math and code
A blog for things related to math, programming, music, and other interests of mine.
Projects:
Build FEniCS 2017.2.0 from source with OpenBLAS
by Evan Cummings
If you are working with a cluster system, or simply want to take advantage of OpenBLAS linear-algebra libraries that are tuned for your particular computer architecture, you’ll have to build some machine code from source. The FEniCS devs are currently working on the latest 2018.1.0 version which will finally no longer support Python 2.7 and also take advantage of the lastest PETSc version. Until this latest version is released, it is required to install some older software versions of the FEniCS dependencies; it is my hope that this letter will provide a demonstration for users to follow in order to get any past or future software which depends on FEniCS version 2017.2.0 up and running.
The steps to follow will build all the dependencies for my glacier simulator cslvr which uses FEniCS, and will be completed by calling the following function, which calls installation scripts for each of the dependencies to be described below:
function build_all()
{
load_environment;
install_dependencies;
install_openblas;
install_python;
install_libarchive;
install_cmake;
install_pybind11;
install_boost;
install_eigen3;
install_swig;
install_hdf5;
install_petsc;
install_slepc;
install_fenics;
install_hsl;
install_ipopt;
install_dolfin_adjoint;
install_basemap;
install_gmsh;
install_cslvr;
}First, define environment variables for the versions of each code we’ll need. Intead of placing all the software in one folder—where each library may become intermingled—I install each in its own directory and manually add each path to my environment:
function load_environment()
{
export PYTHON_VERSION=2.7.15;
export NUMPY_VERSION=1.13;
export SCIPY_VERSION=1.0;
export MATPLOTLIB_VERSION=2.2;
export LIBARCHIVE_VERSION=3.3.2;
export PYBIND11_VERSION=2.2.1;
export BOOST_VERSION=1.67.0;
export EIGEN_VERSION=3.3.4;
export CMAKE_VERSION=3.11.1;
export SWIG_VERSION=3.0.12;
export HDF5_VERSION=1.10.2;
export OPENBLAS_VERSION=0.2.20;
export SLEPC_VERSION=3.8.2;
export PETSC_VERSION=3.8.3;
export PETSC4PY_VERSION=3.8.1;
export SLEPC4PY_VERSION=3.8.0;
export MSHR_VERSION="2017.2.0";
export DOLFIN_VERSION="2017.2.0.post0";
export PYPI_FENICS_VERSION=">=2017.2.0,<2018.1.0";
export DOLFIN_ADJOINT_VERSION="2017.2.0";
export PYADJOINT_VERSION="2017.2.0";
export IPOPT_VERSION=3.12.9;
export PREFIX=$HOME/local;
export SFT_DIR=$HOME/software;
export PYTHON_DIR=${PREFIX}/python-${PYTHON_VERSION};
export LIBARCHIVE_DIR=${PREFIX}/libarchive-${LIBARCHIVE_VERSION};
export PYBIND11_DIR=${PREFIX}/pybind11-${PYBIND11_VERSION};
export CMAKE_DIR=${PREFIX}/cmake-${CMAKE_VERSION};
export SWIG_DIR=${PREFIX}/swig-${SWIG_VERSION};
export BOOST_DIR=${PREFIX}/boost-${BOOST_VERSION};
export EIGEN_DIR=${PREFIX}/eigen-${EIGEN_VERSION};
export HDF5_DIR=${PREFIX}/hdf5-${HDF5_VERSION};
export OPENBLAS_DIR=${PREFIX}/openblas-${OPENBLAS_VERSION};
export SLEPC_DIR=${PREFIX}/slepc-${SLEPC_VERSION};
export PETSC_DIR=${PREFIX}/petsc-${PETSC_VERSION};
export DOLFIN_DIR=${PREFIX}/dolfin-${DOLFIN_VERSION};
export HSL_DIR=${PREFIX}/hsl;
export IPOPT_DIR=${PREFIX}/ipopt-${IPOPT_VERSION};
export LIBADJOINT_DIR=${PREFIX}/libadjoint-${DOLFIN_ADJOINT_VERSION};
export GMSH_DIR=${PREFIX}/gmsh;
export BUILD_THREADS=4;
# make the packages available to paths :
# NOTE: this will produce an error when loading before tools are installed.
source ${DOLFIN_DIR}/share/dolfin/dolfin.conf;
# add dependencies to path :
export LD_LIBRARY_PATH=${LIBARCHIVE_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${PYTHON_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${BOOST_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${HDF5_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${OPENBLAS_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${IPOPT_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${LIBADJOINT_DIR}/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH=${GMSH_DIR}/lib:$LD_LIBRARY_PATH;
export C_INCLUDE_PATH=${LIBARCHIVE_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${PYBIND11_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${BOOST_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${EIGEN_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${HD55_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${OPENBLAS_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${IPOPT_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${LIBADJOINT_DIR}/include:$C_INCLUDE_PATH;
export C_INCLUDE_PATH=${GMSH_DIR}/include:$C_INCLUDE_PATH;
export PATH=${LIBARCHIVE_DIR}/bin:$PATH;
export PATH=${PYTHON_DIR}/bin:$PATH;
export PATH=${CMAKE_DIR}/bin:$PATH;
export PATH=${SWIG_DIR}/bin:$PATH;
export PATH=${HDF5_DIR}/bin:$PATH;
export PATH=${GMSH_DIR}/bin:$PATH;
# add pythonpaths :
export PYTHONPATH=${LIBADJOINT_DIR}/lib/python2.7/site-packages/:$PYTHONPATH
export PYTHONPATH=${GMSH_DIR}/lib/python2.7/site-packages/:$PYTHONPATH
# make the directory to store the source code :
mkdir -p $SFT_DIR;
mkdir -p $PREFIX;
}The function load_environment() can be called after all the software is installed to load all of your packages into your working environment.
We install source code into $SFT_DIR and Python will go into $PYHON_DIR.
While it may be simplier to just throw each of the packages in a single directory—such as $HOME/.local—I prefer to keep each package separated by version numbers so that if I ever want to compile the sources again with a new dependency version, I can simply change the version number at the top to change my entire compilation or operating environment.
If you have access to sudo, install all the Python dependencies the easy way.
Make sure to check the box Source code in your software data sources: press win key (we don’t support planned-obsolescent policies), then type “software & updates”.
Then the command apt-get build-dep will work:
function install_dependencies()
{
# ensure a fortran compiler is available :
sudo apt-get install -y gfortran libgfortran3;
# install python dependencies (make sure to check box `Source code` sources) :
sudo apt-get install -y git build-essential libmpich-dev;
sudo apt-get build-dep -y python2.7;
# install misc dependencies :
sudo apt-get install -y curl slib libuv1-dev qt4-qmake \
libpng-dev zlib1g-dev libpcre3-dev;
# install petsc dependencies :
sudo apt-get install -y git valgrind libbison-dev flex;
# install mshr dependencies :
sudo apt-get install -y libgmp-dev libmpfr-dev;
# install geos for basemap :
sudo apt-get install -y libgeos-dev;
# install gmsh dependencies :
sudo apt-get install -y libfltk1.3-dev libcanberra-gtk-module;
# install cslvr dependencies :
sudo apt-get install -y libnetcdf-dev;
# install latex for plotting with matplotlib :
sudo apt-get install -y texlive-base texlive-latex-base texlive-latex-extra
}If you do not have access to sudo, you’ll have to request help from your system admin or build these dependencies yourself.
Next, build and install OpenBLAS:
function install_openblas()
{
# install openblas :
cd $SFT_DIR;
wget --read-timeout=10 \
-nc https://github.com/xianyi/OpenBLAS/archive/v${OPENBLAS_VERSION}.tar.gz \
-O openblas.tar.gz;
tar -xf openblas.tar.gz;
rm openblas.tar.gz;
cd OpenBLAS-${OPENBLAS_VERSION};
make -j ${BUILD_TREADS} \
USE_THREAD=0 \
NUM_THREADS=1 \
CC=gcc \
FC=gfortran \
PREFIX=${OPENBLAS_DIR};
make install PREFIX=${OPENBLAS_DIR};
}While not a neccessary requirement, let’s build Python version 2.7.15 in a user directory, along with pip, NumPy, SciPy, and Matplotlib, and some other dependencies:
function install_python()
{
# install python :
cd $SFT_DIR;
url="https://www.python.org/ftp/python/${PYTHON_VERSION}/\
Python-${PYTHON_VERSION}.tgz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzf Python-${PYTHON_VERSION}.tgz;
rm Python-${PYTHON_VERSION}.tgz;
cd $SFT_DIR/Python-${PYTHON_VERSION};
./configure --enable-optimizations \
--enable-shared \
--with-system-expat \
--with-system-ffi \
--enable-ipv6 \
--with-threads \
--with-pydebug \
--with-lto \
--prefix=${PYTHON_DIR};
make -j ${BUILD_THREADS};
make install;
# install pip (https://pip.pypa.io/en/stable/installing/) :
cd $SFT_DIR;
wget https://bootstrap.pypa.io/get-pip.py;
python get-pip.py;
rm get-pip.py;
# install various python packages :
pip install sympy \
ipython \
mpi4py \
ply \
sphinx \
cython \
pytest \
nose;
# install numpy with openblas :
# https://leemendelowitz.github.io/blog/installing-numpy-with-openblas.html
cd $SFT_DIR;
git clone https://github.com/numpy/numpy.git;
cd $SFT_DIR/numpy;
git checkout maintenance/${NUMPY_VERSION}.x;
touch site.cfg;
echo [DEFAULT] >> site.cfg;
echo library_dirs = ${OPENBLAS_DIR}/lib >> site.cfg;
echo include_dirs = ${OPENBLAS_DIR}/include >> site.cfg;
echo "" >> site.cfg;
echo [atlas] >> site.cfg;
echo atlas_libs = openblas >> site.cfg;
echo libraries = openblas >> site.cfg;
echo "" >> site.cfg;
echo [openblas] >> site.cfg;
echo libraries = openblas >> site.cfg;
echo library_dirs = ${OPENBLAS_DIR}/lib >> site.cfg;
echo include_dirs = ${OPENBLAS_DIR}/include >> site.cfg;
pip install . -v;
# install scipy ignoring numpy's version (pip will fail, so use setup.py) :
cd $SFT_DIR;
git clone https://github.com/scipy/scipy.git;
cd $SFT_DIR/scipy;
git checkout maintenance/${SCIPY_VERSION}.x;
python setup.py install --record=install_files.txt;
# finally, install matplotlib :
cd $SFT_DIR;
git clone https://github.com/matplotlib/matplotlib;
cd $SFT_DIR/matplotlib;
git checkout v${MATPLOTLIB_VERSION}.x;
pip install . -v;
}The rest of this “tutorial” is rather terse, but you get the idea. Libarchive, needed by HDF5 and CMake:
function install_libarchive()
{
# install libarchive:
cd $SFT_DIR;
url="http://www.libarchive.org/downloads/\
libarchive-${LIBARCHIVE_VERSION}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzf libarchive-${LIBARCHIVE_VERSION}.tar.gz;
rm libarchive-${LIBARCHIVE_VERSION}.tar.gz;
cd $SFT_DIR/libarchive-${LIBARCHIVE_VERSION};
./configure --disable-static \
--prefix=${LIBARCHIVE_DIR};
make -j ${BUILD_THREADS};
make install;
}Next, the lastest version of CMake:
function install_cmake()
{
# install cmake :
cd $SFT_DIR;
url="https://cmake.org/files/v${CMAKE_VERSION%.*}/\
cmake-${CMAKE_VERSION}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzf cmake-${CMAKE_VERSION}.tar.gz;
rm cmake-${CMAKE_VERSION}.tar.gz;
cd $SFT_DIR/cmake-${CMAKE_VERSION};
./bootstrap --parallel=${BUILD_THREADS} \
--prefix=${CMAKE_DIR};
make -j ${BUILD_THREADS};
make install;
}function install_pybind11()
{
# install pybind11 :
cd $SFT_DIR;
url="https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz";
wget -nc $url -O pybind.tgz;
tar -xzf pybind.tgz;
rm pybind.tgz;
mkdir pybind11-${PYBIND11_VERSION}/build;
cd pybind11-${PYBIND11_VERSION}/build;
cmake -D PYBIND11_TEST=OFF \
-D PYTHON_EXECUTABLE:FILEPATH=$(which python) \
-D CMAKE_INSTALL_PREFIX=${PYBIND11_DIR} ..;
make install;
}function install_boost()
{
# install boost (with mpi) :
cd $SFT_DIR;
boost_ver=$(tr "\." "_" <<< ${BOOST_VERSION});
url="https://dl.bintray.com/boostorg/release/${BOOST_VERSION}/\
source/boost_${boost_ver}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
mkdir -p boost-${BOOST_VERSION};
tar -xzf boost_${boost_ver}.tar.gz -C boost-${BOOST_VERSION} \
--strip-components 1;
rm boost_${boost_ver}.tar.gz;
cd $SFT_DIR/boost-${BOOST_VERSION};
./bootstrap.sh --with-toolset=gcc \
--with-python=$(which python) \
--prefix=${BOOST_DIR};
echo "using mpi : mpicxx ;" >> project-config.jam;
./b2 -j ${BUILD_THREADS} toolset=gcc --build-dir=build install;
}function install_eigen3()
{
# install eigen3 :
cd $SFT_DIR;
wget http://bitbucket.org/eigen/eigen/get/${EIGEN_VERSION}.tar.bz2;
mkdir -p eigen-${EIGEN_VERSION};
tar -xf ${EIGEN_VERSION}.tar.bz2 -C eigen-${EIGEN_VERSION} \
--strip-components 1;
rm ${EIGEN_VERSION}.tar.bz2;
rm $SFT_DIR/eigen-${EIGEN_VERSION}/build;
mkdir $SFT_DIR/eigen-${EIGEN_VERSION}/build;
cd $SFT_DIR/eigen-${EIGEN_VERSION}/build;
cmake -D BOOST_ROOT=${BOOST_DIR} \
-D CMAKE_INSTALL_PREFIX=${EIGEN_DIR} ..;
make install;
}SWIG:
function install_swig()
{
# install swig :
cd $SFT_DIR;
url="http://downloads.sourceforge.net/swig/swig-${SWIG_VERSION}.tar.gz";
wget -nc $url -O swig-${SWIG_VERSION}.tar.gz;
tar -xf swig-${SWIG_VERSION}.tar.gz;
rm swig-${SWIG_VERSION}.tar.gz;
cd $SFT_DIR/swig-${SWIG_VERSION};
./configure --with-python=$(which python) \
--with-boost=${BOOST_DIR} \
--prefix=${SWIG_DIR};
make -j ${BUILD_THREADS};
make install;
}HDF5:
function install_hdf5()
{
# install hdf5 :
cd $SFT_DIR;
url="https://support.hdfgroup.org/ftp/HDF5/releases/\
hdf5-${HDF5_VERSION%.*}/hdf5-${HDF5_VERSION}/\
src/hdf5-${HDF5_VERSION}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzf hdf5-${HDF5_VERSION}.tar.gz;
rm hdf5-${HDF5_VERSION}.tar.gz;
rm -rf $SFT_DIR/hdf5-${HDF5_VERSION}/build;
mkdir $SFT_DIR/hdf5-${HDF5_VERSION}/build;
cd $SFT_DIR/hdf5-${HDF5_VERSION}/build;
../configure CC=mpicc \
CXX=mpicxx \
FC=mpifort \
--with-default-api-version=v18 \
--enable-build-mode=production \
--enable-parallel \
--enable-shared \
--enable-fortran \
--with-zlib=yes \
--with-szlib=yes \
--prefix=${HDF5_DIR};
make -j ${BUILD_THREADS};
#make check; # takes forever
make install;
make check-install;
}function install_petsc()
{
# install petsc :
cd $SFT_DIR;
wget -nc https://bitbucket.org/petsc/petsc/get/v${PETSC_VERSION}.tar.gz \
-O ${SFT_DIR}/petsc-${PETSC_VERSION}.tar.gz;
mkdir -p ${SFT_DIR}/petsc-${PETSC_VERSION};
tar -xzf ${SFT_DIR}/petsc-${PETSC_VERSION}.tar.gz \
-C ${SFT_DIR}/petsc-${PETSC_VERSION} \
--strip-components 1;
rm ${SFT_DIR}/petsc-${PETSC_VERSION}.tar.gz;
cd $SFT_DIR/petsc-${PETSC_VERSION};
export PETSC_DIR=$(pwd);
./configure --with-cc=mpicc \
--with-cxx=mpicxx \
--with-fc=mpifort \
--COPTFLAGS="-O2" \
--CXXOPTFLAGS="-O2" \
--FOPTFLAGS="-O2" \
--with-c-support=1 \
--with-cxx-dialect=C++11 \
--with-debugging=0 \
--with-shared-libraries=1 \
--with-boost-dir=${BOOST_DIR} \
--with-hdf5-dir=${HDF5_DIR} \
--with-blas-lib=${OPENBLAS_DIR}/lib/libopenblas.a \
--with-lapack-lib=${OPENBLAS_DIR}/lib/libopenblas.a \
--download-scalapack=1 \
--download-blacs=1 \
--download-hypre=1 \
--download-metis=1 \
--download-mumps=1 \
--download-parmetis=1 \
--download-ptscotch=1 \
--download-spai=1 \
--download-elemental=1 \
--download-ml=1 \
--download-suitesparse=1 \
--download-superlu=1 \
--download-superlu_dist=1 \
--prefix=${PREFIX}/petsc-${PETSC_VERSION};
make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=arch-linux2-c-opt all;
make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=arch-linux2-c-opt install;
export PETSC_DIR=${PREFIX}/petsc-${PETSC_VERSION};
make PETSC_DIR=${PETSC_DIR} PETSC_ARCH="" test;
# install petsc4py
# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/usrman/install.html :
cd $SFT_DIR;
url="https://bitbucket.org/petsc/petsc4py/downloads/\
petsc4py-${PETSC4PY_VERSION}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzvf petsc4py-${PETSC4PY_VERSION}.tar.gz;
rm petsc4py-${PETSC4PY_VERSION}.tar.gz;
cd $SFT_DIR/petsc4py-${PETSC4PY_VERSION};
pip install . -v;
}function install_slepc()
{
# install slepc :
cd $SFT_DIR;
wget -nc http://slepc.upv.es/download/distrib/slepc-${SLEPC_VERSION}.tar.gz \
-O $SFT_DIR/slepc-${SLEPC_VERSION}.tar.gz;
mkdir -p $SFT_DIR/slepc-${SLEPC_VERSION};
tar -xzf $SFT_DIR/slepc-${SLEPC_VERSION}.tar.gz
-C $SFT_DIR/slepc-${SLEPC_VERSION} \
--strip-components 1;
rm $SFT_DIR/slepc-${SLEPC_VERSION}.tar.gz;
cd $SFT_DIR/slepc-${SLEPC_VERSION};
export SLEPC_DIR=$(pwd);
./configure --prefix=${PREFIX}/slepc-${SLEPC_VERSION};
make SLEPC_DIR=${SLEPC_DIR} PETSC_DIR=${PETSC_DIR};
make SLEPC_DIR=${SLEPC_DIR} PETSC_DIR=${PETSC_DIR} install;
export SLEPC_DIR=${PREFIX}/slepc-${SLEPC_VERSION};
make SLEPC_DIR=${SLEPC_DIR} PETSC_DIR=${PETSC_DIR} PETSC_ARCH="" test;
# install slepc4py
# http://slepc.upv.es/slepc4py-current/docs/usrman/install.html :
cd $SFT_DIR;
url="https://bitbucket.org/slepc/slepc4py/\
downloads/slepc4py-${SLEPC4PY_VERSION}.tar.gz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget $url;
tar -xzvf slepc4py-${SLEPC4PY_VERSION}.tar.gz;
rm slepc4py-${SLEPC4PY_VERSION}.tar.gz;
cd $SFT_DIR/slepc4py-${SLEPC4PY_VERSION};
pip install . -v;
}function install_fenics()
{
# install dolfin dependencies :
pip install fenics${PYPI_FENICS_VERSION} -v;
# install dolfin :
cd $SFT_DIR;
git clone https://bitbucket.org/fenics-project/dolfin.git;
cd dolfin;
git checkout ${DOLFIN_VERSION};
rm -rf $SFT_DIR/dolfin/build;
mkdir $SFT_DIR/dolfin/build;
cd $SFT_DIR/dolfin/build;
cmake -D PYTHON_EXECUTABLE:FILEPATH=$(which python) \
-D BLAS_LIBRARIES=${OPENBLAS_DIR}/lib/libopenblas.a \
-D BLAS_LINKER_FLAGS="-I${OPENBLAS_DIR}/include" \
-D LAPACK_LIBRARIES==${OPENBLAS_DIR}/lib/libopenblas.a \
-D LAPACK_LINKER_FLAGS="-I${OPENBLAS_DIR}/include" \
-D SLEPC_INCLUDE_DIRS=${SLEPC_DIR}/include \
-D PETSC_INCLUDE_DIRS=${PETSC_DIR}/include \
-D SWIG_EXECUTABLE=${SWIG_DIR}/bin/swig \
-D BOOST_ROOT=${BOOST_DIR} \
-D HDF5_ROOT=${HDF5_DIR} \
-D BOOST_LIBRARYDIR=${BOOST_DIR}/lib \
-D EIGEN3_INCLUDE_DIR=${EIGEN_DIR}/include/eigen3 \
-D DOLFIN_USE_PYTHON3=false \
-D DOLFIN_ENABLE_HDF5=true \
-D DOLFIN_ENABLE_MPI=true \
-D DOLFIN_ENABLE_DOCS=true \
-D DOLFIN_ENABLE_SPHINX=true \
-D DOLFIN_SKIP_BUILD_TESTS=false \
-D CMAKE_CXX_FLAGS="-O2" \
-D CMAKE_C_FLAGS="-O2" \
-D CMAKE_C_COMPILER=mpicc \
-D CMAKE_CXX_COMPILER=mpicxx \
-D CMAKE_INSTALL_PREFIX=${DOLFIN_DIR} ..;
make -j ${BUILD_THREADS};
make install;
# ensure that dolfin is in all paths :
source ${DOLFIN_DIR}/share/dolfin/dolfin.conf;
# install mshr :
cd $SFT_DIR;
git clone https://bitbucket.org/fenics-project/mshr.git;
cd $SFT_DIR/mshr;
git checkout ${MSHR_VERSION};
rm -rf $SFT_DIR/mshr/build;
mkdir $SFT_DIR/mshr/build;
cd $SFT_DIR/mshr/build;
cmake -D EIGEN3_INCLUDE_DIR=${EIGEN_DIR}/include/eigen3 \
-D SWIG_EXECUTABLE=${SWIG_DIR}/bin/swig \
-D CMAKE_CXX_FLAGS="-O2" \
-D CMAKE_C_FLAGS="-O2" \
-D CMAKE_C_COMPILER=mpicc \
-D CMAKE_CXX_COMPILER=mpicxx \
-D CMAKE_INSTALL_PREFIX=${DOLFIN_DIR} ..;
make -j ${BUILD_THREADS};
make install;
}HSL:
function install_hsl()
{
mkdir -p ${HSL_DIR};
tar -xzf /path/to/coinhsl-linux-x86_64-2015.06.23.tar.gz \
-C ${HSL_DIR} \
--strip-components 1;
}function install_ipopt()
{
# first, build ipopt :
# NOTE: remember to copy hsl to $PREFIX/hsl :
cd $SFT_DIR;
url="https://www.coin-or.org/download/source/Ipopt/\
Ipopt-${IPOPT_VERSION}.tgz";
url=$(tr -d ' ' <<< "$url"); # remove spaces to fit the url within 80 chr
wget -nc $url -O $SFT_DIR/ipopt-${IPOPT_VERSION}.tgz;
mkdir -p $SFT_DIR/ipopt-${IPOPT_VERSION};
tar -xvf $SFT_DIR/ipopt-${IPOPT_VERSION}.tgz \
-C $SFT_DIR/ipopt-${IPOPT_VERSION} \
--strip-components 1;
rm $SFT_DIR/ipopt-${IPOPT_VERSION}.tgz;
cd $SFT_DIR/ipopt-${IPOPT_VERSION};
rm -rf $SFT_DIR/ipopt-${IPOPT_VERSION}/build;
mkdir $SFT_DIR/ipopt-${IPOPT_VERSION}/build;
cd $SFT_DIR/ipopt-${IPOPT_VERSION}/build;
../configure --prefix=${IPOPT_DIR} \
--enable-shared \
--enable-debug \
--with-hsl-lib="-L${HSL_DIR}/lib -lcoinhsl -lmetis" \
--with-hsl-incdir="${HSL_DIR}/include" \
--with-metis-lib="-Wl,-rpath,${PETSC_DIR}/lib \
-L${PETSC_DIR}/lib -lmetis" \
--with-metis-incdir="${PETSC_DIR}/include -I/usr/include/mpi" \
--with-blas-lib=${OPENBLAS_DIR}/lib/libopenblas.a \
--with-blas-incdir=${OPENBLAS_DIR}/include \
--with-lapack-lib=${OPENBLAS_DIR}/lib/libopenblas.a \
--with-lapack-incdir=${OPENBLAS_DIR}/include \
F77=mpifort \
CC=mpicc \
CXX=mpicxx;
make -j ${BUILD_THREADS};
make test;
make install;
# pyipopt :
cd $SFT_DIR;
git clone git@github.com:pf4d/pyipopt.git;
cd $SFT_DIR/pyipopt;
git checkout openblas; # I created this just for you.
# add the additional include directories for our installation :
sed -i "s#library_dirs=\[IPOPT_LIB\]#library_dirs=[IPOPT_LIB, '${PETSC_DIR}/lib', '${HSL_DIR}/lib', '${OPENBLAS_DIR}/lib']#g" setup.py;
sed -i "s#include_dirs=\[numpy_include, IPOPT_INC\]#include_dirs=[numpy_include, IPOPT_INC, '${PETSC_DIR}/include', '${HSL_DIR}/include', '${OPENBLAS_DIR}/include']#g" setup.py;
python setup.py build;
pip install . -v;
}function install_dolfin_adjoint()
{
# install libadjoint :
cd $SFT_DIR;
git clone https://bitbucket.org/dolfin-adjoint/libadjoint;
cd $SFT_DIR/libadjoint;
git checkout libadjoint-${DOLFIN_ADJOINT_VERSION};
rm -rf $SFT_DIR/libadjoint/build;
mkdir $SFT_DIR/libadjoint/build;
cd $SFT_DIR/libadjoint/build;
cmake -D PYTHON_EXECUTABLE:FILEPATH=$(which python) \
-D CMAKE_CXX_FLAGS="-O2" \
-D CMAKE_C_FLAGS="-O2" \
-D CMAKE_C_COMPILER=mpicc \
-D CMAKE_CXX_COMPILER=mpicxx \
-D CMAKE_INSTALL_PREFIX=${LIBADJOINT_DIR} ..;
make;
make install;
# dolfin_adjoint :
cd $SFT_DIR;
git clone https://bitbucket.org/dolfin-adjoint/dolfin-adjoint
cd $SFT_DIR/dolfin-adjoint;
git checkout dolfin-adjoint-${DOLFIN_ADJOINT_VERSION};
pip install . -v;
}function install_basemap()
{
cd $SFT_DIR;
git clone https://github.com/matplotlib/basemap.git;
cd $SFT_DIR/basemap;
pip install . -v;
}Gmsh:
function install_gmsh()
{
# install gmsh :
cd $SFT_DIR
git clone https://gitlab.onelab.info/gmsh/gmsh.git;
rm -rf $SFT_DIR/gmsh/build;
mkdir $SFT_DIR/gmsh/build;
cd $SFT_DIR/gmsh/build;
cmake -D BLAS_LAPACK_LIBRARIES="${OPENBLAS_DIR}/lib/libopenblas.so" \
-D ENABLE_WRAP_PYTHON=ON \
-D ENABLE_FLTK=ON \
-D ENABLE_PRIVATE_API=ON \
-D SWIG_EXECUTABLE=${SWIG_DIR}/bin/swig \
-D PYTHON_EXECUTABLE:FILEPATH=$(which python) \
-D ENABLE_PETSC=OFF \
-D ENABLE_SLEPC=OFF \
-D ENABLE_PETSC4PY=OFF \
-D ENABLE_MPI=ON \
-D CMAKE_C_COMPILER=mpicc \
-D CMAKE_CXX_COMPILER=mpicxx \
-D CMAKE_Fortran_COMPILER=mpifort \
-D CMAKE_INSTALL_PREFIX=${GMSH_DIR} ..;
make -j ${BUILD_THREADS};
make install;
}function install_cslvr()
{
# cslvr dependencies (tifffile requires numpy==1.14 which is incompatible
# with fenics, so ignore its dependencies) :
pip install tifffile --no-deps;
pip install pyproj termcolor colored shapely futures netcdf4 image;
# download cslvr source :
cd $SFT_DIR;
git clone git@github.com:pf4d/cslvr.git;
export PYTHONPATH="$SFT_DIR/cslvr:$PYTHONPATH"
}There, all done!
Now, your $PREFIX directory will contain the software
$ ls $PREFIX
boost-1.67.0 gmsh libadjoint-2017.2.0 python-2.7.15
cmake-3.11.1 hdf5-1.10.2 openblas-0.2.20 slepc-3.8.2
dolfin-2017.2.0.post0 hsl petsc-3.8.3 swig-3.0.12
eigen-3.3.4 ipopt-3.12.9 pybind11-2.2.1Hope this helps! :]
tags: