Coral/archive/nemo.cfg

# Platform dependent configuration functions for the 'cenaero' machine
# (hpc.cenaero.be)

function configure()
{
    # This function should configure all settings/modules needed to
    # later prepare the NEMO run directory and set variables used
    # in the run script


    # Configure paths for building/running NEMO
    nemo_src_dir=${HOME}/modeles/NEMO/3.6
    run_dir=$GLOBALSCRATCH/nemo/run/${exp_name}
    ini_data_dir=$GLOBALSCRATCH/DATA/nemo

    # File for standard output.
    # NOTE: This will be modified for restart jobs!
    #stdout_file=${start_dir}/out/${PBS_JOBNAME}.out

    # Resubmit this job for automatic restarts? [true/false]
    # Also, add options for the resubmit command here.
    resubmit_job=true

    # Configure and load modules
    pre_load_modules_cmd="module purge"
    module_list="module load intel/compilerpro/13.0.1.117 openmpi/1.6.4/intel-13.0.1.117 hdf5/1.8.15p1_intel13_ompi1.6.4 netcdf/intel/4.3.3.1_ompi1.6.4 cdo/intel/1.5.4"

    module load ${module_list}
}

function configure_opa()
{
    # Configure paths for NEMO IC
    [ -f ${ini_data_dir}/INIT/${nem_grid}/coordinates.nc ]                          && ln -s ${ini_data_dir}/INIT/${nem_grid}/coordinates.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/bathy_meter.nc ]                          && ln -s ${ini_data_dir}/INIT/${nem_grid}/bathy_meter.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/runoff_core_monthly.nc ]                  && ln -s ${ini_data_dir}/INIT/${nem_grid}/runoff_core_monthly.nc runoffs_depth.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/ahmcoef.nc ]                              && ln -s ${ini_data_dir}/INIT/${nem_grid}/ahmcoef.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/mask_itf.nc ]                             && ln -s ${ini_data_dir}/INIT/${nem_grid}/mask_itf.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/K1rowdrg.nc ]                             && ln -s ${ini_data_dir}/INIT/${nem_grid}/K1rowdrg.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/M2rowdrg.nc ]                             && ln -s ${ini_data_dir}/INIT/${nem_grid}/M2rowdrg.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/data_1m_potential_temperature_nomask.nc ] && ln -s ${ini_data_dir}/INIT/${nem_grid}/data_1m_potential_temperature_nomask.nc temperature.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/data_1m_salinity_nomask.nc ]              && ln -s ${ini_data_dir}/INIT/${nem_grid}/data_1m_salinity_nomask.nc salinity.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/subbasins.nc ]                            && ln -s ${ini_data_dir}/INIT/${nem_grid}/subbasins.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/resto.nc ]                                && ln -s ${ini_data_dir}/INIT/${nem_grid}/resto.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/chlorophyll.nc ]                          && ln -s ${ini_data_dir}/INIT/${nem_grid}/chlorophyll.nc
    [ -f ${ini_data_dir}/INIT/${nem_grid}/geothermal_heating.nc ]                   && ln -s ${ini_data_dir}/INIT/${nem_grid}/geothermal_heating.nc

    # Configure paths for NEMO Forcings
    ln -sf ${ini_data_dir}/BC/${nem_grid}/${nem_forcing_set}/*.nc .
    [ -f ${ini_data_dir}/BC/${nem_grid}/weights_core_orca2_bicubic_noc.nc ]       && ln -s ${ini_data_dir}/BC/${nem_grid}/weights_core_orca2_bicubic_noc.nc
    [ -f ${ini_data_dir}/BC/${nem_grid}/weights_core_orca2_bilinear_noc.nc ]      && ln -s ${ini_data_dir}/BC/${nem_grid}/weights_core_orca2_bilinear_noc.nc
}

function configure_xios()
{
    # Configure paths for XIOS files
    ln -sf ${ctrl_file_dir}/*.xml .
}

function launch()
{
    # Compute and check the node distribution
    info "======================="
    info "Node/proc distribution:"
    info "-----------------------"
    info "XIOS:  ${xio_numproc}"
    info "NEMO:  ${nem_numproc}"
    info "======================="

    cmd="mpirun"

    while (( "$#" ))
    do
        nranks=$1
        executable=./$(basename $2)
        shift
        shift

        cmd+=" -np $nranks $executable"

        while (( "$#" )) && [ "$1" != "--" ]
        do
            cmd+=" $1"
            shift
        done
        shift || true

        (( "$#" )) && cmd+=" :"
    done

    export OMP_NUM_THREADS=1
    $cmd
}

function finalise()
{
    # This function should execute of any post run functionality, e.g.
    # platform dependent cleaning or a resubmit

    if ${resubmit_job} && [ $(date -d "${leg_end_date}" +%s) -lt $(date -d "${run_end_date}" +%s) ]
    then
        info "Resubmitting job ${start_dir}/${script_name} for leg $((leg_number+1))"
        # Need to go to start_dir to find the run script
        cd ${start_dir}
        # Submit command
        sbatch ./${script_name}
    fi
}