🖥 Computers @CRIUGM

🖥 Computers @CRIUGM#

Login#

To acess CRIUGM computer infrastructure you need a login. Ask Julien and he will redirect you to the right person to get a login.

CPU Clusters#

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 JACARANDA#

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 ELM#

JACARANDA and ELM use Sun grid engine.

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

Create Job Script#

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 “/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'))