README.md

CoRNErS

Containerization of Revised NEMO-ERSEM Employing Singularity (CoRNErS)

The aim is to build a shippable container of a physical ocean model (NEMO) coupled with a biogeochemical model (ERSEM). Ideally, only input data (SeTTe) and output specification (XIOS) are needed to start a full-fledged ocean circulation model (preferably on any HPC you get your hands on).

• the basis for these scripts comes from NOC-MSM/CoNeS and pmlmodelling/NEMO-container
• changes for recent model versions from J Mak NEMO notes
• ERSEM PR version from myself; base version from pmlmodelling/ersem

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Repo containing instructions for creating a singularity container for NEMO-ERSEM. The setup is based heavily on the CoNES repo.

Setup

To create a singularity container, please follow the steps below:

1. Install Docker on host system and create singularity executable with alias singularity='docker run --privileged -it --rm --mount type=bind,source=${PWD},target=/home/singularity quay.io/singularity/singularity:v3.7.3-slim'
   • I hard-coded the alias into the ~/.bashrc file on my WSL
2. Clone and compress NEMO-ERSEM and XIOS folders, this can be done via bash initial-clone-repo.sh.
3. Run singularity build commands
   1. Run singularity build /home/singularity/baseOS.sif /home/singularity/baseOS.def
   2. Run singularity build /home/singularity/fabm.sif /home/singularity/fabm.def
   3. Run singularity build /home/singularity/xios.sif /home/singularity/xios.def
   4. Run singularity build /home/singularity/nemo.sif /home/singularity/nemo.def
4. The next steps could include:
   1. ship containers to HPC
   2. get input data from SETTE
   3. look into XIOS settings to organize the desired model output
   4. run

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NOTE

Make sure that when you build the sif files, you have bound the correct folders to your container.

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