%global pretty_name STEPS
%global module_name steps
# Switch them off if you want
# Best to start with the serial version
%bcond_without mpich
%bcond_without openmpi
%if 0%{?fedora} >= 33 || 0%{?rhel} >= 9
%global blaslib flexiblas
%else
%global blaslib openblas
%endif
# Do not currently use system sundials
# https://bugzilla.redhat.com/show_bug.cgi?id=1820991
%global system_sundials 0
%global _description %{expand:
STEPS is a package for exact stochastic simulation of reaction-diffusion
systems in arbitrarily complex 3D geometries. Our core simulation algorithm is
an implementation of Gillespie's SSA, extended to deal with diffusion of
molecules over the elements of a 3D tetrahedral mesh.
While it was mainly developed for simulating detailed models of neuronal
signaling pathways in dendrites and around synapses, it is a general tool and
can be used for studying any biochemical pathway in which spatial gradients and
morphology are thought to play a role.
STEPS also supports accurate and efficient computational of local membrane
potentials on tetrahedral meshes, with the addition of voltage-gated channels
and currents. Tight integration between the reaction-diffusion calculations and
the tetrahedral mesh potentials allows detailed coupling between molecular
activity and local electrical excitability.
We have implemented STEPS as a set of Python modules, which means STEPS users
can use Python scripts to control all aspects of setting up the model,
generating a mesh, controlling the simulation and generating and analyzing
output. The core computational routines are still implemented as C/C++
extension modules for maximal speed of execution.
STEPS 3.0.0 and above provide early parallel solution for stochastic spatial
reaction-diffusion and electric field simulation.
Documentation can be found here:
http://steps.sourceforge.net/manual/manual_index.html
}
Name: python-%{module_name}
Version: 3.5.0
Release: 5%{?dist}
Summary: STochastic Engine for Pathway Simulation
License: GPLv2
URL: http://steps.sourceforge.net/
Source0: https://github.com/CNS-OIST/STEPS/archive/%{version}/%{module_name}-%{version}.tar.gz
# Header only library, needs cc file
# https://raw.githubusercontent.com/amrayn/easyloggingpp/master/src/easylogging%2B%2B.cc
Source1: easylogging++.cc
# https://raw.githubusercontent.com/amrayn/easyloggingpp/master/src/easylogging%2B%2B.h
Source2: easylogging++.h
# Patches generated from: https://github.com/sanjayankur31/STEPS/tree/fedora-3.5.0
# use system gtest
Patch0: 0001-Unbundle-gtest.patch
%if "%{system_sundials}" == "1"
# Tweak cmake file to stop looking for SUNDIALS_DIR
Patch1: 0002-Update-sundials-cmake.patch
%endif
# Remove flags they set
Patch2: 0003-Remove-flags-set-by-project.patch
# Remove pysteps flags
Patch3: 0004-Remove-pysteps-flags.patch
# We'll install manually, much easier and cleaner
Patch4: 0005-Disable-pyinstall.patch
BuildRequires: cmake
BuildRequires: gcc-c++
BuildRequires: git-core
BuildRequires: gtest-devel
BuildRequires: petsc-devel
BuildRequires: python3-devel
BuildRequires: %{py3_dist Cython}
BuildRequires: %{py3_dist numpy}
BuildRequires: %{py3_dist setuptools}
BuildRequires: %{blaslib}-devel
BuildRequires: Random123-devel
%if "%{system_sundials}" == "1"
BuildRequires: sundials2-devel
%endif
%description
%{_description}
%package -n python3-%{module_name}
Summary: STochastic Engine for Pathway Simulation
Provides: %{module_name} = %{version}-%{release}
%description -n python3-%{module_name}
%{_description}
%if %{with openmpi}
%package -n python3-%{module_name}-openmpi
Summary: %{module_name} built with openmpi
BuildRequires: openmpi-devel
BuildRequires: petsc-openmpi-devel
BuildRequires: rpm-mpi-hooks
BuildRequires: sundials-openmpi-devel
Requires: openmpi
%description -n python3-%{module_name}-openmpi
%{_description}
%endif
%if %{with mpich}
%package -n python3-%{module_name}-mpich
Summary: %{module_name} built with mpich
BuildRequires: mpich-devel
BuildRequires: petsc-mpich-devel
BuildRequires: rpm-mpi-hooks
BuildRequires: sundials-mpich-devel
Requires: mpich
%description -n python3-%{module_name}-mpich
%{_description}
%endif
%prep
%autosetup -n %{pretty_name}-%{version} -S git
# Easyloggingpp
mkdir -pv src/third_party/easyloggingpp/src/
cp %{SOURCE1} src/third_party/easyloggingpp/src/ -v
cp %{SOURCE2} src/third_party/easyloggingpp/src/ -v
# Correct for sundials2
# sed -i.orig 's|^#include.*<cvode/|#include <sundials2/cvode/|g' src/steps/tetode/tetode.cpp
# Build directories
mkdir build
%if %{with openmpi}
mkdir build-openmpi
%endif
%if %{with mpich}
mkdir build-mpich
%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 %{module_name}-%{version}$MPI_COMPILE_TYPE ***"
echo
%set_build_flags
pushd build$MPI_COMPILE_TYPE &&
cmake \\\
-DUSE_BUNDLE_EASYLOGGINGPP:BOOLEAN="ON" \\\
-DUSE_BUNDLE_RANDOM123:BOOLEAN="OFF" \\\
%if "%{system_sundials}" == "1"
-DUSE_BUNDLE_SUNDIALS:BOOLEAN="OFF" \\\
-DSUNDIALS_DIR:PATH=%{_datadir} \\\
-DSUNDIALS_INCLUDE_DIR:PATH=%{_includedir}/sundials2 \\\
-DSUNDIALS_LIBRARY_DIR:PATH=%{_libdir} \\\
%endif
-DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\
-DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \\\
-DLIB_INSTALL_DIR:PATH=%{_libdir} \\\
-DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\
-DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\
-DPYTHON_INSTALL_PREFIX:PATH=$MPI_PYTHON3_SITEARCH \\\
-DCMAKE_SKIP_RPATH:BOOL=ON \\\
-DUSE_MPI:BOOL=$MPI_YES \\\
-DUSE_PETSC:BOOL=False \\\
-DBLAS_LIBRARIES=-l%{blaslib} \\\
-DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\
-DBUILD_SHARED_LIBS:BOOL=ON \\\
%if "%{_lib}" == "lib64"
-DLIB_SUFFIX=64 ../ &&
%else
-DLIB_SUFFIX="" ../ &&
%endif
popd || exit -1;
}
%global do_make_build %{expand: \
make %{?_smp_mflags} -C build$MPI_COMPILE_TYPE &&
pushd pysteps &&
CFLAGS="%{optflags}" LDFLAGS="%{__global_ldflags}" %{__python3} ../build$MPI_COMPILE_TYPE/pysteps/cmake_setup.py build --executable="/usr/bin/python3 -s" --build-base=../build$MPI_COMPILE_TYPE/pysteps/build/ &&
popd || exit -1
}
# Build serial version, dummy arguments
export MPI_COMPILE_TYPE=""
export MPI_COMPILER=serial
export MPI_SUFFIX=""
export MPI_HOME=%{_prefix}
export MPI_BIN=%{_bindir}
export MPI_PYTHON3_SITEARCH=%{python3_sitearch}
export MPI_YES="False"
%{do_cmake_config}
%{do_make_build}
# Build mpich version
%if %{with mpich}
%{_mpich_load}
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES="True"
export MPI_COMPILE_TYPE="-mpich"
%{do_cmake_config}
%{do_make_build}
%{_mpich_unload}
%endif
# Build OpenMPI version
%if %{with openmpi}
%{_openmpi_load}
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES="True"
export MPI_COMPILE_TYPE="-openmpi"
%{do_cmake_config}
%{do_make_build}
%{_openmpi_unload}
%endif
%install
# Install everything
%global do_install %{expand: \
echo
echo "*** INSTALLING %{module_name}-%{version}$MPI_COMPILE_TYPE ***"
echo
make install DESTDIR=$RPM_BUILD_ROOT INSTALL="install -p" CPPROG="cp -p" -C build$MPI_COMPILE_TYPE || exit -1
pushd pysteps &&
CFLAGS="%{optflags}" LDFLAGS="%{__global_ldflags}" %{__python3} ../build$MPI_COMPILE_TYPE/pysteps/cmake_setup.py build --executable="/usr/bin/python3 -s" --build-base=../build$MPI_COMPILE_TYPE/pysteps/build/ install --install-lib=$MPI_PYTHON3_SITEARCH -O1 --skip-build --root $RPM_BUILD_ROOT &&
popd || exit -1
}
# install serial version
export MPI_COMPILE_TYPE=""
export MPI_SUFFIX=""
export MPI_HOME=%{_prefix}
export MPI_BIN=%{_bindir}
export MPI_YES="False"
export MPI_COMPILE_TYPE=""
export MPI_PYTHON3_SITEARCH="%{python3_sitearch}"
%{do_install}
# Install MPICH version
%if %{with mpich}
%{_mpich_load}
export MPI_YES="True"
export MPI_COMPILE_TYPE="-mpich"
%{do_install}
%{_mpich_unload}
%endif
# Install OpenMPI version
%if %{with openmpi}
%{_openmpi_load}
export MPI_YES="True"
export MPI_COMPILE_TYPE="-openmpi"
%{do_install}
%{_openmpi_unload}
%endif
%files -n python3-%{module_name}
%license LICENSE.md
%{python3_sitearch}/%{module_name}
%{python3_sitearch}/%{module_name}-%{version}-py%{python3_version}.egg-info
%if %{with mpich}
%files -n python3-%{module_name}-mpich
%license LICENSE.md
%{python3_sitearch}/mpich/%{module_name}
%{python3_sitearch}/mpich/%{module_name}-%{version}-py%{python3_version}.egg-info
%endif
%if %{with openmpi}
%files -n python3-%{module_name}-openmpi
%license LICENSE.md
%{python3_sitearch}/openmpi/%{module_name}
%{python3_sitearch}/openmpi/%{module_name}-%{version}-py%{python3_version}.egg-info
%endif
%changelog
* Thu Aug 27 2020 Iñaki Úcar <iucar@fedoraproject.org> - 3.5.0-5
- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.5.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
* Thu Jun 25 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.5.0-3
- Explicitly BR setuptools
* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 3.5.0-2
- Rebuilt for Python 3.9
* Sat Apr 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.5.0-1
- Initial rpmbuild