ecearth3/runtime/classic/EC00.sh

#!/bin/bash

#
# Job options 
#
#SBATCH --job-name=EC00
#SBATCH --time=01:59:00
#SBATCH --account=ecearth
#
#SBATCH --nodes=4
#SBATCH --exclusive
#SBATCH --ntasks-per-node=125
##SBATCH --partition=medium
##SBATCH --exclude=cnm016
#SBATCH --partition=debug
##SBATCH --switches=1@47:50:00
#
set -ueo pipefail
#
LOCAL_NODES=4
LOCAL_TASKS=500
#
stdout_file=${SLURM_SUBMIT_DIR-$PWD}/${SLURM_JOB_NAME-"local"}_${SLURM_JOB_ID-"id"}.log
exec > ${stdout_file}
echo "------------------ Job Info --------------------"
echo "jobid : ${SLURM_JOB_ID-"id"}"
echo "jobname : ${SLURM_JOB_NAME-"local"}"
echo "nodename : ${SLURMD_NODENAME-"local"}"
echo "# nodes : ${SLURM_JOB_NUM_NODES-$LOCAL_NODES}"
echo "# tasks : ${SLURM_NTASKS-$LOCAL_TASKS}"
echo "submit dir : ${SLURM_SUBMIT_DIR-$PWD}"

set -ue
#
# Cluster variables
#
NB_CORES_PER_NODES=128
MAX_CORES_PER_NODES=123
LIST_CORES_SOCKET=`seq -s',' 0 $((NB_CORES_PER_NODES-1))`
#
# Directories
start_dir=${SLURM_SUBMIT_DIR-$PWD}

# librunscript defines some helper functions
. ${start_dir}/librunscript.sh

# =============================================================================
# *** BEGIN User configuration
# =============================================================================

# -----------------------------------------------------------------------------
# *** General configuration
# -----------------------------------------------------------------------------

# Component configuration
# (for syntax of the $config variable, see librunscript.sh)
config="ifs nemo lim3 rnfmapper xios:detached oasis"

# Experiment name (exactly 4 letters!)
export exp_name=EC00

# Simulation start and end date. Use any (reasonable) syntax you want.
run_start_date="1970-01-01"
run_end_date="${run_start_date} + 52 years"

# Set $force_run_from_scratch to 'true' if you want to force this run to start
# from scratch, possibly ignoring any restart files present in the run
# directory. Leave set to 'false' otherwise.
# NOTE: If set to 'true' the run directory $run_dir is cleaned!
force_run_from_scratch=true
special_restart=false
special_restart_from=ECE3
special_restart_date="1995-01-01"

# Resolution (TM5 resolution is set at compilation)
ifs_grid=T255L91
nem_grid=ORCA1L75

# Restart frequency. Use any (reasonable) number and time unit you want.
# For runs without restart, leave this variable empty
rst_freq="6 months"

# Number of restart legs to be run in one go
run_num_legs=1

# Directories
ctrl_file_dir=${start_dir}/ctrl
output_control_files_dir=${start_dir}/ctrl

# Architecture
build_arch=ecconf

# This file is used to store information about restarts
ece_info_file="ece.info"

# -----------------------------------------------------------------------------
# *** Read platform dependent configuration
# -----------------------------------------------------------------------------
#. ${start_dir}/ecconf.cfg

# This function should configure all settings/modules needed to
# later prepare the EC-Earth run directory and set variables used
# in the run script

# SCRATCH is not defined in MN3, define it here
# and also make sure it is defined when compiling
export SCRATCH=/gpfs/scratch/acad/ecearth/${USER}

# Configure paths for building/running EC-Earth
ecearth_src_dir=${HOME}/models/ecearth_3.3.1/sources
run_dir=/gpfs/scratch/acad/ecearth/${USER}/ecearth/run/${exp_name}
ini_data_dir=/gpfs/scratch/acad/ecearth/data/bsc32/v3.3.1/inidata
archive_dir=/gpfs/scratch/acad/ecearth/${USER}/ecearth/archive/${exp_name}

# File for standard output.
# NOTE: This will be modified for restart jobs!
stdout_file=${SLURM_SUBMIT_DIR-$PWD}/${SLURM_JOB_NAME-"local"}_${SLURM_JOB_ID-"id"}.log

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

module purge
module load EasyBuild/2023a
MODULEPATH=$MODULEPATH:/gpfs/projects/acad/ecearth/softs/easybuild/modules/all
module load netCDF-Fortran/4.6.1-iompi-2023a
module load imkl/2023.1.0 
module load grib_api/1.24.0-iompi-2023a
module load CDO/1.9.10-iompi-2023a

# Configure grib api paths
export GRIB_DEFINITION_PATH=${HOME}/models/ecearth_3.3.1/sources/util/grib_table_126:${EBROOTGRIB_API}/share/grib_api/definitions
export GRIB_SAMPLES_PATH=${EBROOTGRIB_API}/share/grib_api/ifs_samples/grib1
export GRIB_BIN_PATH=${EBROOTGRIB_API}/bin

# Configure number of processors per node
proc_per_node=128

ulimit -s unlimited

# -----------------------------------------------------------------------------
# *** Time step settings
# -----------------------------------------------------------------------------
case "${ifs_grid}--${nem_grid}" in

    T159L*--ORCA1L*)
        ifs_time_step_sec=3600; nem_time_step_sec=2700; lim_time_step_sec=2700; cpl_freq_atm_oce_sec=10800
        ;;
    T255L*--ORCA1L*)
        ifs_time_step_sec=2700; nem_time_step_sec=2700; lim_time_step_sec=2700; cpl_freq_atm_oce_sec=2700
        ;;
    T511L*--ORCA025L*)
        ifs_time_step_sec=900 ; nem_time_step_sec=900 ; lim_time_step_sec=900 ; cpl_freq_atm_oce_sec=2700
        ;;

    *)  error "Can't set time steps for unknown combination of horizontal grids: ${ifs_grid}-${nem_grid}"
        ;;
esac

# -----------------------------------------------------------------------------
# *** IFS configuration
# -----------------------------------------------------------------------------

ifs_version=36r4

ifs_di_freq=$(( 24 * 3600 / ifs_time_step_sec ))
ifs_ddh_freq=$(( 120 * 3600 / ifs_time_step_sec ))

export ifs_res_hor=$(echo ${ifs_grid} | sed 's:T\([0-9]\+\)L\([0-9]\+\):\1:')
ifs_res_ver=$(echo ${ifs_grid} | sed 's:T\([0-9]\+\)L\([0-9]\+\):\2:')

ifs_numproc=400

ifs_exe_file=${ecearth_src_dir}/ifs-${ifs_version}/bin/ifsmaster-${build_arch}

ifs_lastout=false

# USE FORCING FROM CMIP5 (SOLAR, GHG, AEROSOL, O3)
ifs_cmip5=TRUE
# SWITCH FOR RCP AND HISTORICAL RUNS FOR CMIP5 (0=HISTO 1=RCP 3-PD, 2=RCP 4.5, 3=RCP 6.0, 4=RCP 8.5)
ifs_cmip5_rcp=0
# 1PCTCO2 and A4XCO2 should operate together with ifs_cmip_fixyear years, ie., the baseline GHGs level will use that for year ifs_cmip_fixyear
export ifs_cmip_fixyear=1850

# USE FORCING FROM CMIP6 (HAS PRIORITY OVER LCMIP5)
ifs_cmip6=TRUE
# MAC-SP anthropogenic simple plume model (parameterization of anthropogenic aerosol optical properties)
ifs_mac2sp=TRUE
# Use CMIP6 prescribed preindustrial aerosol
ifs_cmip6piaer=TRUE

# !! scenario 'historical' max 2014
# 1850          (o3_pi)
# 1850 --> 2014 (o3_histo)
# !! other scenarios (> 2014), default: SSP3-7.0
# SSP1-1.9, SSP1-2.6, SSP1-2.6-Ext, SSP2-4.5, SSP3-7.0, SSP3-LowNTCF, SSP4-3.4, SSP5-3.4-OS, SSP4-6.0, SSP5-3.4-OS-Ext, SSP5-8.5, SSP5-8.5-Ext
ifs_cmip6_scenario=historical

# Read CMIP6 stratospheric aerosol data file, vertically integrated version
lcmip6_strataer_simp=FALSE
lcmip6_strataer_full=TRUE
lcmip6_strataer_bckgd=FALSE

# for an abrupt increase of CO2  to 4x the starting year (ifs_cmip_fixyear)
export ifs_A4xCO2=FALSE
# for an 1% per year increase of CO2 until reaching 4x the starting year (ifs_cmip_fixyear)
export ifs_1PCTCO2=FALSE

# Time-varying orbital forcing (Qiong Zhang, SU-2013-09)
# https://dev.ec-earth.org/projects/ecearth3/wiki/Orbital_forcing_in_EC-Earth_3
#
#   ifs_orb_switch=false, no orbital calculations applied
#   ifs_orb_switch=true, use orbital calculations according to ifs_orb_mode
#   ifs_orb_mode="fixed_year", or "variable_year", or "fixed_parameters"
#     fixed_year: calculate the orbital parameters at ifs_orb_iyear, e.g.,1850
#     variable_year: calculate orbital parameters annually start from ifs_orb_iyear
#     fixed_parameters: prescribe orbital parameters for given year
ifs_orb_switch=FALSE
ifs_orb_mode="variable_year"
ifs_orb_iyear=$(date -u -d "${run_start_date}" +%Y)

# IFS tuning parameters
ifs_tuning_parameter_file=${ctrl_file_dir}/ifs-tuning-parameters-${ifs_grid}.sh
if [ -f ${ifs_tuning_parameter_file} ]
then
    source ${ifs_tuning_parameter_file}
else
    error "Sorry, ${ifs_tuning_parameter_file} not found, exiting."
fi

# Select source of vegetation data:
#  ifs       climatology from IFS
#  era20c    vegetation from an off-line LPJ-Guess run forced with ERA20C
#            (currently available only for T255 and T159)
#
ifs_veg_source="era20c"

case ${ifs_veg_source} in
"ifs" )
    # Use Lambert-Beer to compute effective vegetation cover
    n_compute_eff_veg_fraction=2
    ;;
"era20c" )
    # LPJG vegetation is provided as effective cover
    # Don't use Lambert-Beer
    n_compute_eff_veg_fraction=0
    ;;
* )
    error "Vegetation from ${ifs_veg_source} not implemented"
    ;;
esac

# use DMI land ice physics and varying snow albedo
ifs_landice=false

# -----------------------------------------------------------------------------
# *** NEMO/LIM configuration
# -----------------------------------------------------------------------------

# This is only needed if the experiment is started from an existing set of NEMO
# restart files
nem_restart_file_path=${start_dir}/nemo-rst

nem_restart_offset=0

nem_res_hor=$(echo ${nem_grid} | sed 's:ORCA\([0-9]\+\)L[0-9]\+:\1:')

nem_exe_file=${ecearth_src_dir}/nemo-3.6/CONFIG/${nem_grid}_LIM3/BLD/bin/nemo.exe

nem_numproc=98

# -----------------------------------------------------------------------------
# *** Runoff mapper configuration
# -----------------------------------------------------------------------------

rnf_exe_file=${ecearth_src_dir}/runoff-mapper/bin/runoff-mapper.exe
rnf_numproc=1

# -----------------------------------------------------------------------------
# *** OASIS configuration
# -----------------------------------------------------------------------------

# Restart files for the coupling fields (note 8 character limit in OASIS)
#   rstas.nc : atmosphere single-category fields
#   rstam.nc : atmosphere multi-category fields
#   rstos.nc : ocean single-category fields
#   rstom.nc : ocean multi-category fields
oas_rst_files="rstas.nc rstos.nc"

# Decide whether the OASIS weight files for interpolation should be linked from
# the setup directory (true) or not (false). In the latter case, the weights
# are re-computed at the start of the run.
oas_link_weights=true

# Flux correction for runoff (not calving) sent from Oasis to ocean.
# 1.07945 is computed to compensate for a P-E=-0.016 mm/day (valid for std res)
oas_mb_fluxcorr=1.07945

# -----------------------------------------------------------------------------
# *** XIOS configuration
# -----------------------------------------------------------------------------

xio_exe_file=${ecearth_src_dir}/xios-2.5/bin/xios_server.exe

xio_numproc=1

# -----------------------------------------------------------------------------
# *** Extra initial conditions saved during the run
# -----------------------------------------------------------------------------
if has_config save_ic
then
    source ./libsave_ic.sh
    declare -a save_ic_date save_ic_date1 save_ic_sec save_ic_day save_ic_ppt_file save_ic_nemo_ts
fi

# =============================================================================
# *** END of User configuration
# =============================================================================

# =============================================================================
# *** This is where the code begins ...
# =============================================================================

# -----------------------------------------------------------------------------
# *** Create the run dir if necessary and go there
#     Everything is done from here.
# -----------------------------------------------------------------------------
if [ ! -d ${run_dir} ]
then
    mkdir -p ${run_dir}
    if $special_restart
    then
        force_run_from_scratch=false
        echo 'rsync -av --delete ${run_dir}/../${special_restart_from}/ --exclude log --exclude output --exclude restart --exclude="${special_restart_from}_*" --exclude="srf*" --exclude="restart_*" --exclude="debug.*" --ex     clude="output.*" ${run_dir}'
        rsync -av --delete ${run_dir}/../${special_restart_from}/ --exclude log --exclude output --exclude restart --exclude="${special_restart_from}_*" --exclude="srf*" --exclude="restart_*" --exclude="debug.*" --exclude="output.*" ${run_dir}
        cp -f ${nem_exe_file} ${run_dir}
        cp -f ${ifs_exe_file} ${run_dir}
        cp -f ${rnf_exe_file} ${run_dir}
        cp -f ${xio_exe_file} ${run_dir}
        special_year=${special_restart_date:0:4}
        sed -i "/$special_year/q" ${run_dir}/ece.info
        . ${run_dir}/ece.info
        special_restart_leg=$(printf %03d $((leg_number+1)))
        special_restart_leg_oasis=$(printf %03d $((leg_number+2)))
        # PUT HERE THE INSTRUCTIONS TO COPY THE restart files
        rsync -av ${run_dir}/../../archive/${special_restart_from}/restart/ifs/${special_restart_leg}/ ${run_dir}
        rsync -av ${run_dir}/../../archive/${special_restart_from}/restart/oasis/${special_restart_leg_oasis}/ ${run_dir}
        cd ${run_dir}/../../archive/${special_restart_from}/restart/nemo/${special_restart_leg}
        for f in *.nc; do
            nf=${exp_name}${f:4}
            cp $f ${run_dir}/$nf
        done
        cd -
        cd ${run_dir}
        for f in ${exp_name}_????????_restart_???_????.nc; do
            nf=${f:14}
            ln -s $f $nf
        done
        cd -
        rm -f ${run_dir}/ICMCL${special_restart_from}INIT
        mv ${run_dir}/ICMGG${special_restart_from}INIUA ${run_dir}/ICMGG${exp_name}INIUA
        mv ${run_dir}/ICMGG${special_restart_from}INIT ${run_dir}/ICMGG${exp_name}INIT
        mv ${run_dir}/ICMSH${special_restart_from}INIT ${run_dir}/ICMSH${exp_name}INIT
    fi
else
    force_run_from_scratch=false
    special_restart=false
fi
cd ${run_dir}

# -----------------------------------------------------------------------------
# *** Determine the time span of this run and whether it's a restart leg
# -----------------------------------------------------------------------------

# Regularise the format of the start and end date of the simulation
run_start_date=$(date -uR -d "${run_start_date}")
run_end_date=$(date -uR -d "${run_end_date}")


# -----------------------------------------------------------------------------
# *** Set path to grib_set
# -----------------------------------------------------------------------------

grib_set=${GRIB_BIN_PATH}${GRIB_BIN_PATH:+/}grib_set

# Loop over the number of legs
for (( ; run_num_legs>0 ; run_num_legs-- ))
do

    # Check for restart information file and set the current leg start date
    #   Ignore restart information file if force_run_from_scratch is true
    if ${force_run_from_scratch} || ! [ -r ${ece_info_file} ]
    then
        leg_is_restart=false
        leg_start_date=${run_start_date}
        leg_number=1
    else
        leg_is_restart=true
        . ./${ece_info_file}
        leg_start_date=${leg_end_date}
        leg_number=$((leg_number+1))
    fi

    # Compute the end date of the current leg
    if [ -n "${rst_freq}" ]
    then
        leg_end_date=$(date -uR -d "${leg_start_date} + ${rst_freq}")
    else
        leg_end_date=${run_end_date}
    fi

    if [ $(date -u -d "${leg_end_date}" +%s) -ge $(date -u -d "${run_end_date}" +%s) ]
    then
        leg_end_date=${run_end_date}
        ifs_lastout=true
    fi

    # Some time variables needed later
    leg_length_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${leg_start_date}" +%s) ))
    leg_start_sec=$(( $(date -u -d "${leg_start_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
    leg_end_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
    leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d)
    leg_start_date_yyyymm=$(date -u -d "${leg_start_date}" +%Y%m)
    leg_start_date_yyyy=$(date -u -d "${leg_start_date}" +%Y)
    leg_end_date_yyyy=$(date -u -d "${leg_end_date}" +%Y)

    # Check whether there's actually time left to simulate - exit otherwise
    if [ ${leg_length_sec} -le 0 ]
    then
        info "Leg start date equal to or after end of simulation."
        info "Nothing left to do. Exiting."
        exit 0
    fi

    # Initial conditions saved during the run
    do_save_ic=false
    has_config save_ic && save_ic_get_config
    # if you do not use an option with save_ic, you must define 'do_save_ic' and
    # 'save_ic_date_offset' here or in ../libsave_ic.sh/save_ic_get_config()
    ${do_save_ic} && save_ic_define_vars

    # -------------------------------------------------------------------------
    # *** Prepare the run directory for a run from scratch
    # -------------------------------------------------------------------------
    if ! $leg_is_restart
    then
        # ---------------------------------------------------------------------
        # *** Check if run dir is empty. If not, and if we are allowed to do so
        #     by ${force_run_from_scratch}, remove everything
        # ---------------------------------------------------------------------
        if $(ls * >& /dev/null)
        then
            if ${force_run_from_scratch}
            then
                rm -fr ${run_dir}/*
            else
                error "Run directory ${run_dir} not empty and \$force_run_from_scratch not set."
            fi
        fi

        # ---------------------------------------------------------------------
        # *** Copy executables of model components
        # *** Additionally, create symlinks to the original place for reference
        # ---------------------------------------------------------------------
        cp    ${ifs_exe_file} .
        ln -s ${ifs_exe_file} $(basename ${ifs_exe_file}).lnk

        cp    ${nem_exe_file} .
        ln -s ${nem_exe_file} $(basename ${nem_exe_file}).lnk

        cp    ${rnf_exe_file} .
        ln -s ${rnf_exe_file} $(basename ${rnf_exe_file}).lnk

        cp    ${xio_exe_file} .
        ln -s ${xio_exe_file} $(basename ${xio_exe_file}).lnk

        # ---------------------------------------------------------------------
        # *** Files needed for IFS (linked)
        # ---------------------------------------------------------------------

        # Initial data
        ln -s \
        ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMGGECE3INIUA \
                                                            ICMGG${exp_name}INIUA
        ln -s \
        ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMSHECE3INIT \
                                                            ICMSH${exp_name}INIT
        rm -f ICMGG${exp_name}INIT
        cp ${ini_data_dir}/ifs/${ifs_grid}/${leg_start_date_yyyymmdd}/ICMGGECE3INIT \
                                                            ICMGG${exp_name}INIT

        # add bare_soil_albedo to ICMGG*INIT
        tempfile=tmp.$$
        ${grib_set} -s dataDate=$(date -u -d "$run_start_date" +%Y%m%d) \
            ${ini_data_dir}/ifs/${ifs_grid}/climate/bare_soil_albedos.grb \
            ${tempfile}

        cat ${tempfile} >> ICMGG${exp_name}INIT
        rm -f ${tempfile}

        # add land ice mask if needed
        if ${ifs_landice}
        then
            tempfile=tmp.$$
            cdo divc,10 -setcode,82 -selcode,141 ICMGG${exp_name}INIT ${tempfile}
            ${grib_set} -s gridType=reduced_gg ${tempfile} ${tempfile}
            cat ${tempfile} >> ICMGG${exp_name}INIT
            rm -f ${tempfile}
        fi

        # Other stuff
        ln -s ${ini_data_dir}/ifs/rtables/* .

        # Output control (ppt files)
        if [ ! -f ${output_control_files_dir}/pptdddddd0600 ] &&  [ ! -f ${output_control_files_dir}/pptdddddd0300 ];then
           echo "Error from ece-esm.sh: Neither the file pptdddddd0600 or pptdddddd0300 exists in the directory:"
           echo " " ${output_control_files_dir}
           exit -1
        fi
        mkdir postins
        cp ${output_control_files_dir}/ppt* postins/
        if [ -f postins/pptdddddd0600 ];then
           ln -s pptdddddd0600 postins/pptdddddd0000
           ln -s pptdddddd0600 postins/pptdddddd1200
           ln -s pptdddddd0600 postins/pptdddddd1800
        fi
        if [ -f postins/pptdddddd0300 ];then
           ln -s pptdddddd0300 postins/pptdddddd0900
           ln -s pptdddddd0300 postins/pptdddddd1500
           ln -s pptdddddd0300 postins/pptdddddd2100
           if [ ! -f postins/pptdddddd0600 ];then
               ln -s pptdddddd0300 postins/pptdddddd0000
               ln -s pptdddddd0300 postins/pptdddddd0600
               ln -s pptdddddd0300 postins/pptdddddd1200
               ln -s pptdddddd0300 postins/pptdddddd1800
           fi
        fi
        /bin/ls -1 postins/* > dirlist

        # ---------------------------------------------------------------------
        # *** Files needed for NEMO (linked)
        # ---------------------------------------------------------------------

        # Link initialisation files for matching ORCA grid
        for f in \
            bathy_meter.nc coordinates.nc \
            ahmcoef.nc \
            K1rowdrg.nc M2rowdrg.nc mask_itf.nc \
            decay_scale_bot.nc decay_scale_cri.nc \
            mixing_power_bot.nc mixing_power_cri.nc mixing_power_pyc.nc \
            runoff_depth.nc subbasins.nc
        do
            [ -f ${ini_data_dir}/nemo/initial/${nem_grid}/$f ] && ln -s ${ini_data_dir}/nemo/initial/${nem_grid}/$f
        done

        # Link geothermal heating file (independent of grid) and matching weight file
        ln -s ${ini_data_dir}/nemo/initial/Goutorbe_ghflux.nc
        ln -s ${ini_data_dir}/nemo/initial/weights_Goutorbe1_2_orca${nem_res_hor}_bilinear.nc

        # Link the salinity climatology file (needed for diagnostics)
        ln -s ${ini_data_dir}/nemo/climatology/${nem_grid}/sali_ref_clim_monthly.nc

        # Link either restart files or climatology files for the initial state
        if $(has_config nemo:start_from_restart)
        then
            # When linking restart files, we accept three options:
            # (1) Merged files for ocean and ice, i.e.
            #     restart_oce.nc and restart_ice.nc
            # (2) One-file-per-MPI-rank, i.e.
            #     restart_oce_????.nc and restart_ice_????.nc
            #     No check is done whether the number of restart files agrees
            #     with the number of MPI ranks for NEMO!
            # (3) One-file-per-MPI-rank with a prefix, i.e.
            #     <exp_name>_<time_step>_restart_oce_????.nc (similar for the ice)
            #     The prefix is ignored.
            # The code assumes that one of the options can be applied! If more
            # options are applicable, the first is chosen. If none of the
            # options apply, NEMO will crash with missing restart file.
            if   ls -U ${nem_restart_file_path}/restart_[oi]ce.nc > /dev/null 2>&1
            then
                 ln -s ${nem_restart_file_path}/restart_[oi]ce.nc ./

            elif ls -U ${nem_restart_file_path}/restart_[oi]ce_????.nc > /dev/null 2>&1
            then
                 ln -s ${nem_restart_file_path}/restart_[oi]ce_????.nc ./

            else
                for f in ${nem_restart_file_path}/????_????????_restart_[oi]ce_????.nc
                do
                    ln -s $f $(echo $f | sed 's/.*_\(restart_[oi]ce_....\.nc\)/\1/')
                done
            fi
        else

            # Temperature and salinity files for initialisation
            ln -s ${ini_data_dir}/nemo/climatology/absolute_salinity_WOA13_decav_Reg1L75_clim.nc
            ln -s ${ini_data_dir}/nemo/climatology/conservative_temperature_WOA13_decav_Reg1L75_clim.nc
            ln -s ${ini_data_dir}/nemo/climatology/weights_WOA13d1_2_orca${nem_res_hor}_bilinear.nc

            # Grid dependent runoff files
            case ${nem_grid} in
            ORCA1*)   ln -s ${ini_data_dir}/nemo/climatology/runoff-icb_DaiTrenberth_Depoorter_ORCA1_JD.nc ;;
            ORCA025*) ln -s ${ini_data_dir}/nemo/climatology/ORCA_R025_runoff_v1.1.nc ;;
            esac
        fi

        # for ocean_nudging
        if $(has_config nemo:ocenudg) ; then
          ln -fs ${ini_data_dir}/nemo/oce_nudg/resto.nc ./
        fi

        # XIOS files
        . ${ctrl_file_dir}/iodef.xml.sh > iodef.xml
        ln -s ${ctrl_file_dir}/context_nemo.xml
        ln -s ${ctrl_file_dir}/domain_def_nemo.xml
        ln -s ${ctrl_file_dir}/axis_def_nemo.xml
        ln -s ${ctrl_file_dir}/grids_def_nemo.xml
        ln -s ${ctrl_file_dir}/field_def_nemo-lim.xml
        ln -s ${ctrl_file_dir}/field_def_nemo-opa.xml
        ln -s ${ctrl_file_dir}/field_def_nemo-pisces.xml
        ln -s ${ctrl_file_dir}/field_def_nemo-inerttrc.xml
        ln -s ${output_control_files_dir}/file_def_nemo-lim3.xml file_def_nemo-lim.xml
        ln -s ${output_control_files_dir}/file_def_nemo-opa.xml
        ln -s ${output_control_files_dir}/file_def_nemo-pisces.xml

        if [ -f ${ini_data_dir}/xios/ORCA${nem_res_hor}/coordinates_xios.nc ]
        then
            cp ${ini_data_dir}/xios/ORCA${nem_res_hor}/coordinates_xios.nc ./
        else
            info "File 'coordinates_xios.nc' not found. NEMO can not be run with land domain removal!"
        fi

        # ---------------------------------------------------------------------
        # *** Files needed for the Runoff mapper (linked)
        # ---------------------------------------------------------------------

        ln -s ${ini_data_dir}/runoff-mapper/runoff_maps.nc

        # ---------------------------------------------------------------------
        # *** Files needed for OASIS (linked)
        # ---------------------------------------------------------------------

        oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-ORCA${nem_res_hor}

        # Name table file
        ln -s ${ini_data_dir}/oasis/cf_name_table.txt

        # Grid definition files
        ln -s ${oas_grid_dir}/areas.nc
        ln -s ${oas_grid_dir}/grids.nc
        ln -s ${oas_grid_dir}/masks.nc

        # Weight files
        case ${ifs_res_hor} in
            159)  oas_agrd=080
                  ;;
            255)  oas_agrd=128
                  ;;
            511)  oas_agrd=256
                  ;;
            799)  oas_agrd=400
                  ;;
            *)    error "Unsupported horizontal resolution (IFS): ${ifs_res_hor}"
                  ;;
        esac

        case ${nem_res_hor} in
              1)  oas_ogrd=O1t0
                  ;;
            025)  oas_ogrd=Ot25
                  ;;
              *)  error "Unsupported horizontal resolution (NEMO): ${nem_res_hor}"
                  ;;
        esac

        if ${oas_link_weights}
        then
            for f in ${oas_grid_dir}/rmp_????_to_????_GAUSWGT.nc
            do
                ln -s $f
            done
        fi

        for f in ${oas_rst_files}
        do
            cp ${oas_grid_dir}/rst/$f .
        done

    else # i.e. $leg_is_restart == true

        # ---------------------------------------------------------------------
        # *** Remove all leftover output files from previous legs
        # ---------------------------------------------------------------------

        # IFS files
        rm -f ICM{SH,GG}${exp_name}+??????

        # NEMO files
        rm -f ${exp_name}_??_????????_????????_{grid_U,grid_V,grid_W,grid_T,icemod,SBC,scalar,SBC_scalar,diad_T}.nc

    fi # ! $leg_is_restart

    #--------------------------------------------------------------------------
    # *** Surface restoring and ocean nudging options
    #--------------------------------------------------------------------------
    #for ocean_nudging
    if $(has_config nemo:ocenudg) ; then
        ln -fs ${ini_data_dir}/nemo/oce_nudg/temp_sal*.nc ./
    fi

    #for surface restoring
    if $(has_config nemo:surfresto) ; then
        ln -fs ${ini_data_dir}/nemo/surface_restoring/sss_restore_data*.nc  ./
        ln -fs ${ini_data_dir}/nemo/surface_restoring/sst_restore_data*.nc  ./
        ln -fs ${ini_data_dir}/nemo/surface_restoring/mask_restore*.nc ./
    fi

    # -------------------------------------------------------------------------
    # *** Remove land grid-points
    # -------------------------------------------------------------------------
    if $(has_config nemo:elpin)
    then
        if [ ! -f coordinates_xios.nc ]
        then
            error "ELpIN requested, but file 'coordinates_xios.nc' was not found"
        fi
        jpns=($(${ecearth_src_dir}/util/ELPiN/ELPiNv2.cmd ${nem_numproc}))
        info "nemo domain decompostion from ELpIN: ${jpns[@]}"
        nem_numproc=${jpns[0]}
        nem_jpni=${jpns[1]}
        nem_jpnj=${jpns[2]}
    else
        info "nemo original domain decomposition (not using ELPiN)"
    fi

    # -------------------------------------------------------------------------
    # *** Initial conditions saved during the run
    # -------------------------------------------------------------------------
    ${do_save_ic} && save_ic_prepare_output

    # -------------------------------------------------------------------------
    # *** Create some control files
    # -------------------------------------------------------------------------

    # IFS frequency output for namelist
    if [ -f postins/pptdddddd0300 ]
    then
        ifs_output_freq=$(( 3 * 3600 / ifs_time_step_sec ))
    elif [ -f postins/pptdddddd0600 ]
    then
        ifs_output_freq=$(( 6 * 3600 / ifs_time_step_sec ))
    else
        error "IFS output frequency undefined."
    fi

    # IFS, NEMO, LIM namelist and OASIS namcouple files
    . ${ctrl_file_dir}/namelist.ifs.sh                          > fort.4
    . ${ctrl_file_dir}/namelist.nemo.ref.sh                     > namelist_ref
    . ${ctrl_file_dir}/namelist.nemo-${nem_grid}-coupled.cfg.sh > namelist_cfg
    . ${ctrl_file_dir}/namelist.lim3.ref.sh                     > namelist_ice_ref
    . ${ctrl_file_dir}/namelist.lim3-${nem_grid}.cfg.sh         > namelist_ice_cfg

    . ${ctrl_file_dir}/namelist.runoffmapper.sh                 > namelist.runoffmapper

    . ${ctrl_file_dir}/namcouple.sh                             > namcouple


    # -------------------------------------------------------------------------
    # *** Create ICMCL file with vegetation fields
    #     not needed if LPJG is used with feedback
    # -------------------------------------------------------------------------
    tempfile=tmp.$$

    case ${ifs_veg_source} in
    "ifs" )
        # Vegetation from IFS (climatology)

        icmclfile=${ini_data_dir}/ifs/${ifs_grid}/climate/ICMCL_ONLY_VEG_PD

        # Create data for december, the year before the leg starts
        ${grib_set} \
            -s dataDate=$(printf "%04d" $((leg_start_date_yyyy-1)))1215 \
            ${icmclfile}-12 ICMCL${exp_name}INIT

        # Create data for all month in the years of the leg
        for (( y=${leg_start_date_yyyy} ; y<=${leg_end_date_yyyy} ; y++ ))
        do
            yy=$(printf "%04d" $y)
            for m in {1..12}
            do
                mm=$(printf "%02d" $m)
                ${grib_set} -s dataDate=${yy}${mm}15 ${icmclfile}-${mm} ${tempfile}
                cat ${tempfile} >> ICMCL${exp_name}INIT
            done
        done

        # Create data for january, the year after the leg ends
        ${grib_set} \
            -s dataDate=$(printf "%04d" $((leg_end_date_yyyy+1)))0115 \
            ${icmclfile}-01 ${tempfile}
        cat ${tempfile} >> ICMCL${exp_name}INIT
        ;;
    "era20c" )
        # Vegetation from an off-line LPJG run forced with ERA20C (v16)

        rm -f ICMCL${exp_name}INIT

        # Create data for all years of the leg, including one year
        # before and one year after
        for (( yr=leg_start_date_yyyy-1 ; yr<=leg_end_date_yyyy+1 ; yr+=1 ))
        do
            if [ $ifs_cmip_fixyear -le 0 ]
            then
                cat ${ini_data_dir}/ifs/${ifs_grid}/icmcl_v16/icmcl_$yr.grb >> ICMCL${exp_name}INIT
            else
                # Fixed year forcing, requires cdo! (only when not using ifs_veg_source=custom_exp*)
                # If cdo is not available at runtime you need to fix proper
                # icmcl files beforehand and use them here
                cdo setyear,$yr ${ini_data_dir}/ifs/${ifs_grid}/icmcl_v16/icmcl_${ifs_cmip_fixyear}.grb ${tempfile}
                cat ${tempfile} >> ICMCL${exp_name}INIT
            fi
        done
        ;;
    * )
        error "Vegetation from ${ifs_veg_source} not implemented"
        ;;
    esac

    # Clean up
    rm -f ${tempfile}

    # -------------------------------------------------------------------------
    # *** Link the appropriate NEMO restart files of the previous leg
    # -------------------------------------------------------------------------
    if $leg_is_restart && ! $special_restart
    then
        ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec - nem_restart_offset )))
        for (( n=0 ; n<nem_numproc ; n++ ))
        do
            np=$(printf %04d ${n})
            ln -fs ${exp_name}_${ns}_restart_oce_${np}.nc restart_oce_${np}.nc
            ln -fs ${exp_name}_${ns}_restart_ice_${np}.nc restart_ice_${np}.nc
        done

        # Make sure there are no global restart files
        # If links are found, they will be removed. We are cautious and do
        # _not_ remove real files! However, if real global restart files are
        # present, NEMO/LIM will stop because time stamps will not match.
        [ -h restart_oce.nc ] && rm restart_oce.nc
        [ -h restart_ice.nc ] && rm restart_ice.nc
    fi

    # -------------------------------------------------------------------------
    # *** Remove some OASIS files of the previous leg
    # -------------------------------------------------------------------------
    if $leg_is_restart
    then
        rm -f anaisout_*
    fi

    # -------------------------------------------------------------------------
    # *** Start the run
    # -------------------------------------------------------------------------
    export DR_HOOK_IGNORE_SIGNALS='-1'
    export CPLNG='active'

    # Use the launch function from the platform configuration file
    t1=$(date +%s)

    # Compute and check the node distribution
    info "======================="
    info "Node/proc distribution:"
    info "-----------------------"
    info "IFS:    ${ifs_numproc}"
    info "NEMO:   ${nem_numproc}"
    info "XIOS:   ${xio_numproc}"
    info "RUNOFF: ${rnf_numproc}"
    info "======================="
    pwd
    info "======================="
    info "mpirun \
	    -n ${xio_numproc} ./$(basename ${xio_exe_file}) : \
	    -n ${nem_numproc} ./$(basename ${nem_exe_file}) : \
	    -n ${ifs_numproc} ./$(basename ${ifs_exe_file}) -v ecmwf -e ${exp_name} : \
	    -n ${rnf_numproc} ./$(basename ${rnf_exe_file})"
    info "======================="
    
    #exit

    mpirun \
	    -n ${xio_numproc} ./$(basename ${xio_exe_file}) : \
	    -n ${nem_numproc} ./$(basename ${nem_exe_file}) : \
	    -n ${ifs_numproc} ./$(basename ${ifs_exe_file}) -v ecmwf -e ${exp_name} : \
	    -n ${rnf_numproc} ./$(basename ${rnf_exe_file})

    t2=$(date +%s)

    tr=$(date -u -d "0 -$t1 sec + $t2 sec" +%T)

    # -------------------------------------------------------------------------
    # *** Check for signs of success
    #     Note the tests provide no guarantee that things went fine! They are
    #     just based on the IFS and NEMO log files. More tests (e.g. checking
    #     restart files) could be implemented.
    # -------------------------------------------------------------------------

    # Checking for IFS success
    if [ -f ifs.stat ]
    then
        if [ "$(awk 'END{print $3}' ifs.stat)" == "CNT0" ]
        then
            info "Leg successfully completed according to IFS log file 'ifs.stat'."
        else
            error "Leg not completed according to IFS log file 'ifs.stat'."
        fi
    else
        error "IFS log file 'ifs.stat' not found after run."
    fi

    # Check for NEMO success
    if [ -f ocean.output ]
    then
        if [ "$(sed -n '/New day/h; ${g;s:.*\([0-9/]\{10\}\).*:\1:;p;}' ocean.output)" == "$(date -u -d "${leg_end_date} - 1 day" +%Y/%m/%d)" ]
        then
            info "Leg successfully completed according to NEMO log file 'ocean.output'."
        else
            error "Leg not completed according to NEMO log file 'ocean.output'."
        fi

    else
        error "NEMO log file 'ocean.output' not found after run."
    fi

    # -------------------------------------------------------------------------
    # *** Post-process initial conditions saved during the run if requested
    # -------------------------------------------------------------------------
    ${do_save_ic} && save_ic_postproc

    # -------------------------------------------------------------------------
    # *** Move IFS output files to archive directory
    # -------------------------------------------------------------------------
    outdir="${archive_dir}/output/ifs/$(printf %03d $((leg_number)))"
    mkdir -p ${outdir}

    prv_leg=$(printf %03d $((leg_number-1)))

    # This takes care of a special IFS feature: The output for the last time
    # step of each leg is written at the first time step of the new leg. The
    # following code makes sure that the output is appended to the appropriate
    # file. Since GRIB files are just streams, its done with a simple cat
    # command.
    for f in ICMSH${exp_name}+?????? ICMGG${exp_name}+??????
    do
        if [ -f output/ifs/${prv_leg}/${f} ]
        then
            cat ${f} >> output/ifs/${prv_leg}/${f}
            rm -f ${f}
        else
            mv ${f} ${outdir}
        fi
    done

    # -------------------------------------------------------------------------
    # *** Move NEMO output files to archive directory
    # -------------------------------------------------------------------------
    outdir="${archive_dir}/output/nemo/$(printf %03d $((leg_number)))"
    mkdir -p ${outdir}

    for v in grid_U grid_V grid_W grid_T icemod SBC scalar SBC_scalar diad_T \
             grid_T_2D grid_U_2D grid_V_2D grid_W_2D grid_T_3D grid_U_3D grid_V_3D grid_W_3D \
             grid_1point grid_T_3D_ncatice vert_sum \
             grid_ptr_W_3basin_3D grid_ptr_T_3basin_2D grid_ptr_T_2D \
             zoom_700_sum zoom_300_sum zoom_2000_sum
    do
        for f in ${exp_name}_*_????????_????????_*${v}.nc
        do
            test -f $f && mv $f $outdir/
        done
    done

    # -------------------------------------------------------------------------
    # *** Move IFS restart files to archive directory
    # -------------------------------------------------------------------------
    if $leg_is_restart
    then
        outdir="${archive_dir}/restart/ifs/$(printf %03d $((leg_number)))"
        mkdir -p ${outdir}

        # Figure out the time part of the restart files (cf. CTIME on rcf files)
        # NOTE: Assuming that restarts are at full days (time=0000) only!
        nd="$(printf %06d $((leg_start_sec/(24*3600))))0000"

        mv srf${nd}.???? ${outdir}
    fi

    # -------------------------------------------------------------------------
    # *** Move NEMO restart files to archive directory
    # -------------------------------------------------------------------------
    if $leg_is_restart && $(has_config nemo)
    then
        outdir="${archive_dir}/restart/nemo/$(printf %03d $((leg_number)))"
        mkdir -p ${outdir}

        ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec - nem_restart_offset )))
        for f in oce ice
        do
            mv ${exp_name}_${ns}_restart_${f}_????.nc ${outdir}
        done
    fi

    # -------------------------------------------------------------------------
    # *** Copy OASIS restart files to archive directory
    #     NOTE: These files are copied and not moved as they are used in the
    #           next leg!
    #           Note also that the OASIS restart files present at the end of
    #           the leg correspond to the start of the next leg!
    # -------------------------------------------------------------------------
    outdir="${archive_dir}/restart/oasis/$(printf %03d $((leg_number+1)))"
    mkdir -p ${outdir}

    for f in ${oas_rst_files}
    do
        test -f ${f} && cp ${f} ${outdir}
    done

    # -------------------------------------------------------------------------
    # *** Copy rcf files to the archive directory (of the next leg!)
    # -------------------------------------------------------------------------
    outdir="${archive_dir}/restart/ifs/$(printf %03d $((leg_number+1)))"
    mkdir -p ${outdir}

    for f in rcf
    do
        test -f ${f} && cp ${f} ${outdir}
    done

    # -------------------------------------------------------------------------
    # *** Move log files to archive directory
    # -------------------------------------------------------------------------
    outdir="${archive_dir}/log/$(printf %03d $((leg_number)))"
    mkdir -p ${outdir}

    for f in \
        ifs.log ifs.stat fort.4 ocean.output \
        time.step solver.stat \
        nout.000000 debug.??.?????? A*_??.nc O*_??.nc
    do
        test -f ${f} && mv ${f} ${outdir}
    done

    # -------------------------------------------------------------------------
    # *** Write the restart control file
    # -------------------------------------------------------------------------

    # Compute CPMIP performance
    sypd="$(cpmip_sypd $leg_length_sec $(($t2 - $t1)))"
    chpsy="$(cpmip_chpsy  $leg_length_sec $(($t2 - $t1)) $(($ifs_numproc + $nem_numproc + $rnf_numproc + $xio_numproc)))"

    echo "#"                                             | tee -a ${ece_info_file}
    echo "# Finished leg at `date '+%F %T'` after ${tr} (hh:mm:ss)" \
                                                         | tee -a ${ece_info_file}
    echo "# CPMIP performance: $sypd SYPD   $chpsy CHPSY"| tee -a ${ece_info_file}
    echo "leg_number=${leg_number}"                      | tee -a ${ece_info_file}
    echo "leg_start_date=\"${leg_start_date}\""          | tee -a ${ece_info_file}
    echo "leg_end_date=\"${leg_end_date}\""              | tee -a ${ece_info_file}

    # Need to reset force_run_from_scratch in order to avoid destroying the next leg
    force_run_from_scratch=false
    special_restart=false

done # loop over legs

# -----------------------------------------------------------------------------
# *** Platform dependent finalising of the run
# -----------------------------------------------------------------------------
#finalise

if ${resubmit_job} && [ $(date -d "${leg_end_date}" +%s) -lt $(date -d "${run_end_date}" +%s) ]
then
    info "Resubmitting job for leg $((leg_number+1))"
    # Need to go to start_dir to find the run script
    cd ${start_dir}
    # Submit command
    echo "sbatch -N ${SLURM_JOB_NUM_NODES-"1"} -o ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
              -e ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) -d ${SLURM_JOB_ID-"id"} \
              ./${SLURM_JOB_NAME-"run"}.sh"
        # Note: This does not work if you specify a job name with sbatch -J jobname!
        sbatch -N ${SLURM_JOB_NUM_NODES-"1"}                                             \
               -o ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
               -e ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
               -d ${SLURM_JOB_ID-"id"}                                                   \
               ./${SLURM_JOB_NAME-"run"}.sh
fi

exit 0