ecearth3/runtime/classic/ece-lsm.sh.tmpl

#!/usr/bin/env bash

set -ue

# librunscript defines some helper functions
source ./librunscript.sh

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

# -----------------------------------------------------------------------------
# *** General configuration
# -----------------------------------------------------------------------------
# Component configuration (for syntax of the $config variable, see librunscript.sh)
#
# Currently maintained:
#     config="osm"               # OSM (Offline Surface Model, H-TESSEL), forced by IFS output or reanalysis data
#     config="lpjg"              # LPJG-Offline, forced by IFS or OSM output (lpjg_forcing)
                                 #   In this config lpjg can take the option lpjg:spinup to run an offline spinup
#     config="lpjg:fdbck osm"    # LPJG & OSM Coupled via OASIS - option lpjg:fdbck is used to feedback on the OSM

config="lpjg:fdbck osm"

# dummy tm5 coupling - co2 ppm + fluxes
ccycle_co2_init_ppm=0
oas_rst_ifs_tm5=''
if has_config lpjg:cc_coup
then
    # define initial CO2 concentrations in ppm
    ccycle_co2_init_ppm=284.32
    # set to true to write co2 fluxes
    ccycle_debug_fluxes=true
    config+=" tm5:co2 cc_coup"
    export tm5_exch_nlevs=10
    tm5_time_step_sec=[[[MOD:LPJG:TIME_STEP_SEC]]]
    oas_rst_ifs_tm5=$oas_rst_ifs_tm5' l_co2.nc rlpjg.nc'
fi

# minimum sanity
has_config ifs && error "Cannot have ifs in config"
has_config nemo && error "Cannot have nemo in config"
has_config lpjg:spinup osm && error "Cannot have both lpjg:spinup and osm in config"

# add lpjg_forcing to config when needed (lpjg non-spinup and no osm) - do not specify it in the config directly
has_config lpjg_forcing && error "lpjg:lpjg_forcing not allowed in user config"
has_config lpjg && ! has_config lpjg:spinup && ! has_config osm && config+=" lpjg_forcing"
has_config lpjg_forcing osm && error "Cannot have both lpjg_forcing and osm in config"
has_config lpjg:spinup lpjg_forcing && error "Cannot have both lpjg:spinup and lpjg_forcing in config"

# liblsm.sh defines some OSM and LPJG pre/post-processing functions
has_config any osm lpjg lpjg_forcing && source ./liblsm.sh

# Experiment name (exactly 4 letters!)
export exp_name=[[[MOD:GENERAL:EXP_NAME]]]

# Simulation start and end date. Use any (reasonable) syntax you want.
run_start_date="[[[MOD:GENERAL:RUN_START_DATE]]]"
# define run_start_date_as with proper format e.g. 19900101
export run_start_date_as=$(date -u -d "${run_start_date}" +%Y%m%d)
run_end_date="[[[MOD:GENERAL:RUN_END_DATE]]]"

# 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=[[[MOD:GENERAL:FORCE_RUN_FROM_SCRATCH]]]

# Resolution (only T159 and T255 supported)
ifs_grid=[[[MOD:IFS:GRID]]]
#atm_grid=A128

# Restart frequency. Use any (reasonable) number and time unit you want.
# For runs without restart, leave this variable empty
rst_freq="[[[MOD:GENERAL:RST_FREQ]]]"

# Number of restart legs to be run in one go
run_num_legs=[[[MOD:GENERAL:RUN_NUM_LEGS]]]

# Coupling frequencies
has_config lpjg && cpl_freq_atm_lpjg_hrs=[[[MOD:OASIS:CPL_FREQ_ATM_LPJG_HRS]]] #24

# Directories
start_dir=${PWD}
ctrl_file_dir=${start_dir}/ctrl
output_control_files_dir=${start_dir}/[[[MOD:GENERAL:OUTPUT_CONTROL_FILES_DIR]]]

# Architecture
build_arch=[[[PLT:ACTIVE:BUILD_ARCH]]]
use_machinefile=[[[PLT:ACTIVE:USE_MACHINEFILE]]]

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

# -----------------------------------------------------------------------------
# *** Read platform dependent configuration
# -----------------------------------------------------------------------------
source ./ecconf.cfg

configure

[ -z $TMPDIR ] && error "you must define TMPDIR for your platform!!!"


# -----------------------------------------------------------------------------
# *** IFS/OSM configuration - some variables are needed by LPJG
# -----------------------------------------------------------------------------

ifs_version=36r4

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:')

osm_numproc=[[[MOD:OSM:NUMPROC]]] # 

has_config lpjg && osm_exe_file=${ecearth_src_dir}/ifs-${ifs_version}/src/surf/offline/osm/build/bin/master1s_cpl.exe \
    || osm_exe_file=${ecearth_src_dir}/ifs-${ifs_version}/src/surf/offline/osm/build/bin/master1s.exe

osm_forcing_type="[[[MOD:OSM:OSM_FORCING_TYPE]]]"
osm_ifs_output_dir="[[[MOD:OSM:OSM_IFS_OUTPUT_DIR]]]"
osm_forcing_dir="[[[MOD:OSM:OSM_FORCING_DIR]]]"
#uncomment these lines to use era20c/erai forcings, which are generated with the generate_forcing.sh script
#osm_forcing_type="era20c"
#osm_ifs_output_dir=""
#osm_forcing_dir="${SCRATCH}/ECEARTH-RUNS/OSM_FORCING/${osm_forcing_type}/${ifs_grid}"

export ifs_cmip_fixyear=[[[MOD:IFS:CMIP_FIXYEAR]]]

ifs_cmip6=[[[MOD:IFS:CMIP6]]]
ifs_cmip6_scenario=[[[MOD:IFS:CMIP6_SCENARIO]]]
ifs_cmip_fixyear_ch4=[[[MOD:IFS:CMIP_FIXYEAR_CH4]]]
ifs_A4xCO2=[[[MOD:IFS:CMIP6_A4xCO2]]]
ifs_1PCTCO2=[[[MOD:IFS:CMIP6_1PCTCO2]]]
bgc_1PCTCO2=[[[MOD:IFS:CMIP6_1PCTCO2_BGC]]]

# *** Time step settings
# setting ifs_time_step_sec breaks LPJG-offline oasis config so only set it when osm is active for now
# usually we use the IFS time step setting for the target resolution, but for ERA5 forcing
# we use 1h which is the resolution of the forcing
if has_config osm
then

    case "${ifs_grid}" in
        T159L*) ifs_time_step_sec=3600 ;;
        T255L*) ifs_time_step_sec=2700 ;;
        T511L*) ifs_time_step_sec=900  ;;
        *)  error "Can't set time steps for unknown horizontal grid: ${ifs_grid}"
            ;;
    esac

    if [[ "$osm_forcing_type" != "ifs" ]]
    then
        info "Setting OSM time step to 1h because we are using reanalysis forcing"
        ifs_time_step_sec=3600
    fi

    # ifs_output_freq is defined below for ifs in the esm runscript, here it is hard-coded for osm
    ifs_output_freq=$(( 3 * 3600 / ifs_time_step_sec ))
    #ifs_di_freq=$(( 24 * 3600 / ifs_time_step_sec ))
    #ifs_ddh_freq=$(( 120 * 3600 / ifs_time_step_sec ))
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)
#  cmip6     vegetation from an EC-Earth3-Veg (interactive LPJ-Guess) run 
#            (currently available only for T255)
#  custom_exp vegetation from any EC-Earth3-Veg run exp
#            (must contain same variables as era20c & cmip6 and located in icmcl_exp folder)
#  none      don't create an ICMCL file with vegetation data (this is set
#            automatically if LPJG is used with feedback)
#
ifs_veg_source="cmip6"

has_config lpjg:fdbck && ! has_config osm && ifs_veg_source="none"

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

    case "${ifs_grid}" in
        T159L*) veg_version=v29 ;;
        T255L*) veg_version=v16 ;;
        *)  error "Vegetation from off-line LPJ-Guess not available for ${ifs_grid}" ;;
    esac    
    ;;
"cmip6" )
    # LPJG vegetation is provided as effective cover
    # Don't use Lambert-Beer
    n_compute_eff_veg_fraction=0

    case "${ifs_grid}" in
        T255L*) veg_version=v32 ;;
        *)  error "Vegetation from CMIP6 EC-Earth3-Veg not available for ${ifs_grid}" ;;
    esac    
    ;;
"custom_"* )
    # LPJG vegetation is provided as effective cover
    # Don't use Lambert-Beer
    n_compute_eff_veg_fraction=0

    veg_version=${ifs_veg_source:7}
    if [ ! -d ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version} ]
    then
        error "requested IFS_VEG_SOURCE = ${ifs_veg_source} but not found in ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version}"
    fi
    ;;
"none" )
    # LPJG with feedback
    n_compute_eff_veg_fraction=0
    has_config osm && ! has_config lpjg:fdbck && error "OSM requires an offline source of vegetation"
    ;;
* )
    error "Vegetation from ${ifs_veg_source} not implemented"
    ;;
esac

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

# -----------------------------------------------------------------------------
# *** LPJ-GUESS configuration
# -----------------------------------------------------------------------------

lpjg_time_step_sec=[[[MOD:LPJG:TIME_STEP_SEC]]]
lpjg_numproc=[[[MOD:LPJG:NUMPROC]]]

has_config lpjg       && lpjg_on=1
has_config lpjg:fdbck && lpjg_fdbck=1
has_config tm5:co2    && lpjg_fdbck_tm5=1 || lpjg_fdbck_tm5=0

export lpjg_fixNdepafter=[[[MOD:LPJG:LPJG_FIXNDEPAFTER]]]
export lpjg_fixLUafter=[[[MOD:LPJG:LPJG_FIXLUAFTER]]]

info '!!!! CMIP FIX YEAR SETTINGS:'
info "ifs_cmip_fixyear:  $ifs_cmip_fixyear"
info "lpjg_fixNDepAfter: $lpjg_fixNdepafter"
info "lpjg_fixLUAfter:   $lpjg_fixLUafter"
info '!!!!'  

lpjg_res=T${ifs_res_hor}
lpjg_exe_file=${ecearth_src_dir}/lpjg/build/guess_${lpjg_res}

# -----------------------------------------------------------------------------
# *** LPJ-GUESS offline forcing configuration
# -----------------------------------------------------------------------------

lpjg_forcing_exe_file=${ecearth_src_dir}/lpjg/offline/lpjg_forcing
if $(has_config lpjg_forcing)
then
    case "${ifs_grid}" in
        T159L*) lpjg_forcing_exe_file+="_ifs_T159" ;;
        T255L*) lpjg_forcing_exe_file+="_ifs_T255" ;;
        *) has_config lpjg && error "LPJG offline forcing doesn't exist for ifs-grid: ${ifs_grid}" ;;
    esac
fi
lpjg_forcing_numproc=1

ccycle_coupling_exe_file=${ecearth_src_dir}/lpjg/offline/ccycle_coupling
ccycle_coupling_numproc=1

if $(has_config lpjg)
then
    lpjg_ifs_output_dir="[[[MOD:LPJG:LPJG_IFS_OUTPUT_DIR]]]"
    lpjg_forcing_dir="[[[MOD:LPJG:LPJG_FORCING_DIR]]]"
fi

# 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

# =============================================================================
# *** 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}
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
grib_copy=${GRIB_BIN_PATH}${GRIB_BIN_PATH:+/}grib_copy

# 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

    # Check if legs are integer multiples of full years if LPJG is used
    if has_config lpjg
    then
        
        if [[ $(date +%m%d%T -u -d "${leg_start_date}") != "010100:00:00" || \
            $(date +%m%d%T -u -d "${leg_start_date} + ${rst_freq}") != "010100:00:00" ]]
        then
            error "LPJ-GUESS runs must start on Jan 1 and end on Dec 31. Multi-year legs are allowed."
        fi
    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_yyyy=$(date -u -d "${leg_start_date}" +%Y)
    leg_end_date_yyyy=$(date -u -d "${leg_end_date}" +%Y)
    # compute last full year of the leg, used for ICMCL data and OSM forcing when leg ends on Jan 1st
    if [ $(date -u -d "${leg_end_date}" +%m%d) == "0101" ]
    then
      leg_end_date_yyyy_full=$(( leg_end_date_yyyy - 1 ))
    else
      leg_end_date_yyyy_full=$leg_end_date_yyyy
    fi

    # 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

    # -------------------------------------------------------------------------
    # *** 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
        # ---------------------------------------------------------------------
        if $(has_config osm)
        then
            cp    ${osm_exe_file} .
            ln -s ${osm_exe_file} $(basename ${osm_exe_file}).lnk
        fi
        if $(has_config lpjg)
        then
            cp    ${lpjg_exe_file} .
            ln -s ${lpjg_exe_file} $(basename ${lpjg_exe_file}).lnk
        fi
        if $(has_config lpjg_forcing)
        then
          cp ${lpjg_forcing_exe_file} .
        fi
        if $(has_config cc_coup)
        then
          cp ${ccycle_coupling_exe_file} .
        fi

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

        if $(has_config osm)
        then

        # 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 - not used in OSM yet
        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

        fi #osm

        # ---------------------------------------------------------------------
        # *** Files needed for LPJ-GUESS
        # ---------------------------------------------------------------------
        if $(has_config lpjg)
        then
            # Check for valid grid
            if [ $lpjg_res != "T255" -a $lpjg_res != "T159" ]
            then
                error "LPJG-gridlist doesn't exist for ifs-grid: ${ifs_grid}" 
            fi
            # Initial data - saved state for LPJ-GUESS (.bin format)
            lpjgstartdir=$(printf "lpjg_state_%04d" $leg_start_date_yyyy)
            if ! $(has_config lpjg:spinup)
            then
                ln -sf ${ini_data_dir}/lpjg/ini_state/${lpjg_res}/${lpjgstartdir} ${run_dir}/${lpjgstartdir}
            fi

            # Control files (i.e. .ins, landuse, N deposition, soil type files etc.)
            cp  -f ${ecearth_src_dir}/lpjg/data/ins/*.ins .
            # activate the new litterfall scheme for C4MIP - for the coupled model this is done when both pisces and lpjg are activated
            has_config cc_coup && echo -e "!override for EC-Earth-CC in runscript\nifpftlitterfall 1\ncalc_phen_after_restart 0" >> global.ins
            mkdir -p ${run_dir}/landuse
        fi

        # if running an LPJG spinup, create fast forcing files and link to the ifs_spinup_dir expected by LPJG
        if $(has_config lpjg:spinup)
        then
            lpjg_gen_forcing_spinup
            ln -sf $lpjg_forcing_dir ifs_spinup_forcing
        fi

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

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

        # we should use the L128 grid (only in AMIP grid file)
        # but for now let's use the same files as for the coupled runs
        #oas_grid_dir=${ini_data_dir}/oasis/AMIP
        oas_grid_dir=${ini_data_dir}/oasis/${lpjg_res}-ORCA1
        mycp='cp'

        # Grid definition files
        if $(has_config tm5)
        then
            ${mycp} ${oas_grid_dir}/areas.nc gcm_areas.nc
            ${mycp} ${oas_grid_dir}/grids.nc gcm_grids.nc
            ${mycp} ${oas_grid_dir}/masks.nc gcm_masks.nc

            oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-TM5-LPJG
            cp ${oas_grid_dir}/tm5_areas.nc .
            cp ${oas_grid_dir}/tm5_grids.nc .
            cp ${oas_grid_dir}/tm5_masks.nc .

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

            # -- Get restart files for TM5-IFS/LPJG/PISCES 
            for f in ${oas_rst_ifs_tm5}
            do
                cp ${oas_grid_dir}/rst/${tm5_exch_nlevs}-levels/$f .
            done

            # set CO2 concentrations to 1850 levels as in TM5 code
            if true
            then
                for f in l_co2.nc
                do
                    [ -f $f ] && mv -f $f $f.bak && cdo setrtoc,0,1000,${ccycle_co2_init_ppm} $f.bak $f
                done
            fi

            # -- Merge grid definition files
            cdo merge gcm_areas.nc tm5_areas.nc areas.nc
            cdo merge gcm_grids.nc tm5_grids.nc grids.nc
            cdo merge gcm_masks.nc tm5_masks.nc masks.nc

        else
            ln -s ${oas_grid_dir}/areas.nc
            ln -s ${oas_grid_dir}/grids.nc
            ln -s ${oas_grid_dir}/masks.nc
        fi

    else # i.e. $leg_is_restart == true

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

        # IFS/OSM files
        rm -f ICM{SH,GG}${exp_name}+??????
        
    fi # ! $leg_is_restart

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

    # namelist and namcouple files

    has_config lpjg_forcing  && . ${ctrl_file_dir}/namelist.lpjg_forcing.sh                     > namelist.lpjg_forcing
    has_config cc_coup       && . ${ctrl_file_dir}/namelist.ccycle_coupling.sh                  > namelist.ccycle_coupling

    . ${ctrl_file_dir}/namcouple.sh > namcouple

    # -------------------------------------------------------------------------
    # *** LPJ-GUESS initial data
    # -------------------------------------------------------------------------
    if $(has_config lpjg)
    then
        # LPJG runtime rcfile - update with leg dates
        . ${ctrl_file_dir}/namelist.lpjg.sh > lpjg_steps.rc

        # determine lpjg scenario-name and co2-file middle-fix
        case $(echo ${ifs_cmip6_scenario} | tr '[:upper:]' '[:lower:]') in
            hist*)     lpjg_scen="ssp370"; lu_src="AIM"    ; lpjg_sco2_mfix="AIM-ssp370-1-2-1"            ; lu_file_posfix="2018_10_08.txt";;
            ssp1-1.9*) lpjg_scen="ssp119"; lu_src="IMAGE"  ; lpjg_sco2_mfix="IMAGE-ssp119-1-2-1"          ; lu_file_posfix="2019_03_13.txt";;
            ssp1-2.6*) lpjg_scen="ssp126"; lu_src="IMAGE"  ; lpjg_sco2_mfix="IMAGE-ssp126-1-2-1"          ; lu_file_posfix="2018_10_08.txt";;
            ssp2-4.5*) lpjg_scen="ssp245"; lu_src="MESSAGE"; lpjg_sco2_mfix="MESSAGE-GLOBIOM-ssp245-1-2-1"; lu_file_posfix="2018_10_08.txt";;
            ssp3-7.0*) lpjg_scen="ssp370"; lu_src="AIM"    ; lpjg_sco2_mfix="AIM-ssp370-1-2-1"            ; lu_file_posfix="2018_10_08.txt";;
            ssp4-3.4*) lpjg_scen="ssp434"; lu_src="GCAM"   ; lpjg_sco2_mfix="GCAM4-ssp434-1-2-1"            ; lu_file_posfix="2018_10_08.txt";;
            ssp5-3.4*) lpjg_scen="ssp534os"; lu_src="MAGPIE"; lpjg_sco2_mfix="REMIND-MAGPIE-ssp534-over-1-2-1"            ; lu_file_posfix="2019_05_10.txt";;
            ssp5-8.5*) lpjg_scen="ssp585"; lu_src="MAGPIE" ; lpjg_sco2_mfix="REMIND-MAGPIE-ssp585-1-2-1"  ; lu_file_posfix="2018_10_08.txt";;
            *)  error "Scenario ${ifs_cmip6_scenario} not defined for LPJ-GUESS" ;;
        esac

        lpjg_scenario_new="historical + $lpjg_sco2_mfix"
        lpjg_scenario_info=${run_dir}/lpjg_scenario.info

        if [ -f $lpjg_scenario_info ]
        then
            source $lpjg_scenario_info
            if [ "$lpjg_scenario_new" = "$lpjg_scenario" ]
            then
                lpjg_copy_rte=false
            else
                lpjg_copy_rte=true
            fi
        else
            lpjg_copy_rte=true
        fi

        # copy RTE only if necessary (at beginning of a run or when scenario changes)
        if $lpjg_copy_rte
        then
            # write info about installed scenarios to file
            echo "lpjg_scenario=\"historical + $lpjg_sco2_mfix\"" > $lpjg_scenario_info
            # set file prefixes depending on scenario
            lu_file_prefix="1850_2100_luh2_Hist_ScenarioMIP_UofMD"
            lu_file_midfix="2_1_f"

            lu_path="${ini_data_dir}/lpjg/landuse/${lpjg_res}/${lpjg_scen}"

            # copy and reference-link landuse,  gross transitions, crops, n-fertilisation
            for inp in lu gross crop nfert
            do
                if [ $inp == "crop" -o $inp == "nfert" ]
                then
                    lu_src_file="${lu_path}/${inp}_rfirr_${lu_file_prefix}_${lu_src}_${lpjg_scen}_${lu_file_midfix}_${lpjg_res}_${lu_file_posfix}"
                else
                    lu_src_file="${lu_path}/${inp}_${lu_file_prefix}_${lu_src}_${lpjg_scen}_${lu_file_midfix}_${lpjg_res}_${lu_file_posfix}"
                fi
                cp -f $lu_src_file ${run_dir}/landuse/${inp}_luh2.txt
                ln -fs $lu_src_file ${run_dir}/landuse/${inp}_luh2.txt.lnk
            done
            
            # nitrogen deposition files
            mkdir -p ${run_dir}/ndep
            for inp in drynhx2 drynoy2 wetnhx2 wetnoy2
            do
                ndep_src_file="${ini_data_dir}/lpjg/ndep/${lpjg_res}/${lpjg_scen}/${lpjg_scen}_${lpjg_res}_${inp}.nc"
                cp -f  $ndep_src_file ${run_dir}/ndep/${inp}.nc
                ln -fs  $ndep_src_file ${run_dir}/ndep/${inp}.nc.lnk
            done

            # concatenate historic and scenario (2015+) co2 concentration file
            # hist co2 file 
            lpjg_hco2_file="${ini_data_dir}/ifs/cmip6-data/mole-fraction-of-carbon-dioxide-in-air_input4MIPs_GHGConcentrations_CMIP_UoM-CMIP-1-2-0_gr1-GMNHSH_0000-2014.nc"
            # scenario co2 file 
            lpjg_sco2_file="${ini_data_dir}/ifs/cmip6-data/mole-fraction-of-carbon-dioxide-in-air_input4MIPs_GHGConcentrations_ScenarioMIP_UoM-${lpjg_sco2_mfix}_gr1-GMNHSH_2015-2500.nc"
            # combined file
            lpjg_co2_file="${run_dir}/mole_fraction_of_carbon_dioxide_in_air_input4MIPs_lpjg.nc"
            rm -f $lpjg_co2_file
            cdo mergetime $lpjg_hco2_file $lpjg_sco2_file $lpjg_co2_file
        fi

        # Populate or update LPJG run directories
        if $(has_config lpjg:ioopt)
        then
            export lpjg_numproc
            run_node 'echo creating lpjg temp dirs on `hostname` ; rm -rf $TMPDIR/lpjg/run* ; for (( n=1; n<=${lpjg_numproc}; n++ )) ; do mkdir -p $TMPDIR/lpjg/run${n}/output/CMIP6 ; done ; ls -l $TMPDIR/lpjg/'
        fi
        for (( n=1; n<=${lpjg_numproc}; n++ ))
        do
            # if run from scratch or number of procs has been extended
            if ! $leg_is_restart || [ ! -d ${run_dir}/run${n} ]
            then
                # Make output directories
                # add the ioopt config option if running on one node to speed up output
                if $(has_config lpjg:ioopt)
                then
                    mkdir -p ${run_dir}/run${n}
                    ln -sf $TMPDIR/lpjg/run${n}/output ${run_dir}/run${n}/output
                else
                    mkdir -p ${run_dir}/run${n}/output/CMIP6
                fi

                # Copy *.ins, lpjg_steps.rc and OASIS-MCT restart files
                cp ${run_dir}/*.ins ${run_dir}/run${n}

                # Copy output control files
                cp ${output_control_files_dir}/lpjg_cmip6_output.ins ${run_dir}/run${n}
                ln -s ${output_control_files_dir}/lpjg_cmip6_output.ins ${run_dir}/run${n}/lpjg_cmip6_output.ins.lnk

                cp ${ini_data_dir}/lpjg/oasismct/ghg*.txt ${run_dir}/run${n}
                cp ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/ece_gridlist_${lpjg_res}.txt ${run_dir}/run${n}/ece_gridlist.txt
                ln -s ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/ece_gridlist_${lpjg_res}.txt ${run_dir}/run${n}/ece_gridlist.txt.lnk

                # Data only needed by master or spinup
                if [ $n == 1 ]
                then
                    cp ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/*.nc ${run_dir}
                fi
            fi
            # Refresh output-dirs after they hav been removed at end of the last leg
            mkdir -p ${run_dir}/run${n}/output/CMIP6
            mkdir -p ${run_dir}/run${n}/output/CRESCENDO
        done

        if $leg_is_restart
        then
            lpjg_restart_dir="restart/lpjg/$(printf %03d $((leg_number-1)))"
            lpjg_rst_state="${lpjg_restart_dir}/lpjg_state_${leg_start_date_yyyy}"
            if [ -d "$lpjg_rst_state" ]
            then
                ln -sf $lpjg_rst_state
            else
                echo "lpjg restart dir $lpjg_rst_state not available"
                exit -1
            fi
            # get oasis restart files
            oasis_restart_dir="restart/oasis/$(printf %03d $((leg_number)))"
            cp -f ${oasis_restart_dir}/*.nc ${run_dir}/
        fi

        # generate lpjg_forcing files
        if $(has_config lpjg_forcing)
        then
            lpjg_gen_forcing $leg_start_date_yyyy $leg_end_date_yyyy_full
        fi
    fi

    # -------------------------------------------------------------------------
    # *** Create ICMCL file with vegetation fields
    #     not needed if LPJG is used with feedback
    # -------------------------------------------------------------------------
    if $(has_config osm)
    then

    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,stepRange=0 \
            ${icmclfile}-12 ICMCL${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_full} ; y++ ))
        do
            yy=$(printf "%04d" $y)
            for m in {1..12}
            do
                mm=$(printf "%02d" $m)
                ${grib_set} -s dataDate=${yy}${mm}15,stepRange=0 ${icmclfile}-${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_full+1)))0115,stepRange=0 \
            ${icmclfile}-01 ${tempfile}
        cat ${tempfile} >> ICMCL${exp_name}INIT
        ;;
    "era20c"|"cmip6"|"custom_"* )
        # Vegetation from a LPJG run (off-line or EC-Earth3-Veg)

        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_full+1 ; yr+=1 ))
        do

            case ${ifs_veg_source} in
            'era20c' )
                # no scenario needed with era20c
                icmcl_scenario="" ;;
            'custom_'* )
                # no scenario implemented yet with custom_dir
                icmcl_scenario="" ;;
            'cmip6' )
                # select scenario, use SSP3-7.0 as default
                # if not otherwise specified
                icmcl_scenario="historical"
                if ( [ $ifs_cmip_fixyear -le 0 ] && [ $yr -ge 2015 ] ) || \
                     [ $ifs_cmip_fixyear -ge 2015 ]
                then
                    [[ ${ifs_cmip6_scenario} =~ ^SSP ]] \
                        && icmcl_scenario=${ifs_cmip6_scenario} \
                        || icmcl_scenario='SSP3-7.0'
                fi ;;
            esac
            
            if [ $ifs_cmip_fixyear -le 0 ]
            then
                cat ${ini_data_dir}/ifs/${ifs_grid}/icmcl_${veg_version}/${icmcl_scenario}/icmcl_$yr.grb >> ICMCL${exp_name}INIT
            else
                # Fixed year forcing, requires cdo!
                # 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_${veg_version}/${icmcl_scenario}/icmcl_${ifs_cmip_fixyear}.grb ${tempfile}
                cat ${tempfile} >> ICMCL${exp_name}INIT
            fi
        done
        ;;
    "none" )
        info "no ICMCL file is created"
        ;;
    * )
        error "Vegetation from ${ifs_veg_source} not implemented"
        ;;
    esac

    # Clean up
    rm -f ${tempfile}

    fi #osm

    # ---------------------------------------------------------------------
    # *** Create initial & climatological conditions for osm
    # ---------------------------------------------------------------------
    if $(has_config osm)
    then

        ## create initial conditions
        if ! $leg_is_restart
        then
            osm_gen_init_clim
        fi
        
        # used to generate daily veg from an IFS experiment to force the OSM 
        osm_icmcl_ifs=false 
        if $osm_icmcl_ifs
        then   
          if ! [ -r ${osm_forcing_dir}/ICMCL_${leg_start_date_yyyy} ]
          then
            osm_gen_icmcl_from_ifs $leg_start_date_yyyy
            cp ICMCL${exp_name}INIT ${osm_forcing_dir}/ICMCL_${leg_start_date_yyyy}
          else
          # or get it from osm_forcing dir 
            mv ICMCL${exp_name}INIT ICMCL${exp_name}INIT_ORI
            ln -sf ${osm_forcing_dir}/ICMCL_${leg_start_date_yyyy} ICMCL${exp_name}INIT
          fi 
        fi 
        
        # generate surfveg for osm simulation 
        osm_gen_veg 

        ## create forcing 
        osm_gen_forcing $leg_start_date_yyyy $leg_end_date_yyyy_full
        if [[ $leg_start_date_yyyy == $leg_end_date_yyyy_full ]]
        then
            ln -sf ${osm_forcing_dir}/${leg_start_date_yyyy}/* .
        else
            ln -sf ${osm_forcing_dir}/${leg_start_date_yyyy}-${leg_end_date_yyyy_full}/* .
        fi

        ## generate osm namelist 
        . ${ctrl_file_dir}/namelist.osm.sh > input
    fi

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

    # -------------------------------------------------------------------------
    # *** Start the run
    # -------------------------------------------------------------------------
    # Activate OASIS coupling in OSM if necessary
    has_config osm lpjg && export CPLNG='active'

    # Use the launch function from the platform configuration file
    cmd=""
    if $(has_config lpjg)
    then
        [ "${cmd}" != "" ] && cmd=${cmd}" -- "
        has_config lpjg:spinup && lpjg_spinup="-islpjgspinup" || lpjg_spinup=""
        cmd=${cmd}"${lpjg_numproc} ${lpjg_exe_file} guess.ins ${lpjg_spinup} -parallel"
        has_config lpjg_forcing && cmd=${cmd}" -- ${lpjg_forcing_numproc} ${lpjg_forcing_exe_file}"
        has_config cc_coup && cmd=${cmd}" -- ${ccycle_coupling_numproc} ${ccycle_coupling_exe_file}"
    fi
    if $(has_config osm)
    then
        # TODO pass this only to the osm process?
        export OMP_NUM_THREADS=${osm_numproc}
        ### to do: special "launch" function for OpenMP only run
        [ "${cmd}" != "" ] && cmd=${cmd}" -- "
        cmd=${cmd}"1 ${osm_exe_file}"
    fi

    t1=$(date +%s)
    launch $cmd
    t2=$(date +%s)

    tr=$(date -d "0 -$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, NEMO and TM5 log files. More tests (e.g. checking
    #     restart files) could be implemented.
    # -------------------------------------------------------------------------

    # Check for LPJG/OSM success ???

    # -------------------------------------------------------------------------
    # *** Move LPJ-GUESS output files to archive directory
    # -------------------------------------------------------------------------
    if $(has_config lpjg)
    then
        outdir="output/lpjg/$(printf %03d $((leg_number)))"
        if [ -d ${outdir} ]
        then
            rm -rf  ${outdir}
        fi
        mkdir -p ${outdir}

        if $(has_config lpjg:ioopt)
        then
            for (( n=1; n<=${lpjg_numproc}; n++ )) ; do [ -L ${run_dir}/run${n}/output ] && rm -f ${run_dir}/run${n}/output ; done
            export lpjg_numproc run_dir
            run_node 'echo copying lpjg temp dirs from `hostname` ; for (( n=1; n<=${lpjg_numproc}; n++ )) ; do cp -rvf $TMPDIR/lpjg/run${n}/output/ ${run_dir}/run${n} ; done'
        fi

        # LPJG run directories
        # concatenate *.out (or compressed *.out.gz) files from each run* into output dir
        flist=$(cd ${run_dir}/run1/output && find *.out.gz -type f 2>/dev/null || true)
        if [ "$flist" = "" ]
        then
            lpjg_compress_output=false
            flist=$(cd ${run_dir}/run1/output && find *.out -type f 2>/dev/null)
        else
            lpjg_compress_output=true
        fi

        mkdir ${outdir}/CMIP6

        for (( n=1; n<=${lpjg_numproc}; n++ ))
        do
            for ofile in $flist
            do
                if $lpjg_compress_output
                then
                    [ $n == 1 ] && gzip -c ${run_dir}/run${n}/output/`basename ${ofile} .gz`.hdr > ${outdir}/$ofile
                    cat ${run_dir}/run${n}/output/${ofile} >> ${outdir}/$ofile
                else
                    if (( n == 1 ))
                    then
                        cat ${run_dir}/run${n}/output/${ofile} > ${outdir}/$ofile
                    else
                        awk '(FNR!=1){print $0}' ${run_dir}/run${n}/output/${ofile} >> ${outdir}/$ofile
                    fi
                fi
            done
            rm -rf ${run_dir}/run${n}/output
        done
        
        # move monthly file if available
        if [ -f ${run_dir}/LPJ-GUESS_monthlyoutput.txt ]
        then
            mv ${run_dir}/LPJ-GUESS_monthlyoutput.txt ${outdir}
        fi
    fi

    # -------------------------------------------------------------------------
    # *** Move OSM output files to archive directory
    # -------------------------------------------------------------------------
    if $(has_config osm)
    then
      outdir="output/osm/$(printf %03d $((leg_number)))"
      mkdir -p ${outdir}
      mv o_*.nc $outdir
      rm -f Wind.nc Tair.nc Snowf.nc SWdown.nc Rainf.nc Qair.nc PSurf.nc LWdown.nc
            
      #------------------------------------------------------------------------
      # ** Post-process OSM data 
      #------------------------------------------------------------------------
      osm_post_gen_script ${outdir} ${leg_number}
      # run osm_post script now if post_run is in config
      has_config osm:post_run && . ${exp_name}_osm_post_${leg_number}.sh
    fi

    # -------------------------------------------------------------------------
    # *** Move ccycle_coupling output files to archive directory
    # -------------------------------------------------------------------------
    if $(has_config tm5:co2)
    then
      outdir="output/ccycle/$(printf %03d $((leg_number)))"
      mkdir -p ${outdir}
      rm -f GUE_{CNAT,CANT,CNPP}_*.nc
      mv TM5_Land{CNAT,CANT,CNPP}_*.nc ${outdir}
    fi

    # -------------------------------------------------------------------------
    # *** Move LPJ-GUESS restart files to archive directory
    # -------------------------------------------------------------------------
    if $(has_config lpjg) && ! $(has_config lpjg:spinup)
    then
        outdir="restart/lpjg/$(printf %03d $((leg_number)))"
        if [ -d ${outdir} ]
        then
            rm -rf  ${outdir}
        fi
        mkdir -p ${outdir}

        state_dir="./lpjg_state_$(printf %04d $((leg_end_date_yyyy)))"
        mv ${state_dir} ${outdir}
        # LPJG writes into run1 dir, so mv to main rundir
        mv -f run1/lpjgv.nc .
        has_config tm5:co2 lpjg && mv -f run1/rlpjg.nc .

        # remove restart link
        if $leg_is_restart
        then
            old_state_dir="./lpjg_state_$(printf %04d $((leg_start_date_yyyy)))"
            if [ -L $old_state_dir ]
            then
                rm -f "$old_state_dir"
            fi
        fi
    fi

    # -------------------------------------------------------------------------
    # *** Move OSM restart files to archive directory
    # -------------------------------------------------------------------------
    if $(has_config osm)
    then
      outdir="restart/osm/$(printf %03d $((leg_number)))"
      mkdir -p ${outdir}
      mv restartout.nc $outdir/
      rm -f restartin.nc restartin.nc.lnk
      cp -f $outdir/restartout.nc restartin.nc 
      ln -sf $outdir/restartout.nc restartin.nc.lnk
    fi 

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

    for f in \
        guess.log run1/guess0.log \
        nout.000000 debug.??.?????? A*_??.nc O*_??.nc \
        osm.log input
    do
        test -f ${f} && mv ${f} ${outdir}
    done

    # -------------------------------------------------------------------------
    # *** 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="restart/oasis/$(printf %03d $((leg_number+1)))"
    mkdir -p ${outdir}

    for f in vegin.nc lpjgv.nc
    do
        test -f ${f} && cp ${f} ${outdir}
    done

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

    # Compute CPMIP performance
    sypd="$(cpmip_sypd $leg_length_sec $(($t2 - $t1)))"
    ncores=0
    has_config lpjg      && (( ncores+=${lpjg_numproc} )) || :
    has_config lpjg_forcing  && (( ncores+=${lpjg_forcing_numproc} )) || :
    has_config osm       && (( ncores+=${osm_numproc}  )) || :
    chpsy="$(cpmip_chpsy  $leg_length_sec $(($t2 - $t1 +1)) $ncores)" #t_run+1 prevent div zero, just in case

    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

done # loop over legs

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

exit 0