Singularity.nemo

Bootstrap: localimage
From: nemo_baseOS.sif

####
##
## Authors:      James Harle, National Oceanography Centre <jdha@noc.ac.uk>
## Authors:      Chris Wood, EPCC, University of Edinburgh <c.wood@epcc.ed.ac.uk>
## Date:         2021-11-30
## Last updated: 2022-01-28
##
## Definition file for building NEMO/XIOS Singularity Containers using MPICH
##
#####

%files
    input_files/NEMO_in /input_files/NEMO_in
    input_files/MY_SRC.tar.gz /input_files/MY_SRC.tar.gz
    input_files/setup_nemo /input_files/setup_nemo
    input_files/arch/nemo/arch-singularity.fcm /input_files/arch/nemo/arch-singularity.fcm
    input_files/arch/xios/arch-singularity.fcm /input_files/arch/xios/arch-singularity.fcm
    input_files/arch/xios/arch-singularity.env /input_files/arch/xios/arch-singularity.env
    input_files/arch/xios/arch-singularity.path /input_files/arch/xios/arch-singularity.path

%post
    
    . /input_files/NEMO_in

    WORK_DIR=/nemo >> $SINGULARITY_ENVIRONMENT
    cd $WORK_DIR
    chown nemo:nemo -R $WORK_DIR

    PATH=$PATH:/opt/mpi/install/bin:/opt/hdf5/install/bin
    LD_LIBRARY_PATH=/opt/hdf5/install/lib:$LD_LIBRARY_PATH
   
    cd $WORK_DIR

    . /input_files/NEMO_in
   
    chmod u+x /input_files/setup_nemo 
    /input_files/setup_nemo -x /nemo -w /nemo -s /nemo/AMM7_lite -m singularity -v $NEMO_VERSION -c gnu

    cd /nemo/nemo/cfgs/NEMO/EXP00
    
    # Need to put in here if TOP include top namelist etc    
    ln -s ../../SHARED/namelist_ref namelist_ref
    ln -s ../../SHARED/namelist_ice_ref namelist_ice_ref
    ln -s ../../SHARED/grid_def_nemo.xml grid_def_nemo.xml
    ln -s ../../SHARED/field_def_nemo-oce.xml field_def_nemo-oce.xml
    ln -s ../../SHARED/field_def_nemo-ice.xml field_def_nemo-ice.xml
    ln -s ../../SHARED/domain_def_nemo.xml domain_def_nemo.xml
    ln -s ../../SHARED/axis_def_nemo.xml axis_def_nemo.xml
   
    cd $WORK_DIR
    
    mkdir /opt/nemo
    mv /nemo/nemo/cfgs/NEMO/EXP00/nemo /opt/nemo/

    mkdir /opt/xios
    mv /nemo/nemo/cfgs/NEMO/EXP00/xios_server.exe /opt/xios/xios

    # make everything we've built be owned by `nemo` 
    chown -Rv nemo:nemo /opt
    
    # minimal possible permissions: directories executable; binaries read + executable (need to be readable to that library headers can be read!); everything else only readable for g+o
    #chmod -Rv 644 /opt
    #find /opt -type d -print0 | xargs -0 chmod -v 511
    #find /opt -type f -exec file -i {} + | grep ":[^:]*binary[^:]*$" |  sed 's/^\(.*\):[^:]*$/\1/' | xargs chmod -v 555
    
    # The above didn't 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).    

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

    results_dir=$2

    if [[ -z $2 ]]
    then
      results_dir=$SLURM_JOB_ID
    fi

    if [[ -z $results_dir ]]
    then
        echo "Please supply an output directory"
        exit 1
    fi

    if [[ ! -d $results_dir ]]
    then
        mkdir $results_dir
    fi 
    echo "Results directory is: " $results_dir
    cd $results_dir
  
    echo "We are in :" $PWD
    for file in /nemo/nemo/cfgs/NEMO/EXP00/*
    do
        
        # Check if the file is already symlinked to prevent lots of spurious 
        # error messages
        
        linkfile=`basename $file`
 
        echo "linking file: " $linkfile
        
        if ! [[ -L $linkfile ]]
        then
            echo $file $linkfile
            ln -s $file $linkfile
        fi
    done
    echo "done linking"
    if [[ $1 == 'nemo' ]]
    then
        /opt/nemo/nemo
    else
        /opt/xios/xios
    fi

%labels
    Author jdha@noc.ac.uk
    Author c.wood@epcc.ed.ac.uk
    Version v0.0.1

%help
    The definition file used to build NEMO and XIOS:
        - HDF5 (1.10.5)
        - NetCDF C (4.7.1) and Fortran (4.5.2) libraries

    This container

    To build the container, run

        singularity build nemo_mpich.sif Singularity.nemo_mpich_bootstrap