Cluster architecture

Role Hostname CPU (Thread x GHz) RAM (GB) GPU/OpenGL
login psyclogin 16 x 2.1 64 Quadro M5000
master pscmatlab 4 x 3.06 32 No
worker psycmri01 10 x 3.06 32 No
worker psycmri02 10 x 3.06 32 No

Logical architecture

Different nodes have different roles within the cluster:

Login node

As its name suggests, Login node is the entry point to the cluster either via an interactive (VNC) session (How to login) or for file transfer via SFTP (How to access storage). This machine can be used for writing scripts, viewing and editing files, transferring data, etc. You can also submit jobs of your full-fledged pipeline to the scheduler from here.

You can test and debug your scripts in this interactive session locally either on a very small number of subject or running a subset of your pipeline; but :!: you should never run the whole full-fledged pipeline on the Login node locally, because it can clog up the node and incapacitate other users.

Master node

The Master node runs the scheduler that manages the workload across the Worker nodes. Normally, you do not access it.

Worker nodes

Worker nodes are the main computing resources of the cluster. By default, you never access them directly; instead jobs are submitted via the scheduler running on the Master node.

Storage spaces

You have two locations to store items and both of them are available from each node. From your desktop, you can copy files to and from it using an SFTP client program (see Requirements).

Home space

/home/[user name], Desktop icon “[user name]'s Home”

The Home space is private and visible only by you by default. Its main role is to store your configuration settings. You are supposed to use it only as an intermediate storage (e.g. Downloads), which should be transferred either to e.g. the Work space. Scripts you do not want to share may be stored here.
You should not carry out analysis here!

Work space

/MRIWork/MRIWork[PI's number] E.g.: /MRIWork/MRIWork02 for Kathy Rastle

The Work space is private and visible for your group by default. Here, you can store all the data, images, scripts, documents, etc you are working on.
You should carry out analysis also here.

  • If you are a PI, you can create folders for project(s) and give permission to your group members working on that project(s)
  • If you are not a PI, you need to ask your PI to create a folder for you and give you permission for that folder

Archive space

/MRIArchive/MRIWork[PI's number] E.g.: /MRIArchive/MRIWork02 for Kathy Rastle

The Archive space is private and visible for your group by default. Here, you can store all the data, images, scripts, documents, etc you are not working on any more.
You should not carry out analysis here!
File and folder management works in the same way as for Work space.

Software Extra Tools Version(s) Location Configuration (see also Customise shell environment)
MATLAB R2015b
R2018a
R2018b
/usr/local/apps/matlab
source /usr/local/apps/psycapps/config/matlab_bash

(use option “help” for more info)

automaticanalysis 5.4.0 /usr/local/apps/psycapps/automaticanalysis Add required version to MATLAB path
CmapTools 6.0.3 /usr/local/apps/psycapps/CmapTools/CmapTools Not required
conda (python management) 3 (with python 2.7.14 and 3.6.3) /usr/local/apps/psycapps/conda
source /usr/local/apps/psycapps/config/conda_bash

(use option “help” for more info)

CONN 17.f /usr/local/apps/psycapps/CONN
CoSMoMVPA 1.1.0 /usr/local/apps/psycapps/CoSMoMVPA
FreeSurfer 6.0.0 /usr/local/apps/psycapps/freesurfer
source /usr/local/apps/psycapps/config/freesurfer_bash

(use option “help” for more info)

FSL 5.0.9
5.0.10
6.0.0
/usr/local/apps/psycapps/fsl
source /usr/local/apps/psycapps/config/fsl_bash

(use option “help” for more info)

FIX 1.065 /usr/local/apps/psycapps/fsl_utils/fix
FSLNets 0.6.3 /usr/local/apps/psycapps/fsl_utils/fslnets
ICA-AROMA 0.3 /usr/local/apps/psycapps/fsl_utils/ica-aroma
mricron /usr/local/apps/psycapps/mricron/mricron Not required
R 3.4.0 /usr/lib64/R Not required
rstudio 0.98.1103 /usr/local/apps/psycapps/rstudio/rstudio Not required
SPM SPM8
SPM12
SPM12 git (latest)
/usr/local/apps/psycapps/spm Add required version to MATLAB path
Anatomy Toolbox 2.2c /usr/local/apps/psycapps/spm_toolboxes/Anatomy
CAT12 1148
1355
/usr/local/apps/psycapps/spm_toolboxes/CAT12
GIFT 4.0b /usr/local/apps/psycapps/spm_toolboxes/GIFT
LI toolbox 1.3 /usr/local/apps/psycapps/spm_toolboxes/LI_toolbox
rWLS 4.0 /usr/local/apps/psycapps/spm_toolboxes/rWLS
TFCE 121 /usr/local/apps/psycapps/spm_toolboxes/TFCE
marsbar 0.44 /usr/local/apps/psycapps/spm_toolboxes/marsbar

Installation

:!: For members of psycadm group only :!:

Software not requiring system level changes can be installed/copied in /usr/local/apps/psycapps. If you install something here, please, run this script on the main installation folder to set group ownership and permissions:

 /usr/local/apps/psycapps/bin/set_permission.sh <directory> 

The script works recursively, so it also takes care of subfolders.


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