrniv.so.0.0.0 libnrniv.so.0

    ln -sv ./librxdmath.so.0.0.0 librxdmath.so.0

popd

}

%global do_post_install_tweaks %{expand:

# Remove installed libfiles

rm -rfv $RPM_BUILD_ROOT/$MPI_HOME/lib/python/neuron/

# Post install clean up: remove stray object files

# Must be done at end, otherwise it deletes object files required for other builds

find . $RPM_BUILD_ROOT/$MPI_LIB/ -name "*.o" -exec rm -f '{}' \\;

# Remove libtool archives

find . $RPM_BUILD_ROOT/$MPI_LIB/ -name "*.la" -exec rm -f '{}' \\;

# Remove installed copy of libtool

# Remove iv header provided by iv package

rm -rf $RPM_BUILD_ROOT/$MPI_HOME/include/ivstream.h

# Delete installed libtool

rm -fv $RPM_BUILD_ROOT/$MPI_HOME/share/%{tarname}/libtool

# remove package note flag from nrnmech_makefile

pushd $RPM_BUILD_ROOT/$MPI_BIN/

    sed -i "s|-Wl,-dT,.*\.ld||" nrnmech_makefile

popd

# Only needed for MPI builds

if [ x"$MPI_SUFFIX" != "x" ]

then

# Do not install demo files for MPI packages

rm -rf $RPM_BUILD_ROOT/$MPI_HOME/share/%{tarname}/demo

# Renaming MPI bits

pushd $RPM_BUILD_ROOT/$MPI_BIN/

# Rename file references to use MPI_SUFFIX before renaming them

sed -i "s/nrniv\"/nrniv$MPI_SUFFIX\"/g" nrngui

sed -i -e "s/nrniv\"/nrniv$MPI_SUFFIX\"/g" -e "s/nrnmech_makefile/nrnmech_makefile$MPI_SUFFIX/g" -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" nrnivmodl

sed -i -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" nrnmech_makefile

sed -i -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" mkthreadsafe

# Rename files to include $MPI_SUFFIX

for f in modlunit neurondemo nrngui nrniv sortspike mkthreadsafe nocmodl nrnivmodl nrnmech_makefile

do

    mv -v "$f"{,$MPI_SUFFIX}

done

mv -v nrnpyenv{,$MPI_SUFFIX}.sh

mv -v set_nrnpyenv{,$MPI_SUFFIX}.sh

popd

fi

}

# Serial

export MPI_LIB="%{_libdir}"

export MPI_COMPILE_TYPE=""

export MPI_PYTHON3_SITEARCH=%{python3_sitearch}

export MY_CMAKE_BUILDDIR="%_vpath_builddir"

export MPI_HOME="%{_prefix}"

export MPI_BIN="%{_bindir}"

export MPI_SUFFIX=""

%do_install

%do_post_install_tweaks

# Remove duplicate files. These are installed in the correct python locations already

# rm -rf $RPM_BUILD_ROOT/%%{_datadir}/%%{tarname}/lib/python/%%{name}

# mpich

%if %{with mpich}

%{_mpich_load}

export MPI_COMPILE_TYPE="-mpich"

export MY_CMAKE_BUILDDIR="%_vpath_builddir""-mpich"

%do_install

%do_post_install_tweaks

%{_mpich_unload}

%endif

# OpenMPI

%if %{with openmpi}

%{_openmpi_load}

export MPI_COMPILE_TYPE="-openmpi"

export MY_CMAKE_BUILDDIR="%_vpath_builddir""-openmpi"

%do_install

%do_post_install_tweaks

%{_openmpi_unload}

%endif

# The makefiles do not have shebangs

%files

%license Copyright

%{_bindir}/modlunit

%{_bindir}/neurondemo

%{_bindir}/nrngui

%{_bindir}/nrniv

%{_bindir}/sortspike

# Not needed but I'll include them for completeness anyway

%{_bindir}/nrnpyenv.sh

%{_bindir}/set_nrnpyenv.sh

# Libs

%{_libdir}/libnrniv.so.0.0.0

%{_libdir}/libnrniv.so.0

%{_libdir}/librxdmath.so.0.0.0

%{_libdir}/librxdmath.so.0

# other hoc files and data

%dir %{_datadir}/%{tarname}

%{_datadir}/%{tarname}/lib

# Python bits

%files -n python3-%{name}

# The libraries are here

%{python3_sitearch}/%{name}

# Egg info

%{python3_sitearch}/NEURON-*-py%{python3_version}.egg-info

%files devel

%license Copyright

%doc README.md

%{_bindir}/mkthreadsafe

%{_bindir}/nocmodl

%{_bindir}/nrnivmodl

%{_bindir}/nrnmech_makefile

# Headers

%{_includedir}/*.h

%{_includedir}/nrncvode/

# Shared objects

%{_libdir}/libnrniv.so

%{_libdir}/librxdmath.so

# required by neuron

# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890

%{_datadir}/%{tarname}/nrnmain.cpp

%files doc

%license Copyright

%{_datadir}/%{tarname}/demo

%if %{with mpich}

%files mpich

%license Copyright

%{_libdir}/mpich/bin/modlunit_mpich

%{_libdir}/mpich/bin/neurondemo_mpich

%{_libdir}/mpich/bin/nrngui_mpich

%{_libdir}/mpich/bin/nrniv_mpich

%{_libdir}/mpich/bin/sortspike_mpich

# Not needed but I'll include them for completeness anyway

%{_libdir}/mpich/bin/nrnpyenv_mpich.sh

%{_libdir}/mpich/bin/set_nrnpyenv_mpich.sh

# Libs

%{_libdir}/mpich/lib/libnrniv.so.0.0.0

%{_libdir}/mpich/lib/libnrniv.so.0

%{_libdir}/mpich/lib/librxdmath.so.0.0.0

%{_libdir}/mpich/lib/librxdmath.so.0

#

%dir %{_libdir}/mpich/share/%{tarname}

%{_libdir}/mpich/share/%{tarname}/lib

# Python bits

%files -n python3-%{name}-mpich

# The libraries are here

%{python3_sitearch}/mpich/%{name}

# Egg info

%{python3_sitearch}/mpich/NEURON-*-py%{python3_version}.egg-info

%files mpich-devel

%license Copyright

%doc README.md

%{_libdir}/mpich/bin/mkthreadsafe_mpich

%{_libdir}/mpich/bin/nocmodl_mpich

%{_libdir}/mpich/bin/nrnivmodl_mpich

%{_libdir}/mpich/bin/nrnmech_makefile_mpich

# Headers

%{_libdir}/mpich/include/*.h

%{_libdir}/mpich/include/nrncvode/

# Shared objects

%{_libdir}/mpich/lib/libnrniv.so

%{_libdir}/mpich/lib/librxdmath.so

# required by neuron

# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890

%{_libdir}/mpich/share/%{tarname}/nrnmain.cpp

%endif

%if %{with openmpi}

%files openmpi

%license Copyright

%{_libdir}/openmpi/bin/modlunit_openmpi

%{_libdir}/openmpi/bin/neurondemo_openmpi

%{_libdir}/openmpi/bin/nrngui_openmpi

%{_libdir}/openmpi/bin/nrniv_openmpi

%{_libdir}/openmpi/bin/sortspike_openmpi

# Not needed but I'll include them for completeness anyway

%{_libdir}/openmpi/bin/nrnpyenv_openmpi.sh

%{_libdir}/openmpi/bin/set_nrnpyenv_openmpi.sh

# Libs

%{_libdir}/openmpi/lib/libnrniv.so.0.0.0

%{_libdir}/openmpi/lib/libnrniv.so.0

%{_libdir}/openmpi/lib/librxdmath.so.0.0.0

%{_libdir}/openmpi/lib/librxdmath.so.0

#

%dir %{_libdir}/openmpi/share/%{tarname}

%{_libdir}/openmpi/share/%{tarname}/lib

# Python bits

%files -n python3-%{name}-openmpi

# The libraries are here

%{python3_sitearch}/openmpi/%{name}

# Egg info

%{python3_sitearch}/openmpi/NEURON-*-py%{python3_version}.egg-info

%files openmpi-devel

%license Copyright

%doc README.md

%{_libdir}/openmpi/bin/mkthreadsafe_openmpi

%{_libdir}/openmpi/bin/nocmodl_openmpi

%{_libdir}/openmpi/bin/nrnivmodl_openmpi

%{_libdir}/openmpi/bin/nrnmech_makefile_openmpi

# Headers

%{_libdir}/openmpi/include/*.h

%{_libdir}/openmpi/include/nrncvode/

# Shared objects

%{_libdir}/openmpi/lib/libnrniv.so

%{_libdir}/openmpi/lib/librxdmath.so

# required by neuron

# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890

%{_libdir}/openmpi/share/%{tarname}/nrnmain.cpp

%endif

%changelog

%autochangelog