The following instructions list the steps I used to compile MRtrix3 natively on a local HPC cluster or other systems where you may not have admin access. For build instructions on your local machine, please refer to the documentation pages.
Replicating these instructions line-for-line may not work on another system; I’m just providing these instructions here in case they help to point somebody in the right direction, or encourage users to try a native installation rather than resorting to transferring binaries compiled on another system.
Installing a C++11-compliant g++ from source
Note that during this process, there will be three
gcc directories created: one is for the source code (including that of some prerequisites), one is for compilation objects, and one is the target of the final installation (since you almost certainly won’t be able to install this version of
gcc over the top of whatever is provided by the HPC sysadmin).
svn co svn://gcc.gnu.org/svn/gcc/branches/gcc-5-branch gcc_src/
(Don’t checkout the trunk
gcc code; MRtrix3 will currently not compile with it)
gcc dependencies will be built as part of the
gcc compilation, provided that they are placed in the correct location within the
gcc source directory.
wget https://gmplib.org/download/gmp/gmp-6.1.1.tar.bz2 tar -xf gmp-6.1.1.tar.bz2 mv gmp-6.1.1/ gcc_src/gmp/ wget ftp://ftp.gnu.org/gnu/mpc/mpc-1.0.3.tar.gz tar -xf mpc-1.0.3.tar.gz mv mpc-1.0.3/ gcc_src/mpc/ wget http://www.mpfr.org/mpfr-current/mpfr-3.1.4.tar.gz tar -xf mpfr-3.1.4.tar.gz mv mpfr-3.1.4/ gcc_src/mpfr/
With the following, the
configure script (which resides within the
gcc_src directory in this example) must not be executed within that directory; rather, it must be executed from an alternative directory, which will form the target location for the compilation object files. The target installation directory (set using the
--prefix option below) must be a location for which you have write access; most likely somewhere in your home directory.
mkdir gcc_obj; cd gcc_obj/ ../gcc_src/configure --prefix=/path/to/installed/gcc --disable-multilib make && make install
Installing Python3 from source
My local HPC cluster provided Python version 2.6.6, which was not adequate to successfully run the
build scripts in MRtrix3. Therefore this necessitated a manual Python install – a newer version of Python 2 would also work, but downloading Python 3 should result in less ambiguity about which version is being run.
wget https://www.python.org/ftp/python/3.5.2/Python-3.5.2.tgz tar -xf Python-3.5.2.tgz mv Python-3.5.2/ python3/ cd python3/ ./configure ./make cd ../
wget http://bitbucket.org/eigen/eigen/get/3.2.8.tar.gz tar -xf 3.2.8.tar.gz mv eigen* eigen3/
Personally I prefer to install a no-GUI version of MRtrix3 on high-performance computing systems, and transfer files to my local system if I need to view anything; so I use the
-nogui flag for the
git clone https://github.com/MRtrix3/mrtrix3.git cd mrtrix3/ export CXX=/path/to/installed/gcc/bin/g++ export EIGEN_CFLAGS="-isystem /path/to/eigen3/" export LD_LIBRARY_PATH="/path/to/installed/gcc/lib64:$LD_LIBRARY_PATH" ../python3/python configure -nogui ../python3/python build
If you encounter issues when running MRtrix3 commands that resemble the following:
mrconvert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mrconvert)
This indicates that the shared library of the compiler version installed on the cluster is being found before that of the C++11-compliant compiler installed manually. The
lib64/ directory of the manually-installed
gcc version must appear before that of the version installed on the cluster in the
LD_LIBRARY_PATH environment variable.