🖥 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.

VPN#

To reach the CRIUGM machines from outside the CRIUGM network, you need to be connected to the CRIUGM VPN (FortiGate SSL VPN). Use your CRIUGM username and password.

Setting

Value

VPN server

206.167.239.2

Port

443

VPN type

FortiGate (SSL VPN)

Trusted certificate (SHA256)

6864f5458ecef9e9896f8ae6f527681e0a4afc72bcb2c72fbe3feb65b85d85a3

Important

The gateway uses a self-signed certificate, so you need to pin it as trusted (with the SHA256 above). Do not enable “Trust all certs”.

You can use the official FortiClient VPN, but it asks for your credentials at every login. The open-source openfortivpn is a convenient alternative.

The connection is the same on Linux and macOS: the command-line config below works on both, only the installation and GUI options differ.

Install:

sudo apt install openfortivpn

GUI (optional): OpenFortiGUI can store your credentials so you don’t have to type them at each login. Create a new VPN with the settings in the table above:

  • VPN-Device: Fortigate

  • Check “Credentials” and fill in your username/password

  • Leave “Trust all Certs” unchecked and paste the SHA256 in “Trusted-Cert”

Install:

brew install openfortivpn

GUI (optional): you can try openfortivpn-connect, using the settings in the table above.

Command line (Linux and macOS): create a config file, e.g. ~/.config/openfortivpn/criugm.conf:

host = 206.167.239.2
port = 443
username = <CRIUGM_USERNAME>
trusted-cert = 6864f5458ecef9e9896f8ae6f527681e0a4afc72bcb2c72fbe3feb65b85d85a3

Then connect with (you will be prompted for your password):

sudo openfortivpn -c ~/.config/openfortivpn/criugm.conf

Once connected, you can ssh to the clusters below.

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/<GE_USERNAME>

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

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

Activate MATLAB on elm:

module load matlab
matlab

MATLAB - add to path with subfolders:

addpath(genpath('/your_path'))