CRIUGMΒΆ

CPU ClustersΒΆ

elm.criugm.qc.ca (64 cores)
jacaranda.criugm.qc.ca (24 cores)

Note: to run your processings, go to /scratch, it is a much faster disk than the disk where your home directory is, however it is only used for temp files (i.e. clean after use).

Transferring Data from JACARANDAΒΆ

When located in your home directory , you can compress a scan (example myelin_06_rescan) with the following command

tar -zcvhf myelin_06_rescan.tar.gz /unf/dicoms/by_groups/neuropoly/dev/myelin_mapping/myelin_06_rescan/

Once the .tar.gz file has been created, you can download it on your computer using scp or using filezilla (setup connection to sftp server).

Using JACARANDA and ELMΒΆ

JACARANDA and ELM use Sun grid engine.

  • Open a Terminal and run: ssh <username>@jacaranda.criugm.qc.ca

Create Job ScriptΒΆ

Note

Example

#!/bin/bash
#$ -V  # To load environment variables
 
cd /scratch/julien
 
echo "Script started at:"
date
 
# Launch script
sct_testing
 
echo "Script ended at:"
date

* Submit job: `qsub my_job.pbs`
* To see all the jobs currently running type: `qstat`
* use β€œ/scratch” \(faster\)

### Tips & Tricks Elm

Connect to Elm using:

```bash
ssh -Y username@elm.criugm.qc.ca

Copy your files using scp to Elm from your computer:

scp -r /src username@elm.criugm.qc.ca:neuropoly/<GRAMES_USERNAME>

For a faster processing move your data on elm from home to scratch:

cp -r source/ /scratch/julien/neuropoly/<GRAMES_USERNAME>

Activate MATLAB on elm:

module load matlab
matlab

MATLAB - add to path with subfolders:

addpath(genpath('/your_path'))