nemo.def

Bootstrap: localimage
From: fabm.sif

####
##
## Authors:      Michael Wathen, Plymouth Marine Laboratory <miwa@pml.ac.uk>
##
## Definition file for building NEMO Singularity Containers
##
#####

%files
    input_files/arch/nemo-arch/arch-singularity.fcm input_files/arch/nemo-arch/arch-singularity.fcm

%post
    git clone https://github.com/pmlmodelling/NEMO4.0-FABM.git nemo
    cd nemo
    cp /input_files/arch/nemo-arch/* /nemo/arch/PML

    echo "Compiling nemo AMM7 Config"
    ./makenemo -m singularity -r AMM7_FABM -j 8

    mkdir /opt/nemo
    mv /nemo/cfgs/AMM7_FABM/BLD/bin/nemo.exe /opt/nemo

    rm -rf xios
    rm -rf nemo
    # The above didnt seem to work so blanket chmod for time being 
    chmod -Rv 755 /opt

    # Clean up
    rm -rf /var/lib/apt/lists/* /var/lib/dpkg/info/*

%environment
    
    export LD_LIBRARY_PATH=/opt/hdf5/install/lib:$LD_LIBRARY_PATH

%runscript
    #!/bin/bash

    # This runscript will take 2 arguments: program to run (NEMO or XIOS), and an 
    # output directory. By default, the output directory will be the job id 
    # (passed using $SLURM_JOB_ID).    

    if ! [[ $1 == "nemo" || $1 == "xios" ]]    
    then
      echo "The program argument should be either 'nemo' or 'xios'"
      exit 1
    fi

    if [[ $1 == 'nemo' ]]
    then
        /opt/nemo/nemo.exe
    else
        /opt/xios/xios_server.exe
    fi

%labels
    Author miwa@pml.ac.uk

%help
    The definition file used to build XIOS:

    To build the container, run

        singularity build nemo.sif nemo.def