Ferret (Apptainer)

An installation of PyFerret is provided on the NHR system in /sw/container/jupyterhub/ferret.sif

The container can be used on Jupyter HPC for usage inside of iPython notebooks:

%load_ext ferretmagic

%%ferret

cancel data/all
use levitus_climatology
show data

%%ferret -q

shade temp[k=1]; go land

It is also possible to connect to the HPC cluster with X11 forwarding enabled (ssh -X) and start ferret directly:

Note

Note that the $WORK directory currently differs between Emmy Phase 2 and Emmy Phase 3. If your files are on the scratch-emmy WORK filesystem then you can use the Phase 2 large96:shared partition instead of the Phase 3 large96s:shared partition.

srun --partition large96s:shared -c 1 --x11 --pty bash  -c "module load apptainer squashfuse; apptainer run --bind $WORK,$TMPDIR /sw/container/jupyterhub/ferret.sif"

If you want to execute ferret with particular command line arguments you can also first start a shell inside the container:

srun --partition large96s:shared -c 1 --x11 --pty bash  -c "module load apptainer squashfuse; apptainer exec --bind $WORK,$TMPDIR /sw/container/jupyterhub/ferret.sif /bin/bash"