This page overlaps substantially with the page on the module system at MICe (here). As such, non-Pydpiper-specific information here should be merged into that page and this page should probably be deleted.
The MICe machines use the `lmod` software to provide versioned software through a series of "environment modules", which is really just a set of bash functions to automatically set certain paths and some helpful tools for managing these.
For a historical list of quarantines see this page: Registration Quarantines (deprecated)
The module system is enabled by default via
/etc/profile.d/mice_profile.sh as follows (you no longer need such lines in your
A number of modules are loaded by default through the "stdenv" module:
To find additional modules to load, do 'module avail' or 'module spider'. You can give these an argument to limit your search, e.g.:
shows (October 2017):
which is fairly self-explanatory.
python/3.x modules will overwrite your existing
$PYTHONPATH. (This means you might have to do some manual fiddling to use Python software from unusual locations - let me know if this occurs.)
To load, say, the nipy module:
module help, module list, module avail, module spider, module unload, module purge, etc.; if your shell is in a strange state it's often easiest (and safest!) to
module purge or launch a new shell instead.)
Run your PydPiper command as usual:
Note that the PydPiper module sets an environment variable
PYDPIPER_CONFIG_FILE with a bunch of defaults for memory, processors, timeouts, etc., so you generally don't need to concern yourself with these.