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Update run-script example for v3 #6274

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Update run-script example for v3 #6274

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148 changes: 112 additions & 36 deletions run_e3sm.template.sh
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
#!/bin/bash -fe

# E3SM Water Cycle v2 run_e3sm script template.
#
# Inspired by v1 run_e3sm script as well as SCREAM group simplified run script.
# E3SM Coupled Model Group run_e3sm script template.
#
# Bash coding style inspired by:
# http://kfirlavi.herokuapp.com/blog/2012/11/14/defensive-bash-programming
Expand All @@ -18,36 +16,38 @@ main() {
# --- Configuration flags ----

# Machine and project
readonly MACHINE=cori-knl
readonly MACHINE=pm-cpu
# BEFORE RUNNING: CHANGE this to your project
readonly PROJECT="e3sm"

# Simulation
readonly COMPSET="WCYCL1850"
readonly RESOLUTION="ne30pg2_EC30to60E2r2"
readonly RESOLUTION="ne30pg2_r05_IcoswISC30E3r5"
# BEFORE RUNNING : CHANGE the following CASE_NAME to desired value
readonly CASE_NAME="your_casename"
# If this is part of a simulation campaign, ask your group lead about using a case_group label
# readonly CASE_GROUP=""

# Code and compilation
readonly CHECKOUT="20210806"
# BEFORE RUNNING: CHANGE CHECKOUT to date string like 20240301
readonly CHECKOUT="latest"
readonly BRANCH="master"
readonly CHERRY=( )
readonly DEBUG_COMPILE=false

# Run options
readonly MODEL_START_TYPE="hybrid" # 'initial', 'continue', 'branch', 'hybrid'
readonly MODEL_START_TYPE="initial" # 'initial', 'continue', 'branch', 'hybrid'
readonly START_DATE="0001-01-01"

# Additional options for 'branch' and 'hybrid'
readonly GET_REFCASE=TRUE
readonly RUN_REFDIR="/global/cscratch1/sd/forsyth/E3SMv2/v2.LR.piControl/init"
readonly RUN_REFCASE="20210625.v2rc3c-GWD.piControl.ne30pg2_EC30to60E2r2.chrysalis"
readonly RUN_REFDATE="1001-01-01" # same as MODEL_START_DATE for 'branch', can be different for 'hybrid'
#readonly RUN_REFDIR=""
#readonly RUN_REFCASE=""
#readonly RUN_REFDATE="" # same as MODEL_START_DATE for 'branch', can be different for 'hybrid'

# Set paths
readonly CODE_ROOT="${HOME}/E3SMv2/code/${CHECKOUT}"
readonly CASE_ROOT="/global/cscratch1/sd/${USER}/E3SMv2/${CASE_NAME}"
readonly CODE_ROOT="${HOME}/E3SMv3/code/${CHECKOUT}"
readonly CASE_ROOT="/pscratch/sd/r/${USER}/e3sm-scratch/${CASE_NAME}"

# Sub-directories
readonly CASE_BUILD_DIR=${CASE_ROOT}/build
Expand All @@ -59,7 +59,7 @@ readonly CASE_ARCHIVE_DIR=${CASE_ROOT}/archive
# or 'production' for full simulation
readonly run='XS_2x5_ndays'
if [ "${run}" != "production" ]; then

echo "setting up Short test simulations: ${run}"
# Short test simulations
tmp=($(echo $run | tr "_" " "))
layout=${tmp[0]}
Expand Down Expand Up @@ -145,36 +145,111 @@ echo $'\n----- All done -----\n'
user_nl() {

cat << EOF >> user_nl_eam
nhtfrq = 0,-24,-6,-6,-3,-24,0
mfilt = 1,30,120,120,240,30,1
avgflag_pertape = 'A','A','I','A','A','A','I'
fexcl1 = 'CFAD_SR532_CAL', 'LINOZ_DO3', 'LINOZ_DO3_PSC', 'LINOZ_O3CLIM', 'LINOZ_O3COL', 'LINOZ_SSO3', 'hstobie_linoz'
fincl1 = 'extinct_sw_inp','extinct_lw_bnd7','extinct_lw_inp','CLD_CAL', 'TREFMNAV', 'TREFMXAV'
fincl2 = 'FLUT','PRECT','U200','V200','U850','V850','Z500','OMEGA500','UBOT','VBOT','TREFHT','TREFHTMN:M','TREFHTMX:X','QREFHT','TS','PS','TMQ','TUQ','TVQ','TOZ', 'FLDS', 'FLNS', 'FSDS', 'FSNS', 'SHFLX', 'LHFLX', 'TGCLDCWP', 'TGCLDIWP', 'TGCLDLWP', 'CLDTOT', 'T250', 'T200', 'T150', 'T100', 'T050', 'T025', 'T010', 'T005', 'T002', 'T001', 'TTOP', 'U250', 'U150', 'U100', 'U050', 'U025', 'U010', 'U005', 'U002', 'U001', 'UTOP', 'FSNT', 'FLNT'
fincl3 = 'PSL','T200','T500','U850','V850','UBOT','VBOT','TREFHT', 'Z700', 'TBOT:M'
fincl4 = 'FLUT','U200','U850','PRECT','OMEGA500'
fincl5 = 'PRECT','PRECC','TUQ','TVQ','QFLX','SHFLX','U90M','V90M'
fincl6 = 'CLDTOT_ISCCP','MEANCLDALB_ISCCP','MEANTAU_ISCCP','MEANPTOP_ISCCP','MEANTB_ISCCP','CLDTOT_CAL','CLDTOT_CAL_LIQ','CLDTOT_CAL_ICE','CLDTOT_CAL_UN','CLDHGH_CAL','CLDHGH_CAL_LIQ','CLDHGH_CAL_ICE','CLDHGH_CAL_UN','CLDMED_CAL','CLDMED_CAL_LIQ','CLDMED_CAL_ICE','CLDMED_CAL_UN','CLDLOW_CAL','CLDLOW_CAL_LIQ','CLDLOW_CAL_ICE','CLDLOW_CAL_UN'
fincl7 = 'O3', 'PS', 'TROP_P'

! Additional retuning
clubb_tk1 = 268.15D0
gw_convect_hcf = 10.0
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',
'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',
'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','PRECT','U200','V200','U850','V850',
'TCO','SCO','TREFHTMN','TREFHTMX','TREFHT','QREFHT'
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'

! -- chemUCI settings ------------------
history_chemdyg_summary = .true.
history_gaschmbudget_2D = .false.
history_gaschmbudget_2D_levels = .false.
history_gaschmbudget_num = 6 !! no impact if history_gaschmbudget_2D = .false.

! -- MAM5 settings ------------------
is_output_interactive_volc = .true.
EOF

cat << EOF >> user_nl_elm
hist_dov2xy = .true.,.true.
finidat = ''
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
check_finidat_year_consistency = .false.
check_dynpft_consistency = .false.
create_crop_landunit = .false.
EOF

}
Expand Down Expand Up @@ -369,6 +444,7 @@ case_build() {

# 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

fi
Expand Down