#!/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="ifs amip" # "GCM forced-SST" : IFS + AMIP # config="ifs amip lpjg:fdbck tm5:co2" # "C-cycle" : forced-GCM + LPJ-Guess + TM5 # config="ifs amip lpjg:fdbck" # "Veg" : forced-GCM + LPJ-Guess # config="ifs amip tm5:chem,o3,ch4,aero" # "AerChem" : forced-GCM + TM5 # # config="ifs nemo lim3 rnfmapper xios:detached oasis" # "GCM" : IFS+NEMO # config="ifs nemo lim3 rnfmapper xios:detached oasis lpjg:fdbck tm5:co2" # "C-cycle" : GCM+LPJG+TM5 # config="ifs nemo lim3 rnfmapper xios:detached oasis lpjg:fdbck" # "Veg" : GCM+LPJ-Guess # config="ifs nemo lim3 rnfmapper xios:detached oasis tm5:chem,o3,ch4,aero" # "AerChem" : GCM+TM5 config="ifs nemo lim3 rnfmapper xios:detached oasis lpjg:fdbck tm5:co2" # minimum sanity has_config amip nemo && error "Cannot have both nemo and amip in config!!" # 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]]]" 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 $run_dir is cleaned! force_run_from_scratch=[[[MOD:GENERAL:FORCE_RUN_FROM_SCRATCH]]] # Resolution (TM5 resolution is set at compilation) ifs_grid=[[[MOD:IFS:GRID]]] nem_grid=[[[MOD:NEM:GRID]]] # Restart frequency. Use any (reasonable) number and time unit you want. # For runs without restart, leave this variable empty rst_freq="[[[MOD:GENERAL:RST_FREQ]]]" # Number of restart legs to be run in one go run_num_legs=[[[MOD:GENERAL:RUN_NUM_LEGS]]] # Coupling frequencies has_config ifs tm5 && cpl_freq_atm_ctm_hrs=[[[MOD:OASIS:CPL_FREQ_ATM_CHE_HRS]]] has_config ifs lpjg && cpl_freq_atm_lpjg_hrs=[[[MOD:OASIS:CPL_FREQ_ATM_LPJG_HRS]]] # Don't change the coupling frequency because UPDCLIE (where SST and SIC # are updated) is called every 24 hours (hardcoded in ifs-36r4/src/ifs/utility/updtim.F90) has_config amip && cpl_freq_amip_sec=86400 # Directories start_dir=${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]]] # This file is used to store information about restarts ece_info_file="ece.info" # ----------------------------------------------------------------------------- # *** Read platform dependent configuration # ----------------------------------------------------------------------------- source ./ecconf.cfg configure # ----------------------------------------------------------------------------- # *** Time step settings # ----------------------------------------------------------------------------- if has_config ifs 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: ${ifs_grid}" ;; esac fi if has_config nemo then case "${nem_grid}" in ORCA1L*) nem_time_step_sec=2700; lim_time_step_sec=2700 ;; ORCA025L*) nem_time_step_sec=900 ; lim_time_step_sec=900 ;; *) error "Can't set time steps for unknown horizontal grid: ${nem_grid}" ;; esac fi if has_config ifs nemo then case "${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 fi # ----------------------------------------------------------------------------- # *** 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=[[[MOD:IFS:NUMPROC]]] ifs_exe_file=${ecearth_src_dir}/ifs-${ifs_version}/bin/ifsmaster-${build_arch} ifs_lastout=false ifs_cmip5=[[[MOD:IFS:CMIP5]]] ifs_cmip5_rcp=[[[MOD:IFS:CMIP5_RCP]]] ifs_cmip_fixyear=[[[MOD:IFS:CMIP_FIXYEAR]]] ifs_cmip6=[[[MOD:IFS:CMIP6]]] ifs_mac2sp=[[[MOD:IFS:CMIP6]]] ifs_cmip6piaer=[[[MOD:IFS:CMIP6]]] ifs_cmip6_scenario=[[[MOD:IFS:CMIP6_SCENARIO]]] lcmip6_strataer_simp=FALSE lcmip6_strataer_full=[[[MOD:IFS:CMIP6]]] lcmip6_strataer_bckgd=FALSE ifs_A4xCO2=[[[MOD:IFS:CMIP6_A4xCO2]]] ifs_1PCTCO2=[[[MOD:IFS:CMIP6_1PCTCO2]]] # Time-varying orbital forcing (Qiong Zhang, SU-2013-09) # https://dev.ec-earth.org/projects/ecearth3/wiki/Orbital_forcing_in_EC-Earth_3 # # ifs_orb_switch=FALSE, no orbital calculations applied # ifs_orb_switch=TRUE, use orbital calculations according to ifs_orb_mode # ifs_orb_mode="fixed_year", or "variable_year", or "fixed_parameters" # fixed_year: calculate the orbital parameters at ifs_orb_iyear, e.g.,1850 # variable_year: calculate orbital parameters annually start from ifs_orb_iyear # fixed_parameters: prescribe orbital parameters for given year ifs_orb_switch=FALSE ifs_orb_mode="variable_year" ifs_orb_iyear=$(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) # cmip6 vegetation from an EC-Earth3-Veg (interactive LPJ-Guess) run # (currently available only for T255) # 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 && 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 ;; "none" ) # LPJG with feedback n_compute_eff_veg_fraction=0 ! has_config lpjg:fdbck && error "IFS requires an offline source of vegetation" ;; * ) error "Vegetation from ${ifs_veg_source} not implemented" ;; esac # use DMI land ice physics and varying snow albedo ifs_landice=false # ----------------------------------------------------------------------------- # *** NEMO/LIM configuration # ----------------------------------------------------------------------------- # This is only needed if the experiment is started from an existing set of NEMO # restart files nem_restart_file_path=${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=[[[MOD:NEM:NUMPROC]]] # ----------------------------------------------------------------------------- # *** Runoff mapper configuration # ----------------------------------------------------------------------------- rnf_exe_file=${ecearth_src_dir}/runoff-mapper/bin/runoff-mapper.exe rnf_numproc=1 # ----------------------------------------------------------------------------- # *** 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 && lpjg_fdbck_tm5=1 || lpjg_fdbck_tm5=0 export lpjg_fixNdepafter=[[[MOD:LPJG:LPJG_FIXNDEPAFTER]]] export lpjg_fixLUafter=[[[MOD:LPJG:LPJG_FIXLUAFTER]]] if [ $ifs_cmip_fixyear -gt 0 ] then info '!!!! CMIP FIX YEAR SETTINGS:' info "ifs_cmip_fixyear: $ifs_cmip_fixyear" info "lpjg_fixNDepAfter: $lpjg_fixNdepafter" info "lpjg_fixLUAfter: $lpjg_fixLUafter" info '!!!!' fi lpjg_res=T${ifs_res_hor} lpjg_exe_file=${ecearth_src_dir}/lpjg/build/guess_${lpjg_res} # ----------------------------------------------------------------------------- # *** AMIP-reader configuration # ----------------------------------------------------------------------------- amip_exe_file=${ecearth_src_dir}/amip-forcing/bin/amip-forcing.exe amip_numproc=1 # ----------------------------------------------------------------------------- # *** TM5 configuration # ----------------------------------------------------------------------------- if $(has_config tm5) then # With TM5, NPRTRV is set to 1 in the namelist. To avoid some out-of-bound # arrays in IFS, we must limit the number of cores for IFS if (( ifs_numproc > (ifs_res_hor+1) )) then error "too much cores requested for IFS, max is $((ifs_res_hor+1))" fi fi has_config tm5:co2 && export tm5_co2=1 || export tm5_co2=0 tm5_time_step_sec=[[[MOD:TM5:TIME_STEP_SEC]]] tm5_numproc=$(( [[[MOD:TM5:NUMPROC_X]]] * [[[MOD:TM5:NUMPROC_Y]]] )) # nb of coupled levels: nb of levels in either TM5 or IFS (must fit what's used at compilation) export tm5_exch_nlevs=34 # limited number of levels for aerosols, # currently set to lmax_conv export tm5_exch_nlevs_cutoff=23 # executable has_config tm5:co2 && tm5_exe_file=${ecearth_src_dir}/tm5mp/build-co2/appl-tm5-co2.x has_config tm5:chem && tm5_exe_file=${ecearth_src_dir}/tm5mp/build/appl-tm5.x # fields sent back to IFS has_config tm5:o3 && tm5_to_ifs=O3 || tm5_to_ifs= has_config tm5:ch4 && tm5_to_ifs=${tm5_to_ifs},CH4 has_config tm5:aero && tm5_to_ifs=${tm5_to_ifs},"\ N2,SU2,BC2,OC2,N3,SU3,BC3,OC3,SS3,DU3,\ N4,SU4,BC4,OC4,SS4,DU4,N5,BC5,OC5,N6,DU6,N7,DU7,\ NO3,MSA,\ AOD_01,AOD_02,AOD_03,AOD_04,AOD_05,AOD_06,AOD_07,AOD_08,AOD_09,AOD_10,AOD_11,AOD_12,AOD_13,AOD_14,\ SSA_01,SSA_02,SSA_03,SSA_04,SSA_05,SSA_06,SSA_07,SSA_08,SSA_09,SSA_10,SSA_11,SSA_12,SSA_13,SSA_14,\ ASF_01,ASF_02,ASF_03,ASF_04,ASF_05,ASF_06,ASF_07,ASF_08,ASF_09,ASF_10,ASF_11,ASF_12,ASF_13,ASF_14" export tm5_to_ifs=$(echo ${tm5_to_ifs} | sed "s/^,//") # coupled to LPJ-Guess? has_config tm5:co2 lpjg && export cpl_tm_guess=T || export cpl_tm_guess=F # ----------------------------------------------------------------------------- # *** OASIS configuration # ----------------------------------------------------------------------------- # Restart files for the coupling fields (note 8 character limit in OASIS) # rstas.nc : atmosphere single-category fields # rstam.nc : atmosphere multi-category fields # rstos.nc : ocean single-category fields # rstom.nc : ocean multi-category fields oas_rst_ifs_nemo="rstas.nc rstos.nc" oas_rst_ifs_tm5="r_hum.nc r_g2d.nc r_udr.nc r_cc_.nc r_clw.nc r_div.nc \ r_cco.nc r_vor.nc r_ddr.nc r_ciw.nc r_tmp.nc r_dmf.nc \ r_s2d.nc r_ccu.nc r_umf.nc" has_config tm5:o3 || has_config tm5:ch4 && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' o3ch4.nc' has_config tm5:aero && oas_rst_ifs_tm5=$oas_rst_ifs_tm5' C???????' # Decide whether the OASIS weight files for interpolation should be linked from # the setup directory (true) or not (false). In the latter case, the weights # are re-computed at the start of the run. oas_link_weights=true # Flux correction for runoff (not calving) sent from Oasis to ocean. # 1.07945 is computed to compensate for a P-E=-0.016 mm/day has_config nemo && oas_mb_fluxcorr=1.07945 # ----------------------------------------------------------------------------- # *** XIOS configuration # ----------------------------------------------------------------------------- xio_exe_file=${ecearth_src_dir}/xios-2.5/bin/xios_server.exe xio_numproc=[[[MOD:XIO:NUMPROC]]] # ----------------------------------------------------------------------------- # *** 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 oas_rst_files=${oas_rst_ifs_nemo} 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} 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_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 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 if $(has_config amip) then cp ${amip_exe_file} . ln -s ${amip_exe_file} $(basename ${amip_exe_file}).lnk fi if $(has_config nemo) then 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 fi if $(has_config lpjg) then cp ${lpjg_exe_file} . ln -s ${lpjg_exe_file} $(basename ${lpjg_exe_file}).lnk fi if $(has_config tm5) then cp ${tm5_exe_file} . ln -s ${tm5_exe_file} $(basename ${tm5_exe_file}).lnk fi # --------------------------------------------------------------------- # *** 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 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) ln -sf ${ini_data_dir}/lpjg/ini_state/${lpjg_res}/${lpjgstartdir} ${run_dir}/${lpjgstartdir} # Control files (i.e. .ins, landuse, N deposition, soil type files etc.) cp -f ${ecearth_src_dir}/lpjg/data/ins/*.ins . mkdir -p ${run_dir}/landuse fi # --------------------------------------------------------------------- # *** Files needed for NEMO (linked) # --------------------------------------------------------------------- if $(has_config nemo) then # 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. # __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 -s ${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 fi # --------------------------------------------------------------------- # *** Files needed for the Runoff mapper (linked) # --------------------------------------------------------------------- has_config rnfmapper && \ ln -s ${ini_data_dir}/runoff-mapper/runoff_maps.nc # ------------------------------------------------------------------------- # *** File and dir needed for TM5 # ------------------------------------------------------------------------- if $(has_config tm5) then tm5_istart=[[[MOD:TM5:ISTART]]] case ${tm5_istart} in 33|32) ln -s \ ${ini_data_dir}/tm5/restart/TM5_restart_${leg_start_date_yyyymmdd}_0000_glb300x200.nc ;; 31) ln -s ${ini_data_dir}/tm5/restart/tm5_save.hdf ;; 5) ln -s ${ini_data_dir}/tm5/restart/tm5_mmix.hdf ;; 2|9) ;; *) error "Unsupported initial fields option (TM5): ${tm5_istart}" ;; esac # Profiling dir for TM5 mkdir -p ${run_dir}/tm5_profile fi # --------------------------------------------------------------------- # *** Files needed for OASIS (linked) # --------------------------------------------------------------------- # Name table file ln -s ${ini_data_dir}/oasis/cf_name_table.txt # -- Get grid definition and weight files for IFS/NEMO or IFS/AMIP coupling has_config nemo && \ oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-ORCA${nem_res_hor} && \ mycp='cp' has_config amip && \ oas_grid_dir=${ini_data_dir}/oasis/AMIP && \ mycp='cdo -f nc copy' # to enforce nc format, needed for 'cdo merge' to work (have nc4c with Primavera files) # 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 else ln -s ${oas_grid_dir}/areas.nc ln -s ${oas_grid_dir}/grids.nc ln -s ${oas_grid_dir}/masks.nc fi # 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 if $(has_config nemo) then case ${nem_res_hor} in 1) oas_ogrd=O1t0 ;; 025) oas_ogrd=Ot25 ;; *) error "Unsupported horizontal resolution (NEMO): ${nem_res_hor}" ;; esac fi if ${oas_link_weights} then for f in ${oas_grid_dir}/rmp_????_to_????_GAUSWGT.nc do ln -s $f done fi if $(has_config ifs nemo) then for f in ${oas_rst_ifs_nemo} do cp ${oas_grid_dir}/rst/$f . done fi # -- Get grid definition, weight and restart files for IFS/TM5 coupling if $(has_config tm5) then oas_grid_dir=${ini_data_dir}/oasis/T${ifs_res_hor}-TM3x2 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 for f in ${oas_rst_ifs_tm5} do cp ${oas_grid_dir}/rst/$f . done # -- 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 fi 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 # TM5 start file type (33 if you have netcdf4 compiled w/ parallel IO, else to 31) tm5_istart=33 if [ $tm5_istart -eq 31 ] && $(has_config tm5) then ln -sf save_${leg_start_date_yyyymmdd}00_glb300x200.hdf tm5_save.hdf fi fi # ! $leg_is_restart #-------------------------------------------------------------------------- # *** Surface restoring and ocean nudging options #-------------------------------------------------------------------------- if $(has_config nemo:ocenudg) ; then ln -fs ${ini_data_dir}/nemo/oce_nudg/temperature*.nc ./ ln -fs ${ini_data_dir}/nemo/oce_nudg/salinity*.nc ./ fi 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]} elif has_config nemo then info "nemo original domain decomposition (not using ELPiN)" fi # ------------------------------------------------------------------------- # *** Initial conditions saved during the run # ------------------------------------------------------------------------- ${do_save_ic} && save_ic_prepare_output # ------------------------------------------------------------------------- # *** Create some control files # ------------------------------------------------------------------------- # Create TM5 runtime rcfile tm5_start_date=$(date -u -d "${leg_start_date}" +%F\ %T) tm5_end_date=$(date -u -d "${leg_end_date}" +%F\ %T) has_config tm5 && ${ecearth_src_dir}/tm5mp/setup_tm5 --no-compile \ --time-start="${tm5_start_date}" --time-final="${tm5_end_date}" \ --istart=${tm5_istart} ${ctrl_file_dir}/tm5-config-run.rc # IFS frequency output for namelist if [ -f postins/pptdddddd0300 ] then ifs_output_freq=$(( 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, AMIP namelist and OASIS namcouple files has_config ifs && . ${ctrl_file_dir}/namelist.ifs.sh > fort.4 has_config nemo && . ${ctrl_file_dir}/namelist.nemo.ref.sh > namelist_ref has_config nemo && . ${ctrl_file_dir}/namelist.nemo-${nem_grid}-coupled.cfg.sh > namelist_cfg has_config lim3 && . ${ctrl_file_dir}/namelist.lim3.ref.sh > namelist_ice_ref has_config lim3 && . ${ctrl_file_dir}/namelist.lim3-${nem_grid}.cfg.sh > namelist_ice_cfg has_config rnfmapper && . ${ctrl_file_dir}/namelist.runoffmapper.sh > namelist.runoffmapper has_config amip && . ${ctrl_file_dir}/namelist.amip.sh > namelist.amip . ${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";; 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 $lpjg_co2_file fi # Populate or update LPJG run directories for (( n=1; n<=${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 mkdir -p ${run_dir}/run${n}/output # 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 if [ $n == 1 ] then cp ${ini_data_dir}/lpjg/oasismct/${lpjg_res}/*.nc ${run_dir} cp ${ini_data_dir}/lpjg/oasismct/lpjgv.txt ${run_dir}/run${n} 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 fi # ------------------------------------------------------------------------- # *** 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"|"cmip6" ) # 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+1 ; yr+=1 )) do case ${ifs_veg_source} in 'era20c' ) # no scenario needed with era20c 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} # ------------------------------------------------------------------------- # *** Link the appropriate NEMO restart files of the previous leg # ------------------------------------------------------------------------- if $leg_is_restart && $(has_config nemo) then ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec - nem_restart_offset ))) for (( n=0 ; n> output/ifs/${prv_leg}/${f} rm -f ${f} else mv ${f} ${outdir} fi done # ------------------------------------------------------------------------- # *** Move NEMO output files to archive directory # ------------------------------------------------------------------------- if $(has_config nemo) then outdir="output/nemo/$(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 fi # ------------------------------------------------------------------------- # *** 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 ${outdir} # LPJG run directories # concatenate *.out files from each run* into output dir flist=$(find ${run_dir}/run1/output -type f | sed "s%${run_dir}/run1/output\/%%") mkdir ${outdir}/CMIP6 for (( n=1; n<=${lpjg_numproc}; n++ )) do for ofile in $flist do 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 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 TM5 output files to archive directory # ------------------------------------------------------------------------- if $(has_config tm5) then outdir="output/tm5/$(printf %03d $((leg_number)))" mkdir -p ${outdir} set +e mv budget_??????????_??????????_global.hdf ${outdir} mv j_statistics_??????????_??????????.hdf ${outdir} mv mmix_??????????_??????????_glb???x???.hdf ${outdir} mv aerocom?_TM5_*_????????_daily.nc ${outdir} mv aerocom?_TM5_*_??????_monthly.nc ${outdir} mv AOD_????_??_??.nc ${outdir} mv -f TM5MP_${exp_name}_griddef.nc ${outdir} mv TM5MP_${exp_name}_TP_????_??_??.nc ${outdir} mv TM5MP_${exp_name}_vmr3_????_??_??.nc ${outdir} mv general_TM5_${exp_name}_??????????_hourly.nc ${outdir} mv general_TM5_${exp_name}_??????_monthly.nc ${outdir} set -e # move profiling files if any if [ "$(ls -A ${run_dir}/tm5_profile)" ] then outdir="output/tm5/profile_$(printf %03d $((leg_number)))" mkdir -p ${outdir} for f in ${run_dir}/tm5_profile/* do test -f ${f} && mv $f ${outdir} done fi fi # ------------------------------------------------------------------------- # *** Move IFS restart files to archive directory # ------------------------------------------------------------------------- if $leg_is_restart then outdir="restart/ifs/$(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 LPJ-GUESS restart files to archive directory # ------------------------------------------------------------------------- if $(has_config lpjg) then outdir="restart/lpjg/$(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 . # 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 NEMO restart files to archive directory # ------------------------------------------------------------------------- if $leg_is_restart && $(has_config nemo) then outdir="restart/nemo/$(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 # ------------------------------------------------------------------------- # *** Move TM5 restart file to archive directory # ------------------------------------------------------------------------- if $leg_is_restart && $(has_config tm5) then outdir="restart/tm5" mkdir -p ${outdir} case ${tm5_istart} in 33) f=TM5_restart_${leg_start_date_yyyymmdd}_0000_glb300x200.nc ;; 31) f=save_${leg_start_date_yyyymmdd}00_glb300x200.hdf ;; esac mv $f ${outdir} fi # ------------------------------------------------------------------------- # *** Copy OASIS restart files to archive directory # NOTE: These files are copied and not moved as they are used in the # next leg! # Note also that the OASIS restart files present at the end of # the leg correspond to the start of the next leg! # ------------------------------------------------------------------------- outdir="restart/oasis/$(printf %03d $((leg_number+1)))" mkdir -p ${outdir} for f in ${oas_rst_ifs_nemo} ${oas_rst_ifs_tm5} vegin.nc lpjgv.nc do test -f ${f} && cp ${f} ${outdir} done # ------------------------------------------------------------------------- # *** Copy rcf files to the archive directory (of the next leg!) # ------------------------------------------------------------------------- outdir="restart/ifs/$(printf %03d $((leg_number+1)))" mkdir -p ${outdir} for f in rcf do test -f ${f} && cp ${f} ${outdir} done # ------------------------------------------------------------------------- # *** Move log files to archive directory # ------------------------------------------------------------------------- outdir="log/$(printf %03d $((leg_number)))" mkdir -p ${outdir} for f in \ ifs.log ifs.stat fort.4 ocean.output \ time.step solver.stat guess.log run1/guess0.log \ amip.log namelist.amip \ nout.000000 debug.??.?????? A*_??.nc O*_??.nc \ ctm.tm5.log.0 do test -f ${f} && mv ${f} ${outdir} done for f in ctm.tm5.log.* do test -f ${f} && \rm -f ${f} done # ------------------------------------------------------------------------- # *** Write the restart control file # ------------------------------------------------------------------------- # Compute CPMIP performance sypd="$(cpmip_sypd $leg_length_sec $(($t2 - $t1)))" ncores=0 has_config nemo && (( ncores+=${nem_numproc} )) || : has_config ifs && (( ncores+=${ifs_numproc} )) || : has_config xios && (( ncores+=${xio_numproc} )) || : has_config rnfmapper && (( ncores+=${rnf_numproc} )) || : has_config lpjg && (( ncores+=${lpjg_numproc} )) || : has_config tm5 && (( ncores+=${tm5_numproc} )) || : has_config amip && (( ncores+=${amip_numproc} )) || : chpsy="$(cpmip_chpsy $leg_length_sec $(($t2 - $t1)) $ncores)" 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