Changes between Version 55 and Version 56 of Projects/NEMOVAR/Notes


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Timestamp:
14/07/15 11:33:42 (4 years ago)
Author:
cthomas
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  • Projects/NEMOVAR/Notes

    v55 v56  
    279279}}} 
    280280 
    281  
    282 ==== run_nemo_cice ==== 
    283  
    284 The script that steers the job is called `run_nemo_cice`.  
    285 It has different sections for nemo_cice_obsoper and nemo_cice_iau.  
    286  
    287 The common part governs some setup and the running of the model.  
    288 Extracts from the common part are: 
    289 {{{ 
    290 # MODE - ['standalone', 'obsoper', 'iau'] 
    291 # CYCLE_LENGTH - ISO8601 duration specifying the length of this cycle 
    292 # RUNID - identifying string 
    293 # INDIR_EXEC - path to executable 
    294 # INDIR_FLUXES - directory containing fluxes 
    295 # INDIR_ANCILLARY - directory containing ancillary files 
    296 # INDIR_BACKGROUND_RESTARTS - directory containing background restarts 
    297 # OUTDIR_ANALYSIS_RESTARTS - directory in which we put analysis restarts 
    298 # NEMO_IPROC - NEMO processors east-west 
    299 # NEMO_JPROC - NEMO processors north-south 
    300 # NEMO_NPROC - total number of NEMO processors 
    301 # CICE_COL - number of columns for CICE 
    302 # CICE_ROW - number of rows for CICE 
    303  
    304 NEMO_NL=namelist 
    305 CICE_NL=ice_in 
    306  
    307 # Link in common inputs 
    308 mkdir -p $CYLC_TASK_WORK_DIR/fluxes 
    309 ln -sf $INDIR_FLUXES/* $CYLC_TASK_WORK_DIR/fluxes 
    310 ln -sf $INDIR_ANCILLARY/* $CYLC_TASK_WORK_DIR 
    311 ln -sf $INDIR_BACKGROUND_RESTARTS/* $CYLC_TASK_WORK_DIR 
    312  
    313 # Re-link the coordinate and geothermal heating files per processor 
    314 i=0 
    315 while [[ $i -lt $NEMO_NPROC ]]; do 
    316     ln -sf coordinates.nc coordinates_$(printf "%04d" $i).nc 
    317     ln -sf geothermal_heating.nc geothermal_heating_$(printf "%04d" $i).nc 
    318     let i=i+1 
    319 done 
    320  
    321 # Modify main NEMO namelist 
    322 update_namelist $NEMO_NL cn_exp "'${RUNID}o'" 
    323 update_namelist $NEMO_NL ln_rstart .true. 
    324 update_namelist $NEMO_NL nn_rstctl 0 
    325 update_namelist $NEMO_NL nn_it000 1 
    326 update_namelist $NEMO_NL nn_itend ${TIME_STEPS_PER_CYCLE} 
    327 update_namelist $NEMO_NL nn_date0 "$(rose date -c -f %Y%m%d)" 
    328 update_namelist $NEMO_NL nn_leapy ${NEMO_LEAP_YEAR_FLAG} 
    329 update_namelist $NEMO_NL jpni ${NEMO_IPROC} 
    330 update_namelist $NEMO_NL jpnj ${NEMO_JPROC} 
    331 update_namelist $NEMO_NL jpnij ${NEMO_NPROC} 
    332 update_namelist $NEMO_NL nitiaufin ${TIME_STEPS_PER_DAY} 
    333  
    334 # Modify main CICE namelist 
    335 update_namelist $CICE_NL days_per_year ${DAYS_IN_YEAR} 
    336 update_namelist $CICE_NL history_file "'${RUNID}i.${CICE_HISTFREQ_N}${CICE_HISTFREQ}'" #CT - could remove? 
    337 update_namelist $CICE_NL ice_ic "'cice_restart.dat'" 
    338 update_namelist $CICE_NL incond_file "'${RUNID}i_ic'" 
    339 update_namelist $CICE_NL istep0 ${TIME_STEPS_TO_START} 
    340 update_namelist $CICE_NL npt ${TIME_STEPS_PER_CYCLE} 
    341 update_namelist $CICE_NL restart .true. 
    342 update_namelist $CICE_NL restart_file "'cice_restart.dat'" 
    343 update_namelist $CICE_NL use_leap_years ${CICE_LEAP_YEAR_FLAG} 
    344 update_namelist $CICE_NL year_init $(rose date -c -f %Y) 
    345  
    346 echo ${INDIR_EXEC}/nemo.exe:${NEMO_NPROC} > Ocean.conf 
    347 rose mpi-launch -f Ocean.conf 
    348 NEMO_RC=$? 
    349 }}} 
    350  
    351  
    352 === nemo_cice_obsoper === 
    353  
    354 ==== Prerequisites ==== 
    355  
    356 nemo_cice_obsoper depends on `fcm_make_nemo`, `fixed_ancillary`, `fixed_restarts`, `daily_fluxes`, `DAILY_OBSERVATIONS`.  
    357 During the cycling it also depends on the nemo_cice_iau stage.  
    358  
    359 ==== suite.rc ==== 
    360  
    361 In `suite.rc`, all of the nemo_cice variables listed above are inherited. In addition the following environment variables are defined: 
    362 {{{ 
    363             ROSE_APP_OPT_CONF_KEYS = "obsoper" 
    364             INDIR_ALTBIAS=$ALTBIAS_DIR 
    365             INDIR_OBSERVATIONS=$OBSERVATIONS_DIR 
    366             OUTDIR_INNOVATIONS=$INNOVATIONS_DIR 
    367             OUTDIR_ASSIM_BACKGROUND=$ASSIM_BACKGROUND_DIR 
    368 }}} 
    369  
    370 From the rose documentation on `ROSE_APP_OPT_CONF_KEYS`:  
    371 Each KEY in this space delimited list switches on an optional configuration in an application. The configurations are applied in first-to-last order. 
    372281 
    373282==== App ==== 
     
    425334}}} 
    426335 
     336 
     337==== run_nemo_cice ==== 
     338 
     339The script that steers the job is called `run_nemo_cice`.  
     340It has different sections for nemo_cice_obsoper and nemo_cice_iau.  
     341 
     342The common part governs some setup and the running of the model.  
     343Extracts from the common part are: 
     344{{{ 
     345# MODE - ['standalone', 'obsoper', 'iau'] 
     346# CYCLE_LENGTH - ISO8601 duration specifying the length of this cycle 
     347# RUNID - identifying string 
     348# INDIR_EXEC - path to executable 
     349# INDIR_FLUXES - directory containing fluxes 
     350# INDIR_ANCILLARY - directory containing ancillary files 
     351# INDIR_BACKGROUND_RESTARTS - directory containing background restarts 
     352# OUTDIR_ANALYSIS_RESTARTS - directory in which we put analysis restarts 
     353# NEMO_IPROC - NEMO processors east-west 
     354# NEMO_JPROC - NEMO processors north-south 
     355# NEMO_NPROC - total number of NEMO processors 
     356# CICE_COL - number of columns for CICE 
     357# CICE_ROW - number of rows for CICE 
     358 
     359NEMO_NL=namelist 
     360CICE_NL=ice_in 
     361 
     362# Link in common inputs 
     363mkdir -p $CYLC_TASK_WORK_DIR/fluxes 
     364ln -sf $INDIR_FLUXES/* $CYLC_TASK_WORK_DIR/fluxes 
     365ln -sf $INDIR_ANCILLARY/* $CYLC_TASK_WORK_DIR 
     366ln -sf $INDIR_BACKGROUND_RESTARTS/* $CYLC_TASK_WORK_DIR 
     367 
     368# Re-link the coordinate and geothermal heating files per processor 
     369i=0 
     370while [[ $i -lt $NEMO_NPROC ]]; do 
     371    ln -sf coordinates.nc coordinates_$(printf "%04d" $i).nc 
     372    ln -sf geothermal_heating.nc geothermal_heating_$(printf "%04d" $i).nc 
     373    let i=i+1 
     374done 
     375 
     376# Modify main NEMO namelist 
     377update_namelist $NEMO_NL cn_exp "'${RUNID}o'" 
     378update_namelist $NEMO_NL ln_rstart .true. 
     379update_namelist $NEMO_NL nn_rstctl 0 
     380update_namelist $NEMO_NL nn_it000 1 
     381update_namelist $NEMO_NL nn_itend ${TIME_STEPS_PER_CYCLE} 
     382update_namelist $NEMO_NL nn_date0 "$(rose date -c -f %Y%m%d)" 
     383update_namelist $NEMO_NL nn_leapy ${NEMO_LEAP_YEAR_FLAG} 
     384update_namelist $NEMO_NL jpni ${NEMO_IPROC} 
     385update_namelist $NEMO_NL jpnj ${NEMO_JPROC} 
     386update_namelist $NEMO_NL jpnij ${NEMO_NPROC} 
     387update_namelist $NEMO_NL nitiaufin ${TIME_STEPS_PER_DAY} 
     388 
     389# Modify main CICE namelist 
     390update_namelist $CICE_NL days_per_year ${DAYS_IN_YEAR} 
     391update_namelist $CICE_NL history_file "'${RUNID}i.${CICE_HISTFREQ_N}${CICE_HISTFREQ}'" #CT - could remove? 
     392update_namelist $CICE_NL ice_ic "'cice_restart.dat'" 
     393update_namelist $CICE_NL incond_file "'${RUNID}i_ic'" 
     394update_namelist $CICE_NL istep0 ${TIME_STEPS_TO_START} 
     395update_namelist $CICE_NL npt ${TIME_STEPS_PER_CYCLE} 
     396update_namelist $CICE_NL restart .true. 
     397update_namelist $CICE_NL restart_file "'cice_restart.dat'" 
     398update_namelist $CICE_NL use_leap_years ${CICE_LEAP_YEAR_FLAG} 
     399update_namelist $CICE_NL year_init $(rose date -c -f %Y) 
     400 
     401echo ${INDIR_EXEC}/nemo.exe:${NEMO_NPROC} > Ocean.conf 
     402rose mpi-launch -f Ocean.conf 
     403NEMO_RC=$? 
     404}}} 
     405 
     406 
     407=== nemo_cice_obsoper === 
     408 
     409==== Prerequisites ==== 
     410 
     411nemo_cice_obsoper depends on `fcm_make_nemo`, `fixed_ancillary`, `fixed_restarts`, `daily_fluxes`, `DAILY_OBSERVATIONS`.  
     412During the cycling it also depends on the nemo_cice_iau stage.  
     413 
     414==== suite.rc ==== 
     415 
     416In `suite.rc`, all of the nemo_cice variables listed above are inherited. In addition the following environment variables are defined: 
     417{{{ 
     418            ROSE_APP_OPT_CONF_KEYS = "obsoper" 
     419            INDIR_ALTBIAS=$ALTBIAS_DIR 
     420            INDIR_OBSERVATIONS=$OBSERVATIONS_DIR 
     421            OUTDIR_INNOVATIONS=$INNOVATIONS_DIR 
     422            OUTDIR_ASSIM_BACKGROUND=$ASSIM_BACKGROUND_DIR 
     423}}} 
     424 
     425From the rose documentation on `ROSE_APP_OPT_CONF_KEYS`:  
     426Each KEY in this space delimited list switches on an optional configuration in an application. The configurations are applied in first-to-last order. 
     427 
     428==== App ==== 
     429 
    427430Extracts from `opt/rose-app-obsoper.conf`: 
    428431{{{