%global _description %{expand:
Arbor is a high-performance library for Computational Neuroscience simulations.
Some key features include:
- Asynchronous spike exchange that overlaps compute and communication.
- Efficient sampling of voltage and current on all back ends.
- Efficient implementation of all features on GPU.
- Reporting of memory and energy consumption (when available on platform).
- An API for addition of new cell types, e.g. LIF and Poisson spike generators.
- Validation tests against numeric/analytic models and NEURON.
Documentation is available at https://arbor.readthedocs.io/en/latest/
}
# Best to start with the serial version when debugging build failures
%bcond_without mpich
%bcond_without openmpi
%bcond_without tests
%global forgeurl https://github.com/arbor-sim/arbor
Name: arbor
Version: 0.5.2
Release: %autorelease
Summary: Multi-compartment neural network simulation library
%forgemeta
URL: %forgeurl
Source0: %forgesource
# script to run examples
Source1: https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_python_examples.sh
Source2: https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_cpp_examples.sh
License: BSD
# This patch changes ext/CMakeLists.txt for automatically using tinyopt libraries by cmake command.
#Patch1: arbor-tinyopt_cmake.patch
# Random123 does not support these
ExcludeArch: mips64r2 mips32r2 s390
BuildRequires: cmake
BuildRequires: make
BuildRequires: gcc-c++
BuildRequires: git-core
BuildRequires: gtest-devel
BuildRequires: google-benchmark-devel
BuildRequires: json-devel
BuildRequires: libunwind-devel
BuildRequires: pybind11-devel
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: Random123-devel
BuildRequires: tclap-devel
Provides: python3-arbor = %{version}-%{release}
# For validation, but we don't have these BRs
# BuildRequires: julia julia-sundials julia-unitful julia-JSON
%if %{with tests}
BuildRequires: %{py3_dist numpy}
BuildRequires: %{py3_dist pandas}
BuildRequires: %{py3_dist seaborn}
%endif
# Required by arbor
Requires: %{py3_dist numpy}
%description %{_description}
%package devel
Summary: Development files for arbor
Requires: arbor%{?_isa} = %{version}-%{release}
Provides: arbor-static = %{version}-%{release}
%description devel %{_description}
%package doc
# Does not require the main package, since it may be installed by people using
# the MPI builds
Summary: Documentation for arbor
BuildRequires: python3-sphinx
BuildRequires: python3-sphinx_rtd_theme
BuildRequires: python3-svgwrite
%description doc %{_description}
%if %{with mpich}
%package mpich
Summary: MPICH build for arbor
BuildRequires: mpich-devel
BuildRequires: rpm-mpi-hooks
BuildRequires: python3-mpi4py-mpich
Requires: mpich
Requires: python3-mpich
Requires: python3-mpi4py-mpich
Requires: %{py3_dist numpy}
Provides: python3-arbor-mpich = %{version}-%{release}
%description mpich %{_description}
%package mpich-devel
Summary: Development files for arbor-mpich
Requires: arbor-mpich%{?_isa} = %{version}-%{release}
Provides: arbor-mpich-static = %{version}-%{release}
%description mpich-devel %{_description}
%endif
%if %{with openmpi}
%package openmpi
Summary: OpenMPI build for arbor
BuildRequires: openmpi-devel
BuildRequires: rpm-mpi-hooks
BuildRequires: python3-mpi4py-openmpi
Requires: openmpi
Requires: python3-openmpi
Requires: python3-mpi4py-openmpi
Requires: %{py3_dist numpy}
Provides: python3-arbor-openmpi = %{version}-%{release}
%description openmpi %{_description}
%package openmpi-devel
Summary: Development files for arbor-openmpi
Requires: arbor-openmpi%{?_isa} = %{version}-%{release}
Provides: arbor-openmpi-static = %{version}-%{release}
%description openmpi-devel %{_description}
%endif
%prep
%forgesetup
# Disable failing padded test
sed -i '/test_padded.cpp/ d' test/unit/CMakeLists.txt
# should always be included, but is currently included only if bundled pybind11
# is used
sed -i '/add_subdirectory(python)/i \
include(FindPythonModule)' CMakeLists.txt
# Do not build external libraries
sed -i -e 's/ ext-random123//' CMakeLists.txt
# Disable doc build: we built it ourselves
sed -i '/add_subdirectory(doc)/ d' CMakeLists.txt
# Remove ext folders, unbundle libraries
rm -vrf ext/google-benchmark ext/json ext/random123
mv ext/tinyopt/LICENSE ext/tinyopt/LICENSE-tinyopt
# tclap and json are both header only
find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext-json//' {} 2>/dev/null ';'
# Correct Python shebangs in all files
find . -type f -name "*" -exec sed -i 's|^#![ ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';'
# test scripts
cp %{SOURCE1} scripts/
cp %{SOURCE2} scripts/
chmod +x scripts/*.sh
sed -i 's/ python / python3 /' scripts/run_python_examples.sh
sed -i 's|build/|./|' scripts/run_cpp_examples.sh
# builddir for serial
mkdir build-serial
%if %{with mpich}
mkdir build-mpich
%endif
%if %{with openmpi}
mkdir build-openmpi
%endif
%build
# Best to use && so that if anything in the chain fails, the build also fails
# straight away
%global do_cmake_config %{expand: \
echo
echo "*** BUILDING arbor-%{version}$MPI_COMPILE_TYPE ***"
echo
pushd build$MPI_COMPILE_TYPE &&
cmake \\\
-DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\
-DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\
-DINCLUDE_INSTALL_DIR:PATH=$MPI_INCLUDE \\\
-DLIB_INSTALL_DIR:PATH=$MPI_LIB \\\
-DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\
-DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\
-DCMAKE_SKIP_RPATH:BOOL=ON \\\
-DCMAKE_BUILD_TYPE:STRING="release" \\\
-DARB_USE_BUNDLED_LIBS:BOOL=OFF \\\
-DARB_USE_BUNDLED_PYBIND11:BOOL=OFF \\\
%ifarch x86_64 i686 aarch64
-DARB_VECTORIZE:BOOL=ON \\\
%else
-DARB_VECTORIZE:BOOL=OFF \\\
%endif
-DARB_WITH_MPI:BOOL=$MPI_YES \\\
-DARB_WITH_GPU:BOOL=OFF \\\
%ifnarch s390x s390
-DARB_ARCH:STRING="native" \\\
%else
-DARB_ARCH:STRING="none" \\\
%endif
-DCMAKE_INSTALL_LIBDIR=%{_lib} \\\
-DARB_WITH_PYTHON:BOOL=ON \\\
-DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\
%if "%{_lib}" == "lib64"
-DLIB_SUFFIX=64 .. &&
%else
-DLIB_SUFFIX="" .. &&
%endif
popd || exit -1;
# Upstream only supports static libraries
# https://github.com/arbor-sim/arbor/issues/916
# -DBUILD_SHARED_LIBS:BOOL=ON \\\
# Missing BRs
# -DARB_BUILD_VALIDATION_DATA:BOOL=ON \\\
}
%global do_make_build %{expand: \
%make_build -C build$MPI_COMPILE_TYPE || exit -1
%make_build -C build$MPI_COMPILE_TYPE examples || exit -1
%if %{with tests}
%make_build -C build$MPI_COMPILE_TYPE tests || exit -1
%endif
}
# Build serial version, dummy arguments
%global __cc gcc
%global __cxx g++
%set_build_flags
export MPI_SUFFIX=""
export MPI_HOME=%{_prefix}
export MPI_INCLUDE=%{_includedir}
export MPI_LIB=%{_libdir}
export MPI_YES=OFF
export MPI_COMPILE_TYPE="-serial"
export MPI_PYTHON3_SITEARCH=%{python3_sitearch}
%{do_cmake_config}
%{do_make_build}
# Manually make docs in the serial build
sphinx-build-%{python3_version} -b html doc html
# Remove uneeded dotfiles
rm -rfv html/{.buildinfo,.doctrees}
# Build mpich version
%if %{with mpich}
%{_mpich_load}
%global __cc mpicc
%global __cxx mpicxx
%set_build_flags
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES=ON
export MPI_COMPILE_TYPE="-mpich"
%{do_cmake_config}
%{do_make_build}
%{_mpich_unload}
%endif
# Build OpenMPI version
%if %{with openmpi}
%{_openmpi_load}
%global __cc mpicc
%global __cxx mpicxx
%set_build_flags
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES=ON
# Python 3
export MPI_COMPILE_TYPE="-openmpi"
%{do_cmake_config}
%{do_make_build}
%{_openmpi_unload}
%endif
%install
# Install everything
%global do_install %{expand: \
echo
echo "*** INSTALLING arbor-%{version}$MPI_COMPILE_TYPE ***"
echo
%make_install -C build$MPI_COMPILE_TYPE || exit -1
}
# install serial version
export MPI_SUFFIX=""
export MPI_HOME=%{_prefix}
export MPI_BIN=%{_bindir}
export MPI_YES=OFF
export MPI_COMPILE_TYPE="-serial"
%{do_install}
# Install MPICH version
%if %{with mpich}
%{_mpich_load}
export MPI_COMPILE_TYPE="-mpich"
%{do_install}
# Place in correct mpi libdir
%if "%{_lib}" == "lib64"
mv -v $RPM_BUILD_ROOT/%{_libdir}/mpich/lib64 $RPM_BUILD_ROOT/$MPI_LIB/
%endif
pushd $RPM_BUILD_ROOT/$MPI_BIN
mv -v modcc{,$MPI_SUFFIX} -v
popd
%{_mpich_unload}
%endif
# Install OpenMPI version
%if %{with openmpi}
%{_openmpi_load}
export MPI_COMPILE_TYPE="-openmpi"
%{do_install}
# Correct location
%if "%{_lib}" == "lib64"
mv -v $RPM_BUILD_ROOT/%{_libdir}/openmpi/lib64 $RPM_BUILD_ROOT/$MPI_LIB/
%endif
pushd $RPM_BUILD_ROOT/$MPI_BIN
mv -v modcc{,$MPI_SUFFIX} -v
popd
%{_openmpi_unload}
%endif
# https://github.com/arbor-sim/arbor/blob/master/.github/workflows/basic.yml
%if %{with tests}
%check
# General tests
export PYTHONPATH="%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib}"
# these tests segfault, filter out
pushd build-serial
%{python3} ../python/test/unit/runner.py -v2
./bin/unit
./bin/unit-modcc
cp ../scripts/run_cpp_examples.sh .
./run_cpp_examples.sh
popd
./scripts/run_python_examples.sh
# MPICH
%if %{with mpich}
%{_mpich_load}
export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
pushd build-mpich
#./bin/unit --gtest_filter=-*mc_event_delivery*:*fvm_lowered*:*mc_cell_group*
mpirun -n %{_smp_build_ncpus} %{python3} ../python/test/unit_distributed/runner.py -v2
mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
cp ../scripts/run_cpp_examples.sh .
./run_cpp_examples.sh "mpirun -n %{_smp_build_ncpus}"
popd
./scripts/run_python_examples.sh "mpirun -n %{_smp_build_ncpus}"
%{_mpich_unload}
%endif
# OpenMPI
%if %{with openmpi}
%{_openmpi_load}
export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
pushd build-openmpi
mpirun -n %{_smp_build_ncpus} %{python3} ../python/test/unit_distributed/runner.py -v2
mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
cp ../scripts/run_cpp_examples.sh .
./run_cpp_examples.sh "mpirun -n %{_smp_build_ncpus}"
popd
./scripts/run_python_examples.sh "mpirun -n %{_smp_build_ncpus}"
%{_openmpi_unload}
%endif
%endif
%files
%license LICENSE ext/tinyopt/LICENSE-tinyopt
%doc README.md
%{_bindir}/modcc
%{python3_sitearch}/arbor
%files devel
%{_includedir}/arborio
%{_includedir}/arbor
%{_includedir}/arborenv
%{_libdir}/cmake/arbor
%{_libdir}/libarbor.a
%{_libdir}/libarborio.a
%{_libdir}/libarborenv.a
%files doc
%license LICENSE
%doc html
%if %{with mpich}
%files mpich
%doc README.md
%license LICENSE ext/tinyopt/LICENSE-tinyopt
%{_libdir}/mpich/bin/modcc_mpich
%{python3_sitearch}/mpich/arbor
%files mpich-devel
%{_libdir}/mpich/include/arbor
%{_libdir}/mpich/include/arborio
%{_libdir}/mpich/include/arborenv
%{_libdir}/mpich/lib/cmake/arbor
%{_libdir}/mpich/lib/libarbor.a
%{_libdir}/mpich/lib/libarborio.a
%{_libdir}/mpich/lib/libarborenv.a
%endif
%if %{with openmpi}
%files openmpi
%doc README.md
%license LICENSE ext/tinyopt/LICENSE-tinyopt
%{_libdir}/openmpi/bin/modcc_openmpi
%{python3_sitearch}/openmpi/arbor
%files openmpi-devel
%{_libdir}/openmpi/include/arbor
%{_libdir}/openmpi/include/arborio
%{_libdir}/openmpi/include/arborenv
%{_libdir}/openmpi/lib/cmake/arbor
%{_libdir}/openmpi/lib/libarbor.a
%{_libdir}/openmpi/lib/libarborio.a
%{_libdir}/openmpi/lib/libarborenv.a
%endif
%changelog
%autochangelog
* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-10
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 0.3-9
- Rebuilt for Python 3.10
* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
* Mon Oct 05 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.3-7
- Explicitly require setuptools
* Fri Aug 28 2020 Jeff Law <law@redhat.com> - 0.3-6
- Re-enable LTO
- Do not force -march=native on armv7hl so that build architecture does not bleed
into the binaries. This should probably be done on all targets
* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-5
- Second attempt - Rebuilt for
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Mon Jul 27 2020 Jeff Law <law@redhat.com> - 0.3-4
- Disable LTO for armv7hl build
* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Sun Jun 28 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.3-2
- Update build flags to ensure CC and CXX are set correctly
- https://lists.fedoraproject.org/archives/list/scitech@lists.fedoraproject.org/thread/BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT/#BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT
* Mon Jun 08 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-2
- Move Provides lines to runtime packages
- Add patch for using tinyopt libraries
* Sat Jun 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-1
- Release 0.3
* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 0.2.2-8.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
- Rebuilt for Python 3.9
* Thu Apr 02 2020 Björn Esser <besser82@fedoraproject.org> - 0.2.2-7.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
- Fix string quoting for rpm >= 4.16
* Wed Feb 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200226gitfb5d4ea736282dce14c3284bc5db748b082db957
- Use new snapshot that fixes errors on 32 bit systems
- No longer excludes i686 and armv7hl
- Drop unneeded patch.
* Sun Feb 23 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10
- Build from latest upstream snapshot
- Freshen patch
- Add exclude arches
* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.2-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Tue Dec 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-3
- Enable tests
- Add patch for test crash
* Mon Dec 09 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-2
- Remove arch info in provides for static
- Temporarily disable tests
- use python3-devel
- Add documentation in separate sub-package
- add python3-{mpich,openmpi} as requires that own MPI_PYTHON3_SITEARCH directories
- Improve summaries for sub-packages to please rpmlint
* Sat Dec 07 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-1
- Update to latest release
* Sun Jan 13 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.1-1
- Initial rpm package