Install Berkeley Advanced Reconstruction Toolbox without admin rights on a CentOS machine.

bart_centos_installer.bash

#!/bin/bash
# Time-stamp: <2017-07-19 15:06:39 dangom>
# Script for installing BART and dependencies from source on a CentOS machine without admin rights.

# Steps:
# 1. Build OpenBLAS from source to enable support for LAPACKE C API.
# 2. Build FFTW3 from source to enable float32 support (fftw defaults to double precision. BART doesn't)
# 3. Link against Matlab2016, because something changed in Matlab2017 and the BART build breaks.
# 4. Download Cmake >= 3 since cluster ships with old cmake 2.8

# Prerequisites: - gcc
#                - wget
# Piggybackable libs already installed in our cluster, so we don't build from source.
#                - libpng-devel


# On error, exit.
set -e
module unload rsi

# Set a target installation directory.
target_dir="$HOME/bin/bart"


# Define the versions we want (where we expect things to work)
fftw3_version="3.3.6-pl2"
openblas_version="0.2.19"
bart_version="0.4.01"
cmake_version="3.8.2"
matlab_version="R2016a"


fftw3_name="fftw-${fftw3_version}"
openblas_name="v${openblas_version}"
bart_name="v${bart_version}"
cmake_name="cmake-${cmake_version}-Linux-x86_64"


matlab_root="/opt/matlab/${matlab_version}"
matlab_glnxa="${matlab_root}/bin/glnxa64"
matlab_config="-DMATLAB_ENG_LIBRARY=${matlab_glnxa}/libeng.so -DMATLAB_INCLUDE_DIR=${matlab_root}/extern/include -DMATLAB_MAT_LIBRARY=${matlab_glnxa}/libmat.so -DMATLAB_MEX_LIBRARY=${matlab_glnxa}/libmex.so -DMATLAB_MX_LIBRARY=${matlab_glnxa}/libmx.so -DMATLAB_ROOT=${matlab_root}"

# Always be kind.
# Always be kind.
currdir=$(pwd)
builddir=$(mktemp -d)
echo ""
echo ""
echo "Building will take place under $builddir"
echo ""
echo ""
cd $builddir

# Build OpenBLAS
wget -O openblas_${openblas_name}.tar.gz https://github.com/xianyi/OpenBLAS/archive/${openblas_name}.tar.gz
tar xvzf openblas_${openblas_name}.tar.gz && cd OpenBLAS-${openblas_version}
make all
make netlib
make PREFIX=${target_dir}/deps/openblas install
cd -

# Build FFTW3
wget -O fftw_${fftw3_name}.tar.gz http://fftw.org/${fftw3_name}.tar.gz
tar xvzf fftw_${fftw3_name}.tar.gz && cd ${fftw3_name}
CFLAGS="-fPIC" CPPFLAGS="-fPIC" ./configure --prefix=$target_dir/deps/fftw --enable-float --enable-threads # Note the tricky flag: --enable-float
make && make install
cd -

# Download cmake.
wget -O cmake_${cmake_version}.tar.gz https://cmake.org/files/v3.8/${cmake_name}.tar.gz
tar xvzf cmake_${cmake_version}.tar.gz

# Finally, build BART and test it.
wget -O bart_${bart_name}.tar.gz https://github.com/mrirecon/bart/archive/${bart_name}.tar.gz
tar xvzf bart_${bart_name}.tar.gz && cd bart-${bart_version}
mkdir build && cd build

# Compile and link BART against our downloaded dependencies.
# Also make sure it'll use the fftw includes that we downloaded, not the system ones, if available.
CFLAGS="-I${target_dir}/deps/fftw/include -fPIC" $builddir/${cmake_name}/bin/cmake -DCMAKE_INSTALL_PREFIX:PATH=${target_dir} -DLINALG_VENDOR=OpenBLAS -DOpenBLAS_DIR=${target_dir}/deps/openblas ${matlab_config} -DFFTWF_LIB=${target_dir}/deps/fftw/lib/libfftw3f.a -DFFTWF_THREADS_LIB=${target_dir}/deps/fftw/lib/libfftw3f_threads.a ..

sed --in-place 's/bin\/glnxa64 /bin\/glnxa64 -L\/opt\/matlab\/R2016a\/sys\/os\/glnxa64 /' CMakeFiles/mat2cfl.dir/link.txt
sed --in-place 's/glnxa64:/glnxa64:\/opt\/matlab\/R2016a\/sys\/os\/glnxa64:/' CMakeFiles/mat2cfl.dir/link.txt
sed --in-place 's/glnxa64:/glnxa64:\/opt\/matlab\/R2016a\/sys\/os\/glnxa64:/' cmake_install.cmake


make && make test
if [ $? -eq 0 ]; then # Only install if make test returns success.
    make install
    cp mat2cfl ${target_dir}/bin/
    cp -r ../matlab ../startup.m ${target_dir}/bin/
    # Run benchmarks.
    ${target_dir}/bin/bench

    echo "BART successfully installed under ${target_dir}"
    echo "You may add ${target_dir}/bin to your PATH to have BART always available for you!!"
    echo ""
else
    echo "BART installation failed. Sorry for that. Fix the installation script and try again! Good luck!"
fi

cd ${currdir}