- General User's Guide for running coupled E3SM or standalone component model configurations
- Step-by-step guide for running E3SM using a run script
Example run script: run.v3.LR.historical_0101_b2000.pm-cpu.sh
Copy the script to your home directory
mkdir ~/E3SM_scripts
cp -p /global/cfs/cdirs/e3sm/www/Tutorials/2024/scripts/run.v3.LR.historical_0101_b2000.pm-cpu.sh ~/E3SM_scripts/.
Run the script (create case, build, setup, and submit to run for 1 day using 2 nodes)
cd ~/E3SM_scripts
./run.v3.LR.historical_0101_b2000.pm-cpu.sh
cd $PSCRATCH/E3SMv3/Tutorials/v3.LR.historical_0101_b2000.pm-cpu/tests/custom-2_1x1_ndays
- Prepare to run a 1-year coupled simulation
#!/bin/bash -fe # E3SM Coupled Model Group run_e3sm script template. # # Bash coding style inspired by: # http://kfirlavi.herokuapp.com/blog/2012/11/14/defensive-bash-programming main() { # For debugging, uncomment line below #set -x # --- Configuration flags ---- # Machine and projectreadonly MACHINE=pm-cpu
readonly PROJECT="ntrain6"
# Simulation
readonly COMPSET="WCYCL20TR"
readonly RESOLUTION="ne30pg2_r05_IcoswISC30E3r5"
readonly CASE_NAME="v3.LR.historical_0101_b2000.pm-cpu"
# If this is part of a simulation campaign, ask your group lead about using a case_group label # otherwise, comment out readonly CASE_GROUP="Tutorials-2024" # Code and compilation readonly CHECKOUT="20240504"
readonly BRANCH="master" # 2f10b6c2f4b092da4c8dfcf88aba1bc31164b9e1
readonly CHERRY=( ) readonly DEBUG_COMPILE=false # Run options
readonly MODEL_START_TYPE="branch" # 'initial', 'continue', 'branch', 'hybrid'
readonly START_DATE="2000-01-01"# Additional options for 'branch' and 'hybrid' readonly GET_REFCASE=TRUE #readonly RUN_REFDIR="$PSCRATCH/E3SMv3/${CASE_NAME}/init/2000-01-01-00000" readonly RUN_REFDIR="/global/cfs/cdirs/e3sm/terai/E3SM_restarts/v3.LR.historical_0101/2000-01-01-00000" readonly RUN_REFCASE="v3.LR.historical_0101" readonly RUN_REFDATE="2000-01-01" # Set pathsreadonly CODE_ROOT="/global/cfs/cdirs/e3sm/Tutorials/2024/codes/${CHECKOUT}"
readonly CASE_ROOT="$PSCRATCH/E3SMv3/Tutorials/${CASE_NAME}"# Sub-directories readonly CASE_BUILD_DIR=${CASE_ROOT}/build readonly CASE_ARCHIVE_DIR=${CASE_ROOT}/archive
# Define type of run # short tests: 'XS_1x10_ndays', 'XS_2x5_ndays', 'S_1x10_ndays', 'M_1x10_ndays', 'L_1x10_ndays' # or 'production' for full simulation #readonly run='custom-2_1x2_nsteps' #readonly run='custom-2_1x3_nhours' readonly run='custom-2_1x1_ndays'
⏎
#readonly run='custom-2_1x5_ndays' #readonly run='custom-4_1x5_ndays' #readonly run='custom-4_1x1_nmonths' #readonly run='custom-8_1x5_ndays' #readonly run='S_1x10_ndays' #readonly run='S_2x5_ndays' #readonly run='M_1x10_ndays' #readonly run='production' if [[ "${run}" != "production" ]]; then echo "setting up Short test simulations: ${run}" # Short test simulations tmp=($(echo $run | tr "_" " ")) layout=${tmp[0]} units=${tmp[2]} resubmit=$(( ${tmp[1]%%x*} -1 )) length=${tmp[1]##*x} readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/tests/${run}/case_scripts readonly CASE_RUN_DIR=${CASE_ROOT}/tests/${run}/run readonly PELAYOUT=${layout} readonly WALLTIME="2:00:00" readonly STOP_OPTION=${units} readonly STOP_N=${length} readonly REST_OPTION=${STOP_OPTION} readonly REST_N=${STOP_N} readonly RESUBMIT=${resubmit} readonly DO_SHORT_TERM_ARCHIVING=false else echo "setting up ${run}" # Production simulation readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/case_scripts readonly CASE_RUN_DIR=${CASE_ROOT}/run readonly PELAYOUT="custom-8" readonly WALLTIME="6:30:00" readonly STOP_OPTION="nyears" readonly STOP_N="1" readonly REST_OPTION="nmonths" readonly REST_N="3" readonly RESUBMIT="0" readonly DO_SHORT_TERM_ARCHIVING=false fi # Coupler history readonly HIST_OPTION="nyears" readonly HIST_N="1" # Leave empty (unless you understand what it does) readonly OLD_EXECUTABLE="" # --- Toggle flags for what to do ---- do_fetch_code=false do_create_newcase=true do_case_setup=truedo_case_build=true
do_case_submit=true# --- Now, do the work --- # Make directories created by this script world-readable umask 022 # Fetch code from Github fetch_code # Create case create_newcase # Custom PE layout custom_pelayout # Setup case_setup # Build case_build # Configure runtime options runtime_options # Copy script into case_script directory for provenance copy_script # Submit case_submit # All done echo $'\n----- All done -----\n' }
⏎# ======================= # Custom user_nl settings # ======================= user_nl() { cat << EOF >> user_nl_eam cosp_lite = .true. empty_htapes = .true. avgflag_pertape = 'A','A','A','A','I','I' nhtfrq = 0,-24,-6,-3,-1,0 mfilt = 1,30,120,240,720,1 fincl1 = 'AODALL','AODBC','AODDUST','AODPOM','AODSO4','AODSOA','AODSS','AODVIS', 'CLDLOW','CLDMED','CLDHGH','CLDTOT', 'CLDHGH_CAL','CLDLOW_CAL','CLDMED_CAL','CLD_MISR','CLDTOT_CAL', 'CLMODIS','FISCCP1_COSP','FLDS','FLNS','FLNSC','FLNT','FLUT', 'FLUTC','FSDS','FSDSC','FSNS','FSNSC','FSNT','FSNTOA','FSNTOAC','FSNTC', 'ICEFRAC','LANDFRAC','LWCF','OCNFRAC','OMEGA','PRECC','PRECL','PRECSC','PRECSL','PS','PSL','Q', 'QFLX','QREFHT','RELHUM','SCO','SHFLX','SOLIN','SWCF','T','TAUX','TAUY','TCO', 'TGCLDLWP','TMQ','TREFHT','TREFMNAV','TREFMXAV','TS','U','U10','V','Z3', 'SFbc_a1','SFbc_a3','SFbc_a4','SFdst_a1','SFdst_a3','SFmom_a1','SFmom_a2','SFmom_a3','SFmom_a4', 'SFncl_a1','SFncl_a2','SFncl_a3','SFpom_a1','SFpom_a3','SFpom_a4','SFso4_a1','SFso4_a2','SFso4_a3','SFso4_a5', 'SFsoa_a1','SFsoa_a2','SFsoa_a3','bc_a4_CLXF','pom_a4_CLXF','so4_a1_CLXF','so4_a2_CLXF', 'bc_a1DDF','bc_a3DDF','bc_a4DDF','bc_c1DDF','bc_c3DDF','bc_c4DDF', 'dst_a1DDF','dst_a3DDF','dst_c1DDF','dst_c3DDF','mom_a1DDF','mom_a2DDF','mom_a3DDF','mom_a4DDF', 'mom_c1DDF','mom_c2DDF','mom_c3DDF','mom_c4DDF','ncl_a1DDF','ncl_a2DDF','ncl_a3DDF','ncl_c1DDF','ncl_c2DDF','ncl_c3DDF', 'pom_a1DDF','pom_a3DDF','pom_a4DDF','pom_c1DDF','pom_c3DDF','pom_c4DDF','so4_a1DDF','so4_a2DDF','so4_a3DDF','so4_a5DDF', 'so4_c1DDF','so4_c2DDF','so4_c3DDF','so4_c5DDF','soa_a1DDF','soa_a2DDF','soa_a3DDF','soa_c1DDF','soa_c2DDF','soa_c3DDF', 'bc_a1SFWET','bc_a3SFWET','bc_a4SFWET','bc_c1SFWET','bc_c3SFWET','bc_c4SFWET', 'dst_a1SFWET','dst_a3SFWET','dst_c1SFWET','dst_c3SFWET','mom_a1SFWET','mom_a2SFWET','mom_a3SFWET','mom_a4SFWET', 'mom_c1SFWET','mom_c2SFWET','mom_c3SFWET','mom_c4SFWET', 'ncl_a1SFWET','ncl_a2SFWET','ncl_a3SFWET','ncl_c1SFWET','ncl_c2SFWET','ncl_c3SFWET', 'pom_a1SFWET','pom_a3SFWET','pom_a4SFWET','pom_c1SFWET','pom_c3SFWET','pom_c4SFWET', 'so4_a1SFWET','so4_a2SFWET','so4_a3SFWET','so4_a5SFWET','so4_c1SFWET','so4_c2SFWET','so4_c3SFWET','so4_c5SFWET', 'soa_a1SFWET','soa_a2SFWET','soa_a3SFWET','soa_c1SFWET','soa_c2SFWET','soa_c3SFWET', 'Mass_bc','Mass_dst','Mass_mom','Mass_ncl','Mass_pom','Mass_so4','Mass_soa', 'O3','LHFLX', 'O3_2DTDA_trop','O3_2DTDB_trop','O3_2DTDD_trop','O3_2DTDE_trop','O3_2DTDI_trop','O3_2DTDL_trop', 'O3_2DTDN_trop','O3_2DTDO_trop','O3_2DTDS_trop','O3_2DTDU_trop','O3_2DTRE_trop','O3_2DTRI_trop', 'O3_SRF','NO_2DTDS','NO_TDLgt','NO2_2DTDD','NO2_2DTDS','NO2_TDAcf','CO_SRF','TROPE3D_P','TROP_P', 'CDNUMC','SFDMS','so4_a1_sfgaex1','so4_a2_sfgaex1','so4_a3_sfgaex1','so4_a5_sfgaex1','soa_a1_sfgaex1', 'soa_a2_sfgaex1','soa_a3_sfgaex1','GS_soa_a1','GS_soa_a2','GS_soa_a3','AQSO4_H2O2','AQSO4_O3', 'SFSO2','SO2_CLXF','SO2','DF_SO2','AQ_SO2','GS_SO2','WD_SO2','ABURDENSO4_STR','ABURDENSO4_TRO', 'ABURDENSO4','ABURDENBC','ABURDENDUST','ABURDENMOM','ABURDENPOM','ABURDENSEASALT', 'ABURDENSOA','AODSO4_STR','AODSO4_TRO', 'EXTINCT','AODABS','AODABSBC','CLDICE','CLDLIQ','CLD_CAL_TMPLIQ','CLD_CAL_TMPICE','Mass_bc_srf', 'Mass_dst_srf','Mass_mom_srf','Mass_ncl_srf','Mass_pom_srf','Mass_so4_srf','Mass_soa_srf','Mass_bc_850', 'Mass_dst_850','Mass_mom_850','Mass_ncl_850','Mass_pom_850','Mass_so4_850','Mass_soa_850','Mass_bc_500', 'Mass_dst_500','Mass_mom_500','Mass_ncl_500','Mass_pom_500','Mass_so4_500','Mass_soa_500','Mass_bc_330', 'Mass_dst_330','Mass_mom_330','Mass_ncl_330','Mass_pom_330','Mass_so4_330','Mass_soa_330','Mass_bc_200', 'Mass_dst_200','Mass_mom_200','Mass_ncl_200','Mass_pom_200','Mass_so4_200','Mass_soa_200', 'O3_2DTDD','O3_2DCIP','O3_2DCIL','CO_2DTDS','CO_2DTDD','CO_2DCEP','CO_2DCEL','NO_2DTDD', 'FLNTC','SAODVIS', 'H2OLNZ','CH4LNZ','N2OLNZ','NOYLNZ', 'dst_a1SF','dst_a3SF', 'PHIS','CLOUD','TGCLDIWP','TGCLDCWP','AREL', 'CLDTOT_ISCCP','MEANCLDALB_ISCCP','MEANPTOP_ISCCP','CLD_CAL', 'CLDTOT_CAL_LIQ','CLDTOT_CAL_ICE','CLDTOT_CAL_UN', 'CLDHGH_CAL_LIQ','CLDHGH_CAL_ICE','CLDHGH_CAL_UN', 'CLDMED_CAL_LIQ','CLDMED_CAL_ICE','CLDMED_CAL_UN', 'CLDLOW_CAL_LIQ','CLDLOW_CAL_ICE','CLDLOW_CAL_UN', 'CLWMODIS','CLIMODIS' fincl2 = 'PS', 'FLUT','FSNT','FLNT','PRECT','U200','V200','U850','V850','Z500','OMEGA500', 'TCO','SCO','TREFHTMN:M','TREFHTMX:X','TREFHT','QREFHT','TMQ' fincl3 = 'PS', 'PSL','PRECT','TUQ','TVQ','UBOT','VBOT','TREFHT','FLUT','OMEGA500','TBOT','U850','V850','U200','V200','T200','T500','Z700' fincl4 = 'PRECT' fincl5 = 'O3_SRF' fincl6 = 'CO_2DMSD','NO2_2DMSD','NO_2DMSD','O3_2DMSD','O3_2DMSD_trop' fincl7 = 'PS','Q','T','Z3','CLOUD','CONCLD','CLDICE','CLDLIQ','FREQR','REI','REL','PRECT','TMQ','PRECC','TREFHT','QREFHT','OMEGA','CLDTOT','LHFLX','SHFLX','FLDS','FSDS','FLNS','FSNS','FLNSC','FSDSC','FSNSC','AODVIS','AODABS','LS_FLXPRC','LS_FLXSNW','LS_REFFRAIN','ZMFLXPRC','ZMFLXSNW','CCN1','CCN2','CCN3','CCN4','CCN5','num_a1','num_a2','num_a3','num_a4','so4_a1','so4_a2','so4_a3','AREL','TGCLDLWP','AQRAIN','ANRAIN','FREQR','PRECL','RELHUM' fincl7lonlat='262.5e_36.6n','203.4e_71.3n','147.4e_2.0s','166.9e_0.5s','130.9e_12.4s','331.97e_39.09n' ! -- chemUCI settings ------------------ history_chemdyg_summary = .false. history_gaschmbudget_2D = .true. history_gaschmbudget_2D_levels = .true. history_UCIgaschmbudget_2D = .true. history_UCIgaschmbudget_2D_levels = .true. history_gaschmbudget_num = 6 !! no impact if history_gaschmbudget_2D = .false. ! -- MAM5 settings ------------------ is_output_interactive_volc = .true. history_aero_optics = .true. history_aerosol = .true. history_amwg = .true. history_budget = .true. history_verbose = .true. EOF cat << EOF >> user_nl_elm ! default landuse.timeseries file below probably was created using CMIP5 raw land data. Use the updated one. ! flanduse_timeseries = '\${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/landuse.timeseries_0.5x0.5_hist_simyr1850-2015_c191004.nc' flanduse_timeseries = '\${DIN_LOC_ROOT}/lnd/clm2/surfdata_map/landuse.timeseries_0.5x0.5_hist_simyr1850-2015_c240308.nc' hist_dov2xy = .true.,.true. hist_fexcl1 = 'AGWDNPP','ALTMAX_LASTYEAR','AVAIL_RETRANSP','AVAILC','BAF_CROP', 'BAF_PEATF','BIOCHEM_PMIN_TO_PLANT','CH4_SURF_AERE_SAT','CH4_SURF_AERE_UNSAT','CH4_SURF_DIFF_SAT', 'CH4_SURF_DIFF_UNSAT','CH4_SURF_EBUL_SAT','CH4_SURF_EBUL_UNSAT','CMASS_BALANCE_ERROR','cn_scalar', 'COL_PTRUNC','CONC_CH4_SAT','CONC_CH4_UNSAT','CONC_O2_SAT','CONC_O2_UNSAT', 'cp_scalar','CWDC_HR','CWDC_LOSS','CWDC_TO_LITR2C','CWDC_TO_LITR3C', 'CWDC_vr','CWDN_TO_LITR2N','CWDN_TO_LITR3N','CWDN_vr','CWDP_TO_LITR2P', 'CWDP_TO_LITR3P','CWDP_vr','DWT_CONV_CFLUX_DRIBBLED','F_CO2_SOIL','F_CO2_SOIL_vr', 'F_DENIT_vr','F_N2O_DENIT','F_N2O_NIT','F_NIT_vr','FCH4_DFSAT', 'FINUNDATED_LAG','FPI_P_vr','FPI_vr','FROOTC_LOSS','HR_vr', 'LABILEP_TO_SECONDP','LABILEP_vr','LAND_UPTAKE','LEAF_MR','leaf_npimbalance', 'LEAFC_LOSS','LEAFC_TO_LITTER','LFC2','LITR1_HR','LITR1C_TO_SOIL1C', 'LITR1C_vr','LITR1N_TNDNCY_VERT_TRANS','LITR1N_TO_SOIL1N','LITR1N_vr','LITR1P_TNDNCY_VERT_TRANS', 'LITR1P_TO_SOIL1P','LITR1P_vr','LITR2_HR','LITR2C_TO_SOIL2C','LITR2C_vr', 'LITR2N_TNDNCY_VERT_TRANS','LITR2N_TO_SOIL2N','LITR2N_vr','LITR2P_TNDNCY_VERT_TRANS','LITR2P_TO_SOIL2P', 'LITR2P_vr','LITR3_HR','LITR3C_TO_SOIL3C','LITR3C_vr','LITR3N_TNDNCY_VERT_TRANS', 'LITR3N_TO_SOIL3N','LITR3N_vr','LITR3P_TNDNCY_VERT_TRANS','LITR3P_TO_SOIL3P','LITR3P_vr', 'M_LITR1C_TO_LEACHING','M_LITR2C_TO_LEACHING','M_LITR3C_TO_LEACHING','M_SOIL1C_TO_LEACHING','M_SOIL2C_TO_LEACHING', 'M_SOIL3C_TO_LEACHING','M_SOIL4C_TO_LEACHING','NDEPLOY','NEM','nlim_m', 'o2_decomp_depth_unsat','OCCLP_vr','PDEPLOY','PLANT_CALLOC','PLANT_NDEMAND', 'PLANT_NDEMAND_COL','PLANT_PALLOC','PLANT_PDEMAND','PLANT_PDEMAND_COL','plim_m', 'POT_F_DENIT','POT_F_NIT','POTENTIAL_IMMOB','POTENTIAL_IMMOB_P','PRIMP_TO_LABILEP', 'PRIMP_vr','PROD1P_LOSS','QOVER_LAG','RETRANSN_TO_NPOOL','RETRANSP_TO_PPOOL', 'SCALARAVG_vr','SECONDP_TO_LABILEP','SECONDP_TO_OCCLP','SECONDP_vr','SMIN_NH4_vr', 'SMIN_NO3_vr','SMINN_TO_SOIL1N_L1','SMINN_TO_SOIL2N_L2','SMINN_TO_SOIL2N_S1','SMINN_TO_SOIL3N_L3', 'SMINN_TO_SOIL3N_S2','SMINN_TO_SOIL4N_S3','SMINP_TO_SOIL1P_L1','SMINP_TO_SOIL2P_L2','SMINP_TO_SOIL2P_S1', 'SMINP_TO_SOIL3P_L3','SMINP_TO_SOIL3P_S2','SMINP_TO_SOIL4P_S3','SMINP_vr','SOIL1_HR','SOIL1C_TO_SOIL2C','SOIL1C_vr','SOIL1N_TNDNCY_VERT_TRANS','SOIL1N_TO_SOIL2N','SOIL1N_vr', 'SOIL1P_TNDNCY_VERT_TRANS','SOIL1P_TO_SOIL2P','SOIL1P_vr','SOIL2_HR','SOIL2C_TO_SOIL3C', 'SOIL2C_vr','SOIL2N_TNDNCY_VERT_TRANS','SOIL2N_TO_SOIL3N','SOIL2N_vr','SOIL2P_TNDNCY_VERT_TRANS', 'SOIL2P_TO_SOIL3P','SOIL2P_vr','SOIL3_HR','SOIL3C_TO_SOIL4C','SOIL3C_vr', 'SOIL3N_TNDNCY_VERT_TRANS','SOIL3N_TO_SOIL4N','SOIL3N_vr','SOIL3P_TNDNCY_VERT_TRANS','SOIL3P_TO_SOIL4P', 'SOIL3P_vr','SOIL4_HR','SOIL4C_vr','SOIL4N_TNDNCY_VERT_TRANS','SOIL4N_TO_SMINN', 'SOIL4N_vr','SOIL4P_TNDNCY_VERT_TRANS','SOIL4P_TO_SMINP','SOIL4P_vr','SOLUTIONP_vr', 'TCS_MONTH_BEGIN','TCS_MONTH_END','TOTCOLCH4','water_scalar','WF', 'wlim_m','WOODC_LOSS','WTGQ' hist_fincl1 = 'SNOWDP','COL_FIRE_CLOSS','NPOOL','PPOOL','TOTPRODC' hist_fincl2 = 'H2OSNO', 'FSNO', 'QRUNOFF', 'QSNOMELT', 'FSNO_EFF', 'SNORDSL', 'SNOW', 'FSDS', 'FSR', 'FLDS', 'FIRE', 'FIRA' hist_mfilt = 1,365 hist_nhtfrq = 0,-24 hist_avgflag_pertape = 'A','A' EOF # cat << EOF >> user_nl_mosart rtmhist_fincl2 = 'RIVER_DISCHARGE_OVER_LAND_LIQ' rtmhist_mfilt = 1,365 rtmhist_ndens = 2 rtmhist_nhtfrq = 0,-24 EOF } # ===================================== # Customize MPAS stream files if needed # ===================================== patch_mpas_streams() { echo } # ===================================================== # Custom PE layout: custom-N where N is number of nodes # ===================================================== custom_pelayout(){ if [[ ${PELAYOUT} == custom-* ]]; then echo $'\n CUSTOMIZE PROCESSOR CONFIGURATION:' # Number of cores per node (machine specific) if [ "${MACHINE}" == "chrysalis" ]; then ncore=64 hthrd=1 # hyper-threading, default to non-threading elif [ "${MACHINE}" == "pm-cpu" ]; then ncore=128 hthrd=1 # including pm-cpu fi # Extract number of nodes tmp=($(echo ${PELAYOUT} | tr "-" " ")) nnodes=${tmp[1]} # Applicable to all custom layouts pushd ${CASE_SCRIPTS_DIR} ./xmlchange NTASKS=1 ./xmlchange NTHRDS=1 ./xmlchange ROOTPE=0 ./xmlchange MAX_MPITASKS_PER_NODE=$ncore ./xmlchange MAX_TASKS_PER_NODE=$(( $ncore * $hthrd)) # Layout-specific customization if [ "${nnodes}" == "1" ]; then echo Using custom 1 nodes layout with pm-cpu ./xmlchange CPL_NTASKS=128 ./xmlchange ATM_NTASKS=128 ./xmlchange OCN_NTASKS=128 ./xmlchange OCN_ROOTPE=0 ./xmlchange LND_NTASKS=128 ./xmlchange ROF_NTASKS=128 ./xmlchange ICE_NTASKS=128 ./xmlchange LND_ROOTPE=0 ./xmlchange ROF_ROOTPE=0 elif [ "${nnodes}" == "2" ]; then echo Using custom 2 nodes layout with pm-cpu ./xmlchange CPL_NTASKS=256 ./xmlchange ATM_NTASKS=256 ./xmlchange OCN_NTASKS=256 ./xmlchange OCN_ROOTPE=0 ./xmlchange LND_NTASKS=256 ./xmlchange ROF_NTASKS=256 ./xmlchange ICE_NTASKS=256 ./xmlchange LND_ROOTPE=0 ./xmlchange ROF_ROOTPE=0 elif [ "${nnodes}" == "4" ]; then echo Using custom 4 nodes layout with pm-cpu ./xmlchange CPL_NTASKS=512 ./xmlchange ATM_NTASKS=512 ./xmlchange OCN_NTASKS=512 ./xmlchange OCN_ROOTPE=0 ./xmlchange LND_NTASKS=512 ./xmlchange ROF_NTASKS=512 ./xmlchange ICE_NTASKS=512 ./xmlchange LND_ROOTPE=0 ./xmlchange ROF_ROOTPE=0 elif [ "${nnodes}" == "8" ]; then echo Using custom 8 nodes layout with pm-cpu ./xmlchange CPL_NTASKS=1024 ./xmlchange ATM_NTASKS=1024 ./xmlchange OCN_NTASKS=1024 ./xmlchange OCN_ROOTPE=0 ./xmlchange LND_NTASKS=1024 ./xmlchange ROF_NTASKS=1024 ./xmlchange ICE_NTASKS=1024 ./xmlchange LND_ROOTPE=0 ./xmlchange ROF_ROOTPE=0 else echo 'ERRROR: unsupported layout '${PELAYOUT} exit 401 fi popd fi } ###################################################### ### Most users won't need to change anything below ### ###################################################### #----------------------------------------------------- fetch_code() { if [ "${do_fetch_code,,}" != "true" ]; then echo $'\n----- Skipping fetch_code -----\n' return fi echo $'\n----- Starting fetch_code -----\n' local path=${CODE_ROOT} local repo=E3SM echo "Cloning $repo repository branch $BRANCH under $path" if [ -d "${path}" ]; then echo "ERROR: Directory already exists. Not overwriting" exit 20 fi mkdir -p ${path} pushd ${path} # This will put repository, with all code git clone git@github.com:E3SM-Project/${repo}.git . # Check out desired branch git checkout ${BRANCH} # Custom addition if [ "${CHERRY}" != "" ]; then echo ----- WARNING: adding git cherry-pick ----- for commit in "${CHERRY[@]}" do echo ${commit} git cherry-pick ${commit} done echo ------------------------------------------- fi # Bring in all submodule components git submodule update --init --recursive popd } #----------------------------------------------------- create_newcase() { if [ "${do_create_newcase,,}" != "true" ]; then echo $'\n----- Skipping create_newcase -----\n' return fi echo $'\n----- Starting create_newcase -----\n' if [[ ${PELAYOUT} == custom-* ]]; then layout="M" # temporary placeholder for create_newcase else layout=${PELAYOUT} fi # Base arguments args=" --case ${CASE_NAME} \ --output-root ${CASE_ROOT} \ --script-root ${CASE_SCRIPTS_DIR} \ --handle-preexisting-dirs u \ --compset ${COMPSET} \ --res ${RESOLUTION} \ --machine ${MACHINE} \ --walltime ${WALLTIME} \ --pecount ${PELAYOUT}" # Oprional arguments if [ ! -z "${PROJECT}" ]; then args="${args} --project ${PROJECT}" fi if [ ! -z "${CASE_GROUP}" ]; then args="${args} --case-group ${CASE_GROUP}" fi if [ ! -z "${QUEUE}" ]; then args="${args} --queue ${QUEUE}" fi
${CODE_ROOT}/cime/scripts/create_newcase ${args} ⏎
if [ $? != 0 ]; then echo $'\nNote: if create_newcase failed because sub-directory already exists:' echo $' * delete old case_script sub-directory' echo $' * or set do_newcase=false\n' exit 35 fi } #----------------------------------------------------- case_setup() { if [ "${do_case_setup,,}" != "true" ]; then echo $'\n----- Skipping case_setup -----\n' return fi echo $'\n----- Starting case_setup -----\n' pushd ${CASE_SCRIPTS_DIR} # Setup some CIME directories ./xmlchange EXEROOT=${CASE_BUILD_DIR} ./xmlchange RUNDIR=${CASE_RUN_DIR} # Short term archiving ./xmlchange DOUT_S=${DO_SHORT_TERM_ARCHIVING^^} ./xmlchange DOUT_S_ROOT=${CASE_ARCHIVE_DIR} # Build with COSP, except for a data atmosphere (datm) if [ `./xmlquery --value COMP_ATM` == "datm" ]; then echo $'\nThe specified configuration uses a data atmosphere, so cannot activate COSP simulator\n' else echo $'\nConfiguring E3SM to use the COSP simulator\n' ./xmlchange --id CAM_CONFIG_OPTS --append --val='-cosp' fi # Extracts input_data_dir in case it is needed for user edits to the namelist later local input_data_dir=`./xmlquery DIN_LOC_ROOT --value` # Custom user_nl user_nl
# Finally, run CIME case.setup./case.setup --reset ⏎
popd } #----------------------------------------------------- case_build() { pushd ${CASE_SCRIPTS_DIR} # do_case_build = false if [ "${do_case_build,,}" != "true" ]; then echo $'\n----- case_build -----\n' if [ "${OLD_EXECUTABLE}" == "" ]; then # Ues previously built executable, make sure it exists if [ -x ${CASE_BUILD_DIR}/e3sm.exe ]; then echo 'Skipping build because $do_case_build = '${do_case_build} else echo 'ERROR: $do_case_build = '${do_case_build}' but no executable exists for this case.' exit 297 fi else # If absolute pathname exists and is executable, reuse pre-exiting executable if [ -x ${OLD_EXECUTABLE} ]; then echo 'Using $OLD_EXECUTABLE = '${OLD_EXECUTABLE} cp -fp ${OLD_EXECUTABLE} ${CASE_BUILD_DIR}/ else echo 'ERROR: $OLD_EXECUTABLE = '$OLD_EXECUTABLE' does not exist or is not an executable file.' exit 297 fi fi echo 'WARNING: Setting BUILD_COMPLETE = TRUE. This is a little risky, but trusting the user.' ./xmlchange BUILD_COMPLETE=TRUE # do_case_build = true else echo $'\n----- Starting case_build -----\n' # Turn on debug compilation option if requested if [ "${DEBUG_COMPILE^^}" == "TRUE" ]; then ./xmlchange DEBUG=${DEBUG_COMPILE^^} fi
# Run CIME case.build./case.build ⏎
fi # Some user_nl settings won't be updated to *_in files under the run directory # Call preview_namelists to make sure *_in and user_nl files are consistent. echo $'\n----- Preview namelists -----\n' ./preview_namelists popd } #----------------------------------------------------- runtime_options() { echo $'\n----- Starting runtime_options -----\n' pushd ${CASE_SCRIPTS_DIR} # Set simulation start date ./xmlchange RUN_STARTDATE=${START_DATE} # Segment length ./xmlchange STOP_OPTION=${STOP_OPTION,,},STOP_N=${STOP_N} # Restart frequency ./xmlchange REST_OPTION=${REST_OPTION,,},REST_N=${REST_N} # Coupler history ./xmlchange HIST_OPTION=${HIST_OPTION,,},HIST_N=${HIST_N} # Coupler budgets (always on) ./xmlchange BUDGETS=TRUE # Set resubmissions if (( RESUBMIT > 0 )); then ./xmlchange RESUBMIT=${RESUBMIT} fi # Run type # Start from default of user-specified initial conditions if [ "${MODEL_START_TYPE,,}" == "initial" ]; then ./xmlchange RUN_TYPE="startup" ./xmlchange CONTINUE_RUN="FALSE" # Continue existing run elif [ "${MODEL_START_TYPE,,}" == "continue" ]; then ./xmlchange CONTINUE_RUN="TRUE" echo "Prepare the restart files - copy restart-point files over to ../run for the relocated case" elif [ "${MODEL_START_TYPE,,}" == "branch" ] || [ "${MODEL_START_TYPE,,}" == "hybrid" ]; then ./xmlchange RUN_TYPE=${MODEL_START_TYPE,,} ./xmlchange GET_REFCASE=${GET_REFCASE} ./xmlchange RUN_REFDIR=${RUN_REFDIR} ./xmlchange RUN_REFCASE=${RUN_REFCASE} ./xmlchange RUN_REFDATE=${RUN_REFDATE} echo 'Warning: $MODEL_START_TYPE = '${MODEL_START_TYPE} echo '$RUN_REFDIR = '${RUN_REFDIR} echo '$RUN_REFCASE = '${RUN_REFCASE} echo '$RUN_REFDATE = '${START_DATE} else echo 'ERROR: $MODEL_START_TYPE = '${MODEL_START_TYPE}' is unrecognized. Exiting.' exit 380 fi # Patch mpas streams files patch_mpas_streams popd } #----------------------------------------------------- case_submit() { if [ "${do_case_submit,,}" != "true" ]; then echo $'\n----- Skipping case_submit -----\n' return fi echo $'\n----- Starting case_submit -----\n' pushd ${CASE_SCRIPTS_DIR}
# Run CIME case.submit. Add --a="reservation=xxxx" only when using a reservation. # Change below to just ./case.submit for regular use of this script./case.submit -a="--reservation=e3sm_day1" ⏎
popd } #----------------------------------------------------- copy_script() { echo $'\n----- Saving run script for provenance -----\n' local script_provenance_dir=${CASE_SCRIPTS_DIR}/run_script_provenance mkdir -p ${script_provenance_dir} local this_script_name=`basename $0` local script_provenance_name=${this_script_name}.`date +%Y%m%d-%H%M%S` cp -vp ${this_script_name} ${script_provenance_dir}/${script_provenance_name} } #----------------------------------------------------- # Silent versions of popd and pushd pushd() { command pushd "$@" > /dev/null } popd() { command popd "$@" > /dev/null } # Now, actually run the script #----------------------------------------------------- main⏎Customize for a production one-year coupled simulation using 8 nodes
Check the status of previous 1-day runcd $PSCRATCH/E3SMv3/Tutorials/v3.LR.historical_0101_b2000.pm-cpu
ls -l build/e3sm.execd ~/E3SM_scripts
cp -p run.v3.LR.historical_0101_b2000.pm-cpu.sh run.v3.LR.historical_0101_b2000.1-year.pm-cpu.sh
open this file to edit: run.v3.LR.historical_0101_b2000.1-year.pm-cpu.sh
Reset run type/pe-layout ⏎- comment out the line (L58) readonly run='custom-2_1x1_ndays'
- uncomment the line (L67)
#readonly run='production'- change the following from true to false if you previously ran a successful 1-day run (L115)
do_case_build=trueAlternative: copy over a pre-modified script
- cp -p /global/cfs/cdirs/e3sm/www/Tutorials/2024/scripts/run.v3.LR.historical_0101_b2000.1-year.pm-cpu.sh ~/E3SM_scripts/.
./run.v3.LR.historical_0101_b2000.1-year.pm-cpu.sh
cd $PSCRATCH/E3SMv3/Tutorials/v3.LR.historical_0101_b2000.pm-cpu
- uncomment the line (L67)
- comment out the line (L58)