HPC clusters installation

These instructions outline a few issues specific to high-performance computing (HPC) systems.

Installing MRtrix3

Most HPC clusters will run some flavour of GNU/Linux and hence a cluster administrator should be able to follow the steps outlined for a Linux installation. In particular, if your sysadmin is able to install the required dependencies (the preferred option), you should be able to subsequently Build MRtrix3.

However, it is not uncommon for HPC systems to run stable, and hence relatively old distributions, with outdated dependencies. This is particularly problematic since MRtrix3 relies on recent technologies (C++11, OpenGL 3.3), which are only available on recent distributions. There is therefore a good chance these dependencies simply cannot be installed (certainly not without a huge amount of effort on the part of your sysadmin). In such cases, one can instead attempt a Standalone installation on Linux. Alternatively, if you (and your sysadmin) are comfortable with installation of dependencies from source within your home directory, you can try the instructions below.

Installation of MRtrix3 and dependencies from source

The following instructions list the steps I used to compile MRtrix3 natively on a local HPC cluster. 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)

    The following 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 configure and 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/
    cd ../
  • Installing Eigen3

    wget http://bitbucket.org/eigen/eigen/get/3.2.8.tar.gz
    tar -xf 3.2.8.tar.gz
    mv eigen* eigen3/
  • Installing MRtrix3

    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 configure script.

    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.

Remote display

Most people would expect to be able to run mrview on the server using X11 forwarding. Unfortunately, this will not work without some effort - please refer to Display issues for details.


There are a number of parameters that can be set in the configuration file that are highly relevant in a HPC environment, particularly when the user’s home folder is stored over a network-based filesystem (as is often the case). The MRtrix3 configuration file is located either system-wide in /etc/mrtrix.conf, and/or in each user’s home folder in ~/.mrtrix.conf. Entries consist of key: value entries, one per line, stored as ASCII text.

  • NumberOfThreads (default: hardware concurrency, as reported by the system): by default, MRtrix3 will use as many threads as the system reports being able to run concurrently. You may want to change that number to a lower value, to prevent MRtrix3 from taking over the system entirely. This is particularly true if you anticipate many users running many MRtrix3 commands concurrently.
  • TmpFileDir (default: ‘/tmp’): any image data passed from one MRtrix3 command to the next using a Unix pipeline is actually stored in a temporary file, and its filename passed to the next command. While this is fine if the filesystem holding the temporary file is locally backed and large enough, it can cause significant slowdown and bottlenecks if it resides on a networked filesystems, as the temporary file will most likely need to be transferred in its entirety over the network and back again. Also, if the filesystem is too small, MRtrix3 commands may abort when processing large files. In general, the /tmp folder is likely to be the most appropriate (especially if mounted as tmpfs). If however it is not locally mounted, or too small, you may want to set this folder to some other more suitable location.
  • TrackWriterBufferSize (default: 16777216). When writing out track files, MRtrix3 will buffer up the output and write out in chunks of 16MB, to limit the frequency of write() calls and the amount of IO requests. More importantly, when several instances of MRtrix3 are generating tracks concurrently and writing to the same filesystem, frequent small writes will result in massive fragmentation of the output files. By setting a large buffer size, the chances of writes being concurrent is reduced drastically, and the output files are much less likely to be badly fragmented. Note that fragmentation can seriously affect the performance of subsequent commands that need to read affected data. Depending on the type of operations performed, it may be beneficial to use larger buffer sizes, for example 256MB. Note that larger numbers imply greater RAM usage to hold the data prior to write-out, so it is best to keep this much smaller than the total RAM capacity.