HPC clusters installation¶
These instructions outline a few issues specific to high-performance computing (HPC) systems.
Most HPC clusters will run some flavour of GNU/Linux and hence a cluster administrator should be able to follow the steps outlined to Building MRtrix3 from source. 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However, it is not uncommon for HPC systems to run stable, and hence relatively old distributions, with outdated dependencies.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 <https://community.mrtrix.org/t/standalone-installation-on-linux/3549>. Alternatively, if you (and your sysadmin) are comfortable with installation of dependencies from source within your home directory, you can try the instructions suggested on the wiki section of the MRtrix3 community forum.
Most people would expect to be able to run
mrview on the server using
X11 forwarding. Unfortunately, this will not work without some effort.
The most up-to-date details on attempts to use
mrview in this way
can be found in the relevant Wiki entry
of the MRtrix3 community forum.
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
/etc/mrtrix.conf, and/or in each user’s home folder
~/.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 filesystem, 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
/tmpfolder 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.