Revision 3657e4066889b03de1ae808db02c049a13ccca7d authored by Alan V Di Vittorio on 08 December 2023, 23:14:38 UTC, committed by Alan V Di Vittorio on 08 December 2023, 23:14:38 UTC
The model successfully runs to completion for ZLND with functional CO2 downscaling. The linearly downscaled CO2 data have been verified within the GCAM repo code, but not yet in the fortran ehc code (giac repo). Convergence downscaling has not been verified. Restarts work properly. The gcam namelist has been updated to add several options for convergence downscaling and the gcam co2 passing namelist item has been corrected in name. A shell script has been added to gcam/tools that generates the new input base co2 gridded files. The fortran floating point exception checks are still off because the model still fails due to untrapped GCAM nans if these are on (which usually is only when DEBUG=TRUE). This allows for DEBUG to be set to TRUE and for the model to run. The configuration for the boost library for the ehc/gcam now points to the files in the gcam repo for portability. The xerces library configuration has been removed as it is no longer needed by GCAM. The three repo branches (e3sm, giac, gcam) at this commit work together (at least for ZLND), and thse branches are set in the .gitmodules files.
1 parent 2cf7280
run_e3sm.template.sh
#!/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.
#
# Bash coding style inspired by:
# http://kfirlavi.herokuapp.com/blog/2012/11/14/defensive-bash-programming
# TO DO:
# - custom pelayout
main() {
# For debugging, uncomment line below
#set -x
# --- Configuration flags ----
# Machine and project
readonly MACHINE=cori-knl
readonly PROJECT="e3sm"
# Simulation
readonly COMPSET="WCYCL1850"
readonly RESOLUTION="ne30pg2_EC30to60E2r2"
# 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"
readonly BRANCH="master"
readonly CHERRY=( )
readonly DEBUG_COMPILE=false
# Run options
readonly MODEL_START_TYPE="hybrid" # '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'
# Set paths
readonly CODE_ROOT="${HOME}/E3SMv2/code/${CHECKOUT}"
readonly CASE_ROOT="/global/cscratch1/sd/${USER}/E3SMv2/${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_2x5_ndays', 'XS_1x10_ndays', 'S_1x10_ndays',
# 'M_1x10_ndays', 'M2_1x10_ndays', 'M80_1x10_ndays', 'L_1x10_ndays'
# or 'production' for full simulation
readonly run='XS_2x5_ndays'
if [ "${run}" != "production" ]; then
# Short test simulations
tmp=($(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
# Production simulation
readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/case_scripts
readonly CASE_RUN_DIR=${CASE_ROOT}/run
readonly PELAYOUT="L"
readonly WALLTIME="34:00:00"
readonly STOP_OPTION="nyears"
readonly STOP_N="50"
readonly REST_OPTION="nyears"
readonly REST_N="5"
readonly RESUBMIT="9"
readonly DO_SHORT_TERM_ARCHIVING=false
fi
# Coupler history
readonly HIST_OPTION="nyears"
readonly HIST_N="5"
# Leave empty (unless you understand what it does)
readonly OLD_EXECUTABLE=""
# --- Toggle flags for what to do ----
do_fetch_code=true
do_create_newcase=true
do_case_setup=true
do_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
# 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
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
EOF
cat << EOF >> user_nl_elm
hist_dov2xy = .true.,.true.
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
}
patch_mpas_streams() {
echo
}
######################################################
### 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 .
# Setup git hooks
rm -rf .git/hooks
git clone git@github.com:E3SM-Project/E3SM-Hooks.git .git/hooks
git config commit.template .git/hooks/commit.template
# 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 $'\n----- Starting create_newcase -----\n'
if [[ -z "$CASE_GROUP" ]]; then
${CODE_ROOT}/cime/scripts/create_newcase \
--case ${CASE_NAME} \
--output-root ${CASE_ROOT} \
--script-root ${CASE_SCRIPTS_DIR} \
--handle-preexisting-dirs u \
--compset ${COMPSET} \
--res ${RESOLUTION} \
--machine ${MACHINE} \
--project ${PROJECT} \
--walltime ${WALLTIME} \
--pecount ${PELAYOUT}
else
${CODE_ROOT}/cime/scripts/create_newcase \
--case ${CASE_NAME} \
--case-group ${CASE_GROUP} \
--output-root ${CASE_ROOT} \
--script-root ${CASE_SCRIPTS_DIR} \
--handle-preexisting-dirs u \
--compset ${COMPSET} \
--res ${RESOLUTION} \
--machine ${MACHINE} \
--project ${PROJECT} \
--walltime ${WALLTIME} \
--pecount ${PELAYOUT}
fi
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
# 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.
./preview_namelists
fi
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 [ "${MODEL_START_TYPE,,}" == "continue" ]; then
./xmlchange CONTINUE_RUN="TRUE"
elif [ "${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
./case.submit
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
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