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 ~/.bashrc):

. /axiom2/projects/software/arch/linux-xenial-xerus/lmod/7.6.5/lmod/lmod/init/bash
module use /axiom2/projects/software/arch/linux-xenial-xerus/modulefiles/

A number of modules are loaded by default through the "stdenv" module:


$ module list
Currently Loaded Modules:
  1) OCCIviewer              6) pyminc/0.51                11) R/3.4.1
  2) minc-toolkit/1.9.15     7) minc-stuffs/0.1.21         12) Fiji/1.51n
  3) python/3.6.2            8) pydpiper/2.0.9             13) slurm/17.02.7
  4) parallel/20170822       9) tagtoxfm_bspline/f5639af3  14) brain-view2/0.1.2
  5) qbatch/1.0.1-318bdd42  10) MICe-lab/0.15              15) stdenv/1.0.1

To find additional modules to load, do 'module avail' or 'module spider'.  You can give these an argument to limit your search, e.g.:

module avail pydpiper

shows (October 2017):

------------------- /axiom2/projects/software/arch/linux-xenial-xerus/modulefiles --------------------
   pydpiper/2.0.8    pydpiper/2.0.9 (L,D)
  Where:
   L:  Module is loaded
   D:  Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". # 

which is fairly self-explanatory.


Loading 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 load nipy  # or nipy/0.4.1 or ...

(Try also 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:

twolevel_model_building.py ...

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.

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