Compute Canada - PaulBautin/tpil_dmri GitHub Wiki

First you must connect to compute canada with command ssh [email protected]. To not type full command each time you can define a bash alias in $HOME/.bashrc : alias graham="ssh [email protected]"

the first step is to make sure you have the right python version installed

module avail python

for example you can choose (python>3.6) ex: module load python/3.7.4

To enable the use of Singularity on CC systems: module load singularity

With each version of python CC provides the virtualenv tool that allows users to create virtual environments within which you can easily install Python packages.

To create a virtual environment, make sure you have selected a Python version with module load python as shown above in section Loading a Python module. If you expect to use any of the packages listed in section SciPy stack above, also run module load scipy-stack. Then enter the following command, where ENV is the name of the directory for your new environment: virtualenv --no-download ENV

Once the virtual environment has been created, it must be activated: source ENV/bin/activate

You should also upgrade pip in the environment: pip install --no-index --upgrade pip

To exit the virtual environment, simply enter the command deactivate: deactivate

Globus is the preferred tool for transferring data between Compute Canada systems, and if it can be used, it should.

To launch the sbatch: sbatch -A <def-user> <script_name>.sh

To check if it has been launched: squeue -u <USER>

To quit the cluster: exit

To analyse disk usage, use diskusage_report to see if you are at or over your quota: diskusage_report

To request interactive processors, use: salloc --time=DD-HH:MM --mem-per-cpu=<number>G --ntasks=<number> --account=<your_account>

if [ -z "${SLURM_CPUS_PER_TASK+x}" ]; then
    export OMP_NUM_THREADS=1
else
    export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
fi