adapt workflow for HPC using udocker / singularity

[backeb]

• [ ] clone repo to HPC, e.g. GRNET
• [x] test running the delft3dfm singularity container
• [ ] test running the delft3dfm docker container with udocker https://github.com/c-scale-community/workflow-coastal-hydrowaq/pull/52
• [ ] if udocker works, figure out how to make snakemake rules / make alternative Snakefile to run with udocker
• [ ] if udocker fails, add an if statement to run delft3fm rule to use singularity if compute_type is set to hpc in workflow/config.yml

cc @sebastian-luna-valero

[backeb]

Information about Deltares Docker and Singularity: https://publicwiki.deltares.nl/pages/viewpage.action?spaceKey=DSCMEET&title=Singularity+and+Docker+Containers+For+Delft3D+FM

[backeb]

SSH access to GRNET ARIS HPC: ssh -i ~/.ssh/id_rsa bbackeberg2@login03.aris.grnet.gr

[backeb]

First working on #46 to publish our docker containers.

[lorincmeszaros]

Steps to run on ARIS with Singularity:

• in the fm_model folder (where dimr.xml is present), place run_FM.sh

This points to the singularity container (in this case delft3dfm_2022.01)

• submit job with sbatch: run_all.sh