[Dart-dev] [5469] DART/branches/development/models/cam/shell_scripts: More appropriate name ...
nancy at ucar.edu
nancy at ucar.edu
Wed Dec 28 11:54:29 MST 2011
Revision: 5469
Author: thoar
Date: 2011-12-28 11:54:29 -0700 (Wed, 28 Dec 2011)
Log Message:
-----------
More appropriate name ... will make it obvious what is different between
a 'startup' run (CESM_setup_startup.csh) and a 'hybrid' run (CESM_setup_hybrid.csh).
Added Paths:
-----------
DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh
Removed Paths:
-------------
DART/branches/development/models/cam/shell_scripts/CESM_notes_TJH.csh
-------------- next part --------------
Deleted: DART/branches/development/models/cam/shell_scripts/CESM_notes_TJH.csh
===================================================================
--- DART/branches/development/models/cam/shell_scripts/CESM_notes_TJH.csh 2011-12-27 21:47:41 UTC (rev 5468)
+++ DART/branches/development/models/cam/shell_scripts/CESM_notes_TJH.csh 2011-12-28 18:54:29 UTC (rev 5469)
@@ -1,469 +0,0 @@
-#!/bin/csh
-#
-# DART software - Copyright 2004 - 2011 UCAR. This open source software is
-# provided by UCAR, "as is", without charge, subject to all terms of use at
-# http://www.image.ucar.edu/DAReS/DART/DART_download
-#
-# $Id$
-
-# ---------------------
-# Purpose
-# ---------------------
-#
-# The real purpose of this set of notes is to record what is needed to configure
-# and build a CESM instance that has CAM, CLM, and CICE as active components
-# in a multi-instance configuration over a single data ocean ... etc.
-# Despite looking like a script, it might best be used as a set of notes.
-# ---------------------
-# How to set the script
-# ---------------------
-# -- Copy this script into your directory
-# -- Choose a case name (by changing "setenv case" ) and save the script as $case.csh
-# -- Set the case options at the top of the script
-# -- If you have source mods, the script assumes that your mods are in: mods_$case.
-# So, if you have source mods, create a subdirectory mods_$case that contains your mods.
-# If you don t have any source mods, the script creates an empty subdirectory mods_$case.
-# -- If you have namelist mods, you need to add them to the namelist template: user_nl_cam_$case
-# Set your namelist variables over there (without modifying the syntax to create user_nl_cam_$case
-# -- Now, you are ready to go. Save your script and submit your run with the command: ./$case.csh
-# The script creates your case, configure, compile and submit your job.
-# -- The script also creates a subdirectory (nml_$case) that contains your namelists.
-#
-# ---------------------
-# Important features
-# ---------------------
-#
-# If you want to change something in your case other than the runtime settings,
-# you need to delete everything and start the run from scratch.
-#
-# ./${CASENAME}.*.clean_build
-# ./configure -cleanall
-
-# ====================================================================
-# ==== Set case options
-# ====================================================================
-
-# ======================
-# case settings
-# ======================
-
-#setenv case F_AMIP_CN
-#setenv compset F_AMIP_CN
- setenv case F2000
- setenv compset F_2000
-setenv ccsmtag cesm1_1_beta06
-setenv resolution f09_f09
-setenv num_instances 10
-
-# had to edit the following to remove the LSB_PJL_... word too long error
-# /glade/home/thoar/cesm1_1_beta04/scripts/ccsm_utils/Machines/mkbatch.bluefire
-# as long as OMP_NUM_THREADS == 1 ... the default is fine.
-
-# ================================
-# define machines and directories
-# ================================
-
-setenv mach bluefire ;# machine
-setenv DARTdir /glade/home/thoar/svn/DART/dev ;# DART executables, scripts and input
-
-setenv cesm_public /glade/proj3/cseg ;# location of public CESM sandbox
-setenv cesm_datadir /glade/proj3/cseg/inputdata
-setenv ccsmroot ${cesm_public}/collections/${ccsmtag} ;# location of the public cesm code
-setenv ccsmroot /glade/home/thoar/${ccsmtag} ;# location of your personal cesm code
-setenv caseroot /glade/user/thoar/cases/${case} ;# your (future) cesm case directory
-setenv rundir /glade/scratch/thoar/${case} ;# (future) run-time directory
-setenv archdir /glade/scratch/thoar/archive/${case} ;# (future) short-term archive directory
-
-# ======================
-# clear out previous builds
-# ======================
-
-echo "removing old files from ${caseroot} and ${rundir}"
-\rm -fr ${caseroot}
-\rm -fr ${rundir}
-
-# ======================
-# configure settings
-# ======================
-
-setenv run_startdate 2008-10-31
-
-setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
-setenv year_start 1850
-setenv year_end 2010
-
-# ======================
-# runtime settings
-# ======================
-
-setenv resubmit 0
-setenv stop_n 12
-setenv stop_option nhours
-
-# ======================
-# job settings
-# ======================
-
-setenv proj 93300315
-setenv timewall 5:00
-setenv queue regular
-
-# ======================
-# namelist variables
-# ======================
-# Create namelist templates that get copied once the case has been configured.
-
-setenv this_dir `pwd`
-
-cat <<EOF >! user_nl_cam_${case}
-&camexp
- inithist = 'ENDOFRUN'
- div24del2flag = 4
- bndtvghg = '${cesm_datadir}/atm/cam/ggas/ghg_rcp45_1765-2500_c100405.nc'
- prescribed_ozone_datapath = '${cesm_datadir}/atm/cam/ozone'
- prescribed_ozone_file = 'ozone_1.9x2.5_L26_1850-2015_rcp45_c101108.nc'
- prescribed_ozone_name = 'O3'
- prescribed_ozone_type = 'INTERP_MISSING_MONTHS'
- prescribed_volcaero_datapath = '${cesm_datadir}/atm/cam/volc'
- prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
- solar_data_file = '${cesm_datadir}/atm/cam/solar/SOLAR_TSI_Lean_1610-2140_annual_c100301.nc'
- prescribed_aero_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
- prescribed_aero_file = 'aero_rcp45_v1_1.9x2.5_L26_1995-2105_c100316.nc'
- aerodep_flx_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
- aerodep_flx_file = 'aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
-/
-EOF
-
-cat <<EOF >! user_nl_clm_${case}
-&clmexp
- fpftdyn = '${cesm_datadir}/lnd/clm2/surfdata/surfdata.pftdyn_0.9x1.25_rcp4.5_simyr1850-2100_c100406.nc'
- faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
-/
-EOF
-
-# ====================================================================
-# ==== End of case options
-# ====================================================================
-
-# ====================================================================
-# Create a new case, configure, and build.
-# For list of the cases: ./create_newcase -list
-# ====================================================================
-
-${ccsmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
- -res ${resolution} -compset ${compset} -skip_rundb
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be created."
- exit 1
-endif
-
-# Change Tools/Templates/cam.cpl7.template
-# ncdata = '${RUN_REFCASE}.cam.i.${RUN_REFDATE}-00000.nc'
-# to
-# ncdata = '${RUN_REFCASE}.cam_\$INST_ATM.i.${RUN_REFDATE}-${RUN_REFTOD}.nc'
-
-# Add the RUN_REFTOD xml crap
-# cesm1_1_beta04/scripts/ccsm_utils/Case.template/config_definition.xml
-
-
-cd ${caseroot}
-
-./xmlchange -file env_build.xml -id EXEROOT -val ${rundir}
-./xmlchange -file env_build.xml -id USE_ESMF_LIB -val TRUE
-#./xmlchange -file env_build.xml -id ESMF_LIBDIR -val ${nancy_scratch}/esmf-mpi
-
-set num_tasks_per_instance = 16
-set nthreads = 1
-@ total_nt = $num_instances * $num_tasks_per_instance
-
-./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val $total_nt
-./xmlchange -file env_mach_pes.xml -id NTHRDS_ATM -val $nthreads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_ATM -val 0
-./xmlchange -file env_mach_pes.xml -id NINST_ATM -val $num_instances
-
-./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val $total_nt
-./xmlchange -file env_mach_pes.xml -id NTHRDS_LND -val $nthreads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_LND -val 0
-./xmlchange -file env_mach_pes.xml -id NINST_LND -val $num_instances
-
-./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val $total_nt
-./xmlchange -file env_mach_pes.xml -id NTHRDS_ICE -val $nthreads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_ICE -val 0
-./xmlchange -file env_mach_pes.xml -id NINST_ICE -val $num_instances
-
-./xmlchange -file env_conf.xml -id RUN_TYPE -val hybrid
-./xmlchange -file env_conf.xml -id RUN_STARTDATE -val $run_startdate
-./xmlchange -file env_conf.xml -id RUN_REFDATE -val $run_startdate
-./xmlchange -file env_conf.xml -id RUN_REFCASE -val ref_${case}
-./xmlchange -file env_conf.xml -id GET_REFCASE -val FALSE
-
-#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_FILENAME -val $sst_dataset #TJH WARNING not being set in F2000!
-#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_START -val $year_start
-#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_END -val $year_end
-./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val '-rtm off'
-#./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val '-bgc cn -rtm off'
-
-./xmlchange -file env_run.xml -id RESUBMIT -val $resubmit
-./xmlchange -file env_run.xml -id STOP_OPTION -val $stop_option
-./xmlchange -file env_run.xml -id STOP_N -val $stop_n
-./xmlchange -file env_run.xml -id CALENDAR -val GREGORIAN
-
-# Substantial archiving changes exist in the Tools/st_archive.sh script.
-# DOUT_S is to turn on/off the short-term archiving
-# DOUT_L_MS is to store to the HPSS (formerly "MSS")
-./xmlchange -file env_run.xml -id DOUT_S_ROOT -val ${archdir}
-./xmlchange -file env_run.xml -id DOUT_S -val TRUE
-./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val TRUE
-./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE
-./xmlchange -file env_run.xml -id DOUT_L_HTAR -val TRUE
-
-# ====================================================================
-# Create namelist template: user_nl_cam
-# ====================================================================
-
-\mv -f ${this_dir}/user_nl_cam_{$case} ${caseroot}/user_nl_cam
-\mv -f ${this_dir}/user_nl_clm_{$case} ${caseroot}/user_nl_clm
-
-# ====================================================================
-# Update source files if need be
-# ====================================================================
-
-\cp -rf ~/${ccsmtag}/SourceMods/* ${caseroot}/SourceMods/
-if ( $status == 0) then
- echo "FYI - Local Source Modifications used for this case:"
- ls -lr ${caseroot}/SourceMods/*
-else
- echo "FYI - No SourceMods for this case"
-endif
-
-# ====================================================================
-# Configure
-# ====================================================================
-
-cd ${caseroot}
-./configure -case
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be configured."
- exit 2
-endif
-
-# ====================================================================
-# Stage a copy of the DART assimilate.csh script HERE
-# ====================================================================
-
-cd ${caseroot}
-
-\mv Tools/st_archive.sh Tools/st_archive.sh.org
-\cp -f ${DARTdir}/models/cam/shell_scripts/st_archive.sh Tools/st_archive.sh
-
-\cp -f ${DARTdir}/models/cam/shell_scripts/assimilate.csh .
-
-# ====================================================================
-# update the namelists and scripts as needed
-# ====================================================================
-
-echo ''
-echo 'Editing the Buildconf/{cam,cice,clm}.buildnml.csh files'
-echo ''
-
-cd ${caseroot}/Buildconf
-
-cp -f cam.buildnml.csh cam.buildnml.csh.org
-cp -f cice.buildnml.csh cice.buildnml.csh.org
-cp -f clm.buildnml.csh clm.buildnml.csh.org
-
-# The CAM buildnml script only needs changing in one place.
-
-ex cam.buildnml.csh <<ex_end
-/cam_inparm/
-/ncdata/
-s;= '.*';= "cam_initial_\${atm_inst_counter}.nc";
-wq
-ex_end
-
-# The CICE buildnml script only needs changing in one place.
-
-ex cice.buildnml.csh <<ex_end
-/setup_nml/
-/ice_ic/
-s;= '.*';= "ice_restart_\${ice_inst_counter}.nc";
-wq
-ex_end
-
-# The CLM buildnml script needs changing in MANY places.
-
-@ n = 1
-while ($n <= $num_instances)
- set inst = `printf "%04d" $n`
- ex clm.buildnml.csh <<ex_end
-/lnd_in_$inst/
-/finidat/
-s;= '.*';= "clm_restart_${n}.nc";
-wq
-ex_end
- @ n++
-end
-
-# ====================================================================
-# The *.run script must be modified to call the DART assimilate script.
-# The modifications are contained in a "here" document that MUST NOT
-# expand the wildcards etc., before it is run. This is achieved by
-# double-quoting the characters used to delineate the start/stop of
-# the "here" document. No kidding. It has to be "EndOfText"
-# ====================================================================
-
-cd ${caseroot}
-
-echo ''
-echo 'Adding the call to assimilate.csh to the *.run script.'
-echo ''
-
-cat << "EndOfText" >! add_to_run.txt
-
-# -------------------------------------------------------------------------
-# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
-# perform an assimilation with DART.
-# -------------------------------------------------------------------------
-
-set CplLogFile = `ls -1t cpl.log* | head -1`
-if ($CplLogFile == "") then
- echo 'ERROR: Model did not complete - no cpl.log file present - exiting'
- echo 'ERROR: Assimilation will not be attempted.'
- exit -4
-endif
-
-grep 'SUCCESSFUL TERMINATION' $CplLogFile
-if ( $status == 0 ) then
- ${CASEROOT}/assimilate.csh
-
- if ( $status == 0 ) then
- echo "`date` -- DART HAS FINISHED"
- else
- echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
- exit -5
- endif
-endif
-
-# END OF DART BLOCK
-# -------------------------------------------------------------------------
-
-"EndOfText"
-
-# Now that the "here" document is created,
-# determine WHERE to insert it.
-
-set MYSTRING = `grep --line-number "CSM EXECUTION HAS FINISHED" ${case}.${mach}.run`
-set MYSTRING = `echo $MYSTRING | sed -e "s#:# #g"`
-
-@ orglen = `cat ${case}.${mach}.run | wc -l`
-@ keep = $MYSTRING[1]
-@ lastlines = $orglen - $keep
-
-mv ${case}.${mach}.run ${case}.${mach}.run.orig
-
-head -$keep ${case}.${mach}.run.orig >! ${case}.${mach}.run
-cat add_to_run.txt >> ${case}.${mach}.run
-tail -$lastlines ${case}.${mach}.run.orig >> ${case}.${mach}.run
-
-# ====================================================================
-# IMPORTANT: All resubmits must be coldstarts.
-# Change Tools/ccsm_postrun.csh line 83 to CONTINUE_RUN -val FALSE'
-# ====================================================================
-
-cd ${caseroot}/Tools
-
-echo ''
-echo 'Changing Tools/ccsm_postrun.csh such that all the resubmits are coldstarts,'
-echo 'which means CONTINUE_RUN should be FALSE in ccsm_postrun.csh'
-echo ''
-
-# TJH turning off to see what happens with a BRANCH run
-#ex ccsm_postrun.csh <<ex_end
-#/use COMP_RUN_BARRIERS as surrogate for timing run logical/
-#/CONTINUE_RUN/
-#s;TRUE;FALSE;
-#wq
-#ex_end
-
-# ====================================================================
-# build
-# ====================================================================
-
-cd ${caseroot}
-
-echo ''
-echo 'Building the case'
-echo ''
-
-./$case.$mach.build
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be built."
- exit 3
-endif
-
-# ====================================================================
-# Stage the restarts now that the run directory exists
-# ====================================================================
-
-# 20081031 ... /ptmp/thoar/restarts
-# 20080801 ... /glade/proj3/DART/raeder/FV1deg_4.0/Exp1/obs_0000
-set stagedir = /glade/proj3/DART/raeder/FV1deg_4.0/Exp1/obs_0000
-
-echo ''
-echo "Staging the restarts from {$stagedir}"
-echo ''
-
-@ n = 1
-while ($n <= $num_instances)
-
- echo "Staging restarts for instance $n of $num_instances"
- cp ${stagedir}/CAM/caminput_${n}.nc ${rundir}/run/cam_initial_${n}.nc
- cp ${stagedir}/CLM/clminput_${n}.nc ${rundir}/run/clm_restart_${n}.nc
- cp ${stagedir}/ICE/iceinput_${n}.nc ${rundir}/run/ice_restart_${n}.nc
-
- @ n++
-end
-
-echo 'If inflation is being used ... '
-echo "must stage a ${rundir}/[prior,pos]_inflate_restart.YYYY-MM-DD-SSSSS"
-
-# ====================================================================
-# Edit the run script to reflect project, queue, and wallclock
-# ====================================================================
-
-set PROJ=`grep BSUB $case.$mach.run | grep -e '-P' `
-sed s/$PROJ[3]/$proj/ < $case.$mach.run >! temp
-/bin/mv temp $case.$mach.run
-
-set TIMEWALL=`grep BSUB $case.$mach.run | grep -e '-W' `
-sed s/$TIMEWALL[3]/$timewall/ < $case.$mach.run >! temp
-/bin/mv temp $case.$mach.run
-
-set QUEUE=`grep BSUB $case.$mach.run | grep -e '-q' `
-sed s/$QUEUE[3]/$queue/ < $case.$mach.run >! temp
-/bin/mv temp $case.$mach.run
-
-chmod 0744 $case.$mach.run
-
-# ====================================================================
-# Submit job
-# ====================================================================
-
-set MYSTRING = `grep "set DARTDIR" assimilate.csh`
-set DARTDIR = $MYSTRING[4]
-
-echo ''
-echo 'case is ready to submit after you check the'
-echo "DART settings in ${DARTDIR}/input.nml"
-echo 'After you check them,'
-echo "cd into ${caseroot} and run: ./$case.$mach.submit"
-echo ''
-
-exit
-
-cd ${caseroot}
-./$case.$mach.submit
-
Copied: DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh (from rev 5468, DART/branches/development/models/cam/shell_scripts/CESM_notes_TJH.csh)
===================================================================
--- DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh (rev 0)
+++ DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh 2011-12-28 18:54:29 UTC (rev 5469)
@@ -0,0 +1,469 @@
+#!/bin/csh
+#
+# DART software - Copyright 2004 - 2011 UCAR. This open source software is
+# provided by UCAR, "as is", without charge, subject to all terms of use at
+# http://www.image.ucar.edu/DAReS/DART/DART_download
+#
+# $Id$
+
+# ---------------------
+# Purpose
+# ---------------------
+#
+# The real purpose of this set of notes is to record what is needed to configure
+# and build a CESM instance that has CAM, CLM, and CICE as active components
+# in a multi-instance configuration over a single data ocean ... etc.
+# Despite looking like a script, it might best be used as a set of notes.
+# ---------------------
+# How to set the script
+# ---------------------
+# -- Copy this script into your directory
+# -- Choose a case name (by changing "setenv case" ) and save the script as $case.csh
+# -- Set the case options at the top of the script
+# -- If you have source mods, the script assumes that your mods are in: mods_$case.
+# So, if you have source mods, create a subdirectory mods_$case that contains your mods.
+# If you don t have any source mods, the script creates an empty subdirectory mods_$case.
+# -- If you have namelist mods, you need to add them to the namelist template: user_nl_cam_$case
+# Set your namelist variables over there (without modifying the syntax to create user_nl_cam_$case
+# -- Now, you are ready to go. Save your script and submit your run with the command: ./$case.csh
+# The script creates your case, configure, compile and submit your job.
+# -- The script also creates a subdirectory (nml_$case) that contains your namelists.
+#
+# ---------------------
+# Important features
+# ---------------------
+#
+# If you want to change something in your case other than the runtime settings,
+# you need to delete everything and start the run from scratch.
+#
+# ./${CASENAME}.*.clean_build
+# ./configure -cleanall
+
+# ====================================================================
+# ==== Set case options
+# ====================================================================
+
+# ======================
+# case settings
+# ======================
+
+#setenv case F_AMIP_CN
+#setenv compset F_AMIP_CN
+ setenv case F2000
+ setenv compset F_2000
+setenv ccsmtag cesm1_1_beta06
+setenv resolution f09_f09
+setenv num_instances 10
+
+# had to edit the following to remove the LSB_PJL_... word too long error
+# /glade/home/thoar/cesm1_1_beta04/scripts/ccsm_utils/Machines/mkbatch.bluefire
+# as long as OMP_NUM_THREADS == 1 ... the default is fine.
+
+# ================================
+# define machines and directories
+# ================================
+
+setenv mach bluefire ;# machine
+setenv DARTdir /glade/home/thoar/svn/DART/dev ;# DART executables, scripts and input
+
+setenv cesm_public /glade/proj3/cseg ;# location of public CESM sandbox
+setenv cesm_datadir /glade/proj3/cseg/inputdata
+setenv ccsmroot ${cesm_public}/collections/${ccsmtag} ;# location of the public cesm code
+setenv ccsmroot /glade/home/thoar/${ccsmtag} ;# location of your personal cesm code
+setenv caseroot /glade/user/thoar/cases/${case} ;# your (future) cesm case directory
+setenv rundir /glade/scratch/thoar/${case} ;# (future) run-time directory
+setenv archdir /glade/scratch/thoar/archive/${case} ;# (future) short-term archive directory
+
+# ======================
+# clear out previous builds
+# ======================
+
+echo "removing old files from ${caseroot} and ${rundir}"
+\rm -fr ${caseroot}
+\rm -fr ${rundir}
+
+# ======================
+# configure settings
+# ======================
+
+setenv run_startdate 2008-10-31
+
+setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
+setenv year_start 1850
+setenv year_end 2010
+
+# ======================
+# runtime settings
+# ======================
+
+setenv resubmit 0
+setenv stop_n 12
+setenv stop_option nhours
+
+# ======================
+# job settings
+# ======================
+
+setenv proj 93300315
+setenv timewall 5:00
+setenv queue regular
+
+# ======================
+# namelist variables
+# ======================
+# Create namelist templates that get copied once the case has been configured.
+
+setenv this_dir `pwd`
+
+cat <<EOF >! user_nl_cam_${case}
+&camexp
+ inithist = 'ENDOFRUN'
+ div24del2flag = 4
+ bndtvghg = '${cesm_datadir}/atm/cam/ggas/ghg_rcp45_1765-2500_c100405.nc'
+ prescribed_ozone_datapath = '${cesm_datadir}/atm/cam/ozone'
+ prescribed_ozone_file = 'ozone_1.9x2.5_L26_1850-2015_rcp45_c101108.nc'
+ prescribed_ozone_name = 'O3'
+ prescribed_ozone_type = 'INTERP_MISSING_MONTHS'
+ prescribed_volcaero_datapath = '${cesm_datadir}/atm/cam/volc'
+ prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
+ solar_data_file = '${cesm_datadir}/atm/cam/solar/SOLAR_TSI_Lean_1610-2140_annual_c100301.nc'
+ prescribed_aero_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
+ prescribed_aero_file = 'aero_rcp45_v1_1.9x2.5_L26_1995-2105_c100316.nc'
+ aerodep_flx_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
+ aerodep_flx_file = 'aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+/
+EOF
+
+cat <<EOF >! user_nl_clm_${case}
+&clmexp
+ fpftdyn = '${cesm_datadir}/lnd/clm2/surfdata/surfdata.pftdyn_0.9x1.25_rcp4.5_simyr1850-2100_c100406.nc'
+ faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+/
+EOF
+
+# ====================================================================
+# ==== End of case options
+# ====================================================================
+
+# ====================================================================
+# Create a new case, configure, and build.
+# For list of the cases: ./create_newcase -list
+# ====================================================================
+
+${ccsmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
+ -res ${resolution} -compset ${compset} -skip_rundb
+
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be created."
+ exit 1
+endif
+
+# Change Tools/Templates/cam.cpl7.template
+# ncdata = '${RUN_REFCASE}.cam.i.${RUN_REFDATE}-00000.nc'
+# to
+# ncdata = '${RUN_REFCASE}.cam_\$INST_ATM.i.${RUN_REFDATE}-${RUN_REFTOD}.nc'
+
+# Add the RUN_REFTOD xml crap
+# cesm1_1_beta04/scripts/ccsm_utils/Case.template/config_definition.xml
+
+
+cd ${caseroot}
+
+./xmlchange -file env_build.xml -id EXEROOT -val ${rundir}
+./xmlchange -file env_build.xml -id USE_ESMF_LIB -val TRUE
+#./xmlchange -file env_build.xml -id ESMF_LIBDIR -val ${nancy_scratch}/esmf-mpi
+
+set num_tasks_per_instance = 16
+set nthreads = 1
+@ total_nt = $num_instances * $num_tasks_per_instance
+
+./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val $total_nt
+./xmlchange -file env_mach_pes.xml -id NTHRDS_ATM -val $nthreads
+./xmlchange -file env_mach_pes.xml -id ROOTPE_ATM -val 0
+./xmlchange -file env_mach_pes.xml -id NINST_ATM -val $num_instances
+
+./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val $total_nt
+./xmlchange -file env_mach_pes.xml -id NTHRDS_LND -val $nthreads
+./xmlchange -file env_mach_pes.xml -id ROOTPE_LND -val 0
+./xmlchange -file env_mach_pes.xml -id NINST_LND -val $num_instances
+
+./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val $total_nt
+./xmlchange -file env_mach_pes.xml -id NTHRDS_ICE -val $nthreads
+./xmlchange -file env_mach_pes.xml -id ROOTPE_ICE -val 0
+./xmlchange -file env_mach_pes.xml -id NINST_ICE -val $num_instances
+
+./xmlchange -file env_conf.xml -id RUN_TYPE -val hybrid
+./xmlchange -file env_conf.xml -id RUN_STARTDATE -val $run_startdate
+./xmlchange -file env_conf.xml -id RUN_REFDATE -val $run_startdate
+./xmlchange -file env_conf.xml -id RUN_REFCASE -val ref_${case}
+./xmlchange -file env_conf.xml -id GET_REFCASE -val FALSE
+
+#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_FILENAME -val $sst_dataset #TJH WARNING not being set in F2000!
+#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_START -val $year_start
+#./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_END -val $year_end
+./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val '-rtm off'
+#./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val '-bgc cn -rtm off'
+
+./xmlchange -file env_run.xml -id RESUBMIT -val $resubmit
+./xmlchange -file env_run.xml -id STOP_OPTION -val $stop_option
+./xmlchange -file env_run.xml -id STOP_N -val $stop_n
+./xmlchange -file env_run.xml -id CALENDAR -val GREGORIAN
+
+# Substantial archiving changes exist in the Tools/st_archive.sh script.
+# DOUT_S is to turn on/off the short-term archiving
+# DOUT_L_MS is to store to the HPSS (formerly "MSS")
+./xmlchange -file env_run.xml -id DOUT_S_ROOT -val ${archdir}
+./xmlchange -file env_run.xml -id DOUT_S -val TRUE
+./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val TRUE
+./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE
+./xmlchange -file env_run.xml -id DOUT_L_HTAR -val TRUE
+
+# ====================================================================
+# Create namelist template: user_nl_cam
+# ====================================================================
+
+\mv -f ${this_dir}/user_nl_cam_{$case} ${caseroot}/user_nl_cam
+\mv -f ${this_dir}/user_nl_clm_{$case} ${caseroot}/user_nl_clm
+
+# ====================================================================
+# Update source files if need be
+# ====================================================================
+
+\cp -rf ~/${ccsmtag}/SourceMods/* ${caseroot}/SourceMods/
+if ( $status == 0) then
+ echo "FYI - Local Source Modifications used for this case:"
+ ls -lr ${caseroot}/SourceMods/*
+else
+ echo "FYI - No SourceMods for this case"
+endif
+
+# ====================================================================
+# Configure
+# ====================================================================
+
+cd ${caseroot}
+./configure -case
+
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be configured."
+ exit 2
+endif
+
+# ====================================================================
+# Stage a copy of the DART assimilate.csh script HERE
+# ====================================================================
+
+cd ${caseroot}
+
+\mv Tools/st_archive.sh Tools/st_archive.sh.org
+\cp -f ${DARTdir}/models/cam/shell_scripts/st_archive.sh Tools/st_archive.sh
+
+\cp -f ${DARTdir}/models/cam/shell_scripts/assimilate.csh .
+
+# ====================================================================
+# update the namelists and scripts as needed
+# ====================================================================
+
+echo ''
+echo 'Editing the Buildconf/{cam,cice,clm}.buildnml.csh files'
+echo ''
+
+cd ${caseroot}/Buildconf
+
+cp -f cam.buildnml.csh cam.buildnml.csh.org
+cp -f cice.buildnml.csh cice.buildnml.csh.org
+cp -f clm.buildnml.csh clm.buildnml.csh.org
+
+# The CAM buildnml script only needs changing in one place.
+
+ex cam.buildnml.csh <<ex_end
+/cam_inparm/
+/ncdata/
+s;= '.*';= "cam_initial_\${atm_inst_counter}.nc";
+wq
+ex_end
+
+# The CICE buildnml script only needs changing in one place.
+
+ex cice.buildnml.csh <<ex_end
+/setup_nml/
+/ice_ic/
+s;= '.*';= "ice_restart_\${ice_inst_counter}.nc";
+wq
+ex_end
+
+# The CLM buildnml script needs changing in MANY places.
+
+@ n = 1
+while ($n <= $num_instances)
+ set inst = `printf "%04d" $n`
+ ex clm.buildnml.csh <<ex_end
+/lnd_in_$inst/
+/finidat/
+s;= '.*';= "clm_restart_${n}.nc";
+wq
+ex_end
+ @ n++
+end
+
+# ====================================================================
+# The *.run script must be modified to call the DART assimilate script.
+# The modifications are contained in a "here" document that MUST NOT
+# expand the wildcards etc., before it is run. This is achieved by
+# double-quoting the characters used to delineate the start/stop of
+# the "here" document. No kidding. It has to be "EndOfText"
+# ====================================================================
+
+cd ${caseroot}
+
+echo ''
+echo 'Adding the call to assimilate.csh to the *.run script.'
+echo ''
+
+cat << "EndOfText" >! add_to_run.txt
+
+# -------------------------------------------------------------------------
+# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
+# perform an assimilation with DART.
+# -------------------------------------------------------------------------
+
+set CplLogFile = `ls -1t cpl.log* | head -1`
+if ($CplLogFile == "") then
+ echo 'ERROR: Model did not complete - no cpl.log file present - exiting'
+ echo 'ERROR: Assimilation will not be attempted.'
+ exit -4
+endif
+
+grep 'SUCCESSFUL TERMINATION' $CplLogFile
+if ( $status == 0 ) then
+ ${CASEROOT}/assimilate.csh
+
+ if ( $status == 0 ) then
+ echo "`date` -- DART HAS FINISHED"
+ else
+ echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
+ exit -5
+ endif
+endif
+
+# END OF DART BLOCK
+# -------------------------------------------------------------------------
+
+"EndOfText"
+
+# Now that the "here" document is created,
+# determine WHERE to insert it.
+
+set MYSTRING = `grep --line-number "CSM EXECUTION HAS FINISHED" ${case}.${mach}.run`
+set MYSTRING = `echo $MYSTRING | sed -e "s#:# #g"`
+
+@ orglen = `cat ${case}.${mach}.run | wc -l`
+@ keep = $MYSTRING[1]
+@ lastlines = $orglen - $keep
+
+mv ${case}.${mach}.run ${case}.${mach}.run.orig
+
+head -$keep ${case}.${mach}.run.orig >! ${case}.${mach}.run
+cat add_to_run.txt >> ${case}.${mach}.run
+tail -$lastlines ${case}.${mach}.run.orig >> ${case}.${mach}.run
+
+# ====================================================================
+# IMPORTANT: All resubmits must be coldstarts.
+# Change Tools/ccsm_postrun.csh line 83 to CONTINUE_RUN -val FALSE'
+# ====================================================================
+
+cd ${caseroot}/Tools
+
+echo ''
+echo 'Changing Tools/ccsm_postrun.csh such that all the resubmits are coldstarts,'
+echo 'which means CONTINUE_RUN should be FALSE in ccsm_postrun.csh'
+echo ''
+
+# TJH turning off to see what happens with a BRANCH run
+#ex ccsm_postrun.csh <<ex_end
+#/use COMP_RUN_BARRIERS as surrogate for timing run logical/
+#/CONTINUE_RUN/
+#s;TRUE;FALSE;
+#wq
+#ex_end
+
+# ====================================================================
+# build
+# ====================================================================
+
+cd ${caseroot}
+
+echo ''
+echo 'Building the case'
+echo ''
+
+./$case.$mach.build
+
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be built."
+ exit 3
+endif
+
+# ====================================================================
+# Stage the restarts now that the run directory exists
+# ====================================================================
+
+# 20081031 ... /ptmp/thoar/restarts
+# 20080801 ... /glade/proj3/DART/raeder/FV1deg_4.0/Exp1/obs_0000
+set stagedir = /glade/proj3/DART/raeder/FV1deg_4.0/Exp1/obs_0000
+
+echo ''
+echo "Staging the restarts from {$stagedir}"
+echo ''
+
+@ n = 1
+while ($n <= $num_instances)
+
+ echo "Staging restarts for instance $n of $num_instances"
+ cp ${stagedir}/CAM/caminput_${n}.nc ${rundir}/run/cam_initial_${n}.nc
+ cp ${stagedir}/CLM/clminput_${n}.nc ${rundir}/run/clm_restart_${n}.nc
+ cp ${stagedir}/ICE/iceinput_${n}.nc ${rundir}/run/ice_restart_${n}.nc
+
+ @ n++
+end
+
+echo 'If inflation is being used ... '
+echo "must stage a ${rundir}/[prior,pos]_inflate_restart.YYYY-MM-DD-SSSSS"
+
+# ====================================================================
+# Edit the run script to reflect project, queue, and wallclock
+# ====================================================================
+
+set PROJ=`grep BSUB $case.$mach.run | grep -e '-P' `
+sed s/$PROJ[3]/$proj/ < $case.$mach.run >! temp
+/bin/mv temp $case.$mach.run
+
+set TIMEWALL=`grep BSUB $case.$mach.run | grep -e '-W' `
+sed s/$TIMEWALL[3]/$timewall/ < $case.$mach.run >! temp
+/bin/mv temp $case.$mach.run
+
+set QUEUE=`grep BSUB $case.$mach.run | grep -e '-q' `
+sed s/$QUEUE[3]/$queue/ < $case.$mach.run >! temp
+/bin/mv temp $case.$mach.run
+
+chmod 0744 $case.$mach.run
+
+# ====================================================================
+# Submit job
+# ====================================================================
+
+set MYSTRING = `grep "set DARTDIR" assimilate.csh`
+set DARTDIR = $MYSTRING[4]
+
+echo ''
+echo 'case is ready to submit after you check the'
+echo "DART settings in ${DARTDIR}/input.nml"
+echo 'After you check them,'
+echo "cd into ${caseroot} and run: ./$case.$mach.submit"
+echo ''
+
+exit
+
+cd ${caseroot}
+./$case.$mach.submit
+
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