Using Compute Canada / ACENET HPC

This guide explains how to connect to the Digital Research Alliance of Canada (Compute Canada) or ACENET clusters, create a working directory in scratch, transfer files with Globus, and submit jobs using SLURM.

1. Connect to the HPC via SSH

Determine which cluster to use (examples):
- Graham: graham.computecanada.ca
- Cedar: cedar.computecanada.ca
- Beluga: beluga.computecanada.ca
- Niagara: niagara.scinet.utoronto.ca
- ACENET: login1.acenet.ca
Open a terminal and connect via SSH:
```
ssh username@graham.computecanada.ca
```
When prompted, confirm the host fingerprint and enter your password.

2. Create a Folder in Scratch

Your $SCRATCH directory is a temporary workspace for large data and computations. It is purged after 60 days of inactivity.

After logging in:

cd $SCRATCH
mkdir my_project
cd my_project

Confirm your path:

pwd
# Example output: /scratch/username/my_project

3. Install and Use Globus for File Transfers

Globus is a fast, reliable tool for large file transfers. It requires a small local agent called Globus Connect Personal.

Install Globus Connect Personal

Linux:

wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz
tar xzf globusconnectpersonal-latest.tgz
cd globusconnectpersonal*
./globusconnectpersonal -setup

macOS:
Download and install from: https://www.globus.org/globus-connect-personal
Windows:
Download the installer from the same link and follow the setup wizard.

After installation, your local computer will appear as a Globus endpoint.

Transfer Files

Visit https://app.globus.org and log in using Compute Canada credentials.
In the web app, choose two endpoints:
- Source: Your local computer or institutional storage.
- Destination: Your HPC endpoint (for example, Compute Canada Graham Scratch).
Navigate to your target scratch folder (/scratch/username/my_project).
Select files and click Start Transfer.

Globus will handle transfers asynchronously and resume interrupted transfers automatically.

4. Submit Jobs to ACENET with SLURM

Job submissions use the SLURM scheduler. Create a batch file describing your job resources and commands.

Example job script (`job.slurm`)

#!/bin/bash
#SBATCH --job-name=my_analysis
#SBATCH --account=def-yourprof
#SBATCH --time=2:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --mem=8G
#SBATCH --output=output_%j.log

module load python/3.11
source ~/myenv/bin/activate

python my_script.py

Submit and Monitor Jobs

sbatch job.slurm        # Submit job
squeue -u username      # Check status
scancel job_id          # Cancel job

View Results

After completion, check output logs:

less output_<jobid>.log

5. Useful Commands

module avail             # List available software modules
module load python/3.11  # Load a module
df -h $SCRATCH           # Check scratch usage
quota -s                 # Check your disk quota

6. References

Alliance Docs: https://docs.alliancecan.ca/wiki/Technical_documentation
ACENET Training: https://www.ace-net.ca/training/
Globus Setup: https://www.globus.org/globus-connect-personal

3.5 KiB Raw Blame History