Compile FreeSurfer on ppc64.
Using the docker container in this repo, which compiles itk 4.13 from source and mostly following along here with minor modifications to the FreeSurfer dev branch which
- disable the compilation of
mri_watershed
- this is the only binary that includes
affine.hpp
which seems hard coded to x86
- this is the only binary that includes
- diabled staticlly linking of fortran binaries
- hard coded for now, ideally this would be a cmake option that can be set independently of architecture
make
It gets tagged as fs-src
mkdir ~/fs
cd ~/fs
mkdir bin
git clone [email protected]:pwighton/freesurfer.git
cd freesurfer
git checkout 20191115-ppc64
TODO: get the Freesurfer git annex data (this will compile and install, recon-all wont run without it.
docker run -it --rm -v ~/fs:/fs fs-src /bin/bash
Then build FreeSurfer. Might have to tweak:
-DGFORTRAN_LIBRARIES="/usr/lib/gcc/ppc64le-redhat-linux/4.8.2/libgfortran.so"
cd /fs/freesurfer
rm -f ./CMakeCache.txt
cmake . \
-DBUILD_GUIS=OFF \
-DMINIMAL=ON \
-DMAKE_BUILD_TYPE=Release \
-DINSTALL_PYTHON_DEPENDENCIES=OFF \
-DDISTRIBUTE_FSPYTHON=OFF \
-DCMAKE_INSTALL_PREFIX="/fs/bin" \
-DFS_PACKAGES_DIR="/usr" \
-DPPC64=ON \
-DCMAKE_CXX_FLAGS="-DPPC64" \
-DCMAKE_C_FLAGS="-DPPC64" \
-DGFORTRAN_LIBRARIES="/usr/lib/gcc/ppc64le-redhat-linux/4.8.2/libgfortran.so"
make -j 4
make install