[Dart-dev] [5449] DART/branches/development/models/cam/shell_scripts: Updates to the scripts to run the Zagar test on hopper.
nancy at ucar.edu
nancy at ucar.edu
Wed Dec 14 16:28:56 MST 2011
Revision: 5449
Author: nancy
Date: 2011-12-14 16:28:55 -0700 (Wed, 14 Dec 2011)
Log Message:
-----------
Updates to the scripts to run the Zagar test on hopper.
Should be in sync with tim's scripts to run the same
test on bluefire.
Modified Paths:
--------------
DART/branches/development/models/cam/shell_scripts/setup_cesm_case.ned.csh
DART/branches/development/models/cam/shell_scripts/setup_cesm_case.pmo.csh
-------------- next part --------------
Modified: DART/branches/development/models/cam/shell_scripts/setup_cesm_case.ned.csh
===================================================================
--- DART/branches/development/models/cam/shell_scripts/setup_cesm_case.ned.csh 2011-12-14 23:24:07 UTC (rev 5448)
+++ DART/branches/development/models/cam/shell_scripts/setup_cesm_case.ned.csh 2011-12-14 23:28:55 UTC (rev 5449)
@@ -1,58 +1,66 @@
#!/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: setup_cesm_case.hopper.csh 5404 2011-11-16 15:30:00Z nancy $
-#
-# ====================================================================
-#
+# $Id: CESM_setup_zagar.csh 5444 2011-12-14 22:22:12Z thoar $
+
# ---------------------
# 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.
+# -- 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_$case.
+# If you don t have any source mods, the script creates an empty subdirectory mods_$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: ./$case.csh
-# The script creates your case, configure, compile and submit your job.
+# -- Now, you are ready to go. Save your script and submit your run with the command: ./$case.csh
+# The script creates your case, configure, compile and submit your job.
# -- The script also creates a subdirectory (nml_$case) that contains your namelists.
-#
+#
# ---------------------
# Important features
# ---------------------
-# -- If you want to change something in your case other than the runtime settings above,
-# you need to delete everything and start the run from scratch.
+#
+# If you want to change something in your case other than the runtime settings,
+# you need to delete everything and start the run from scratch.
+#
+# ./${CASENAME}.*.clean_build
+# ./configure -cleanall
# ====================================================================
# ==== Set case options
-# ====================================================================
+# ====================================================================
# ======================
-# case settings
+# case settings
# ======================
-# according to docs, F == F_2000
# beta05 is also available, but i'm still using 04 for now
# because i have a fixed copy in my home directory.
-setenv ccsmtag cesm1_1_beta04
-setenv case F_ZAGAR3
-setenv compset F_2000
-setenv resolution f09_f09
+setenv ccsmtag cesm1_1_beta04
+setenv case F_ZAGAR3
+setenv compset F_2000
+setenv resolution f09_f09
+setenv num_instances 80
+# 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
+# define machines and directories
# ================================
# my home, and temp/scratch space
@@ -60,7 +68,7 @@
setenv my_scratch $SCRATCH
setenv mach hopp2 ;# machine - must match cesm names
-setenv cesm_public /project/projectdirs/ccsm1
+setenv cesm_datadir /project/projectdirs/ccsm1/inputdata
setenv ccsmroot ${my_home}/${ccsmtag} ;# this is where the cesm code lives
#setenv ccsmroot ${cesm_public}/collections/${ccsmtag} ;# this is where the cesm code lives
@@ -69,6 +77,8 @@
setenv lockroot ${my_home}/locked_cases ;## locked cases
setenv rundir ${my_scratch}/${case}
+setenv DARTdir ${my_home}/devel
+
# for data files not in the public cems area
setenv my_datadir ${my_scratch}/cesm_datafiles
@@ -76,192 +86,207 @@
# clear out previous builds
# ======================
-echo removing old files from $caseroot and $rundir
-rm -fr $caseroot
-rm -fr $rundir
+echo "removing old files from ${caseroot} and ${rundir}"
+\rm -fr ${caseroot}
+\rm -fr ${rundir}
# ======================
# configure settings
# ======================
-setenv num_instances 80
-
setenv run_startdate 2008-08-01
-setenv sst_dataset $my_datadir/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
+setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
setenv year_start 1850
setenv year_end 2010
# ======================
-# job settings to alter in run script
+# runtime settings
# ======================
-setenv queue premium
-setenv timewall 02:00:00
+setenv resubmit 0
+setenv stop_n 12
+setenv stop_option nhours
# ======================
-# runtime settings
+# job settings
# ======================
-# each 'job' is 12 hours, so 8 resubmits should be 4 full days
-setenv resubmit 0
-setenv stop_n 12
-setenv stop_option nhours
+setenv timewall 01:45:00
+setenv queue premium
# ======================
# namelist variables
# ======================
-# We create namelist templates that get copied once the case has been configured.
+# Create namelist templates that get copied once the case has been configured.
setenv this_dir `pwd`
cat <<EOF >! user_nl_cam_${case}
&camexp
- inithist = 'ENDOFRUN'
- div24del2flag = 4
- bndtvghg = '${cesm_public}/inputdata/atm/cam/ggas/ghg_rcp45_1765-2500_c100405.nc'
- prescribed_ozone_datapath = '${cesm_public}/inputdata/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 = "$my_datadir"
- prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
- solar_data_file = '${cesm_public}/inputdata/atm/cam/solar/SOLAR_TSI_Lean_1610-2140_annual_c100301.nc'
- prescribed_aero_datapath = '${cesm_public}/inputdata/atm/cam/chem/trop_mozart_aero/aero'
- prescribed_aero_file = 'aero_rcp45_v1_1.9x2.5_L26_1995-2105_c100316.nc'
- aerodep_flx_datapath = "$my_datadir"
- aerodep_flx_file = 'aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+ inithist = 'ENDOFRUN'
+ div24del2flag = 4
+ aerodep_flx_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
+ aerodep_flx_file = 'aerosoldep_monthly_1849-2006_1.9x2.5_c090803.nc'
+ aerodep_flx_cycle_yr = 2000
+ aerodep_flx_type = 'CYCLICAL'
+ iradae = -12
+ empty_htapes = .true.
+ nhtfrq = -12
/
EOF
- #aerodep_flx_datapath = '${cesm_public}/inputdata/atm/cam/chem/trop_mozart_aero/aero'
- #prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
-
cat <<EOF >! user_nl_clm_${case}
&clmexp
- fsurdat = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr1850_c091006.nc'
- fpftdyn = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_0.9x1.25_rcp2.6_simyr1850-2100_c100323.nc'
- faerdep = "$my_datadir/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc"
+ fatmgrid = '${cesm_datadir}/lnd/clm2/griddata/griddata_0.9x1.25_070212.nc'
+ faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+ outnc_large_files = .true.
+ hist_nhtfrq = -12
+ hist_empty_htapes = .true.
/
EOF
- #fsurdat = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr2000_c100505.nc'
-
-
# ====================================================================
# ==== End of case options
-# ====================================================================
+# ====================================================================
# ====================================================================
-# Create a new case, configure, and build
-# for list of the cases: ./create_newcase -list
+# Create a new case, configure, and build.
+# For list of the cases: ./create_newcase -list
# ====================================================================
-cd $ccsmroot/scripts
-./create_newcase -case $caseroot -mach $mach -res $resolution -compset $compset -skip_rundb
+${ccsmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
+ -res ${resolution} -compset ${compset} -skip_rundb
-cd $caseroot
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be created."
+ exit 1
+endif
+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 ${my_scratch}/esmf-mpi
+#./xmlchange -file env_build.xml -id ESMF_LIBDIR -val ${nancy_scratch}/esmf-mpi
-# number of instances == ensemble size
-./xmlchange -file env_mach_pes.xml -id NINST_ATM -val $num_instances
-./xmlchange -file env_mach_pes.xml -id NINST_LND -val $num_instances
-./xmlchange -file env_mach_pes.xml -id NINST_ICE -val $num_instances
-
-# was 12 when nthreads was 1
set num_tasks_per_instance = 2
set nthreads = 6
@ 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 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 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 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 startup
./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 DOCN_SSTDATA_FILENAME -val $sst_dataset
-./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 '-bgc cn -rtm off'
+./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_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
+./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
-# Have not sorted out the archiving just yet ... turning it off for now.
+# 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 -val 'TRUE'
-./xmlchange -file env_run.xml -id DOUT_L_MS -val 'TRUE'
-./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val 'TRUE'
+./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
-#------------------
+# ====================================================================
+# 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
-# FIXME: updated source files
+# ====================================================================
+# Update source files if need be
+# ====================================================================
cp ~/cesm_mods/seq*F90 $caseroot/SourceMods/src.drv
cp ~/cesm_mods/hist*F90 $caseroot/SourceMods/src.clm
-echo updated source files not in standard distribution:
-ls -l $caseroot/SourceMods/src.drv/*
-ls -l $caseroot/SourceMods/src.clm/*
-#------------------
-# configure
-#------------------
+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
- cd $caseroot
- ./configure -case
+# ====================================================================
+# Configure
+# ====================================================================
-#------------------
-# Stage a copy of the DART assimilate.csh script HERE
-#------------------
+cd ${caseroot}
+./configure -case
- cd $caseroot
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be configured."
+ exit 2
+endif
- setenv SCRIPTHOME $HOME/devel/models/cam/shell_scripts/
- ln -sf $SCRIPTHOME/assimilate.ned.csh .
- ln -sf $SCRIPTHOME/st_archive.sh Tools/
+# ====================================================================
+# 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 ${DARTdir}/models/cam/shell_scripts/assimilate.ned.csh assimilate.csh
+
+# ====================================================================
# update the namelists and scripts as needed
-#------------------
+# ====================================================================
-
-echo
+echo ''
echo 'Editing the Buildconf/{cam,cice,clm}.buildnml.csh files'
-echo
+echo ''
-cd Buildconf
-mv cam.buildnml.csh cam.buildnml.csh.orig
-sed -e '/ ncdata/c ncdata = "cam_initial_${atm_inst_counter}.nc" ' cam.buildnml.csh.orig >! cam.buildnml.csh
-chmod 0755 cam.buildnml.csh
+cd ${caseroot}/Buildconf
-mv cice.buildnml.csh cice.buildnml.csh.orig
-sed -e '/ ice_ic/c ice_ic = "ice_restart_${ice_inst_counter}.nc" ' cice.buildnml.csh.orig >! cice.buildnml.csh
-chmod 0755 cice.buildnml.csh
+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
-#mv clm.buildnml.csh clm.buildnml.csh.orig
-#sed -e '/ finidat/c finidat = "clm_restart_X.nc" ' clm.buildnml.csh.orig >! clm.buildnml.csh
-cp -f clm.buildnml.csh clm.buildnml.csh.orig
+# 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" $n`
@@ -271,145 +296,146 @@
s;= '.*';= "clm_restart_${n}.nc";
wq
ex_end
- @ n++
+ @ n++
end
chmod 0755 clm.buildnml.csh
-cd ..
+# ====================================================================
+# 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"
+# ====================================================================
-echo
-echo 'Adding the call to assimilate.ned.csh to the *.run script.'
-echo
+cd ${caseroot}
-# save original file minus the last 4 lines; insert the
-# call to the assimilate script in front of those 4 lines.
-# could also do this with an ex script
+echo ''
+echo 'Adding the call to assimilate.csh to the *.run script.'
+echo ''
-cat <<"EOF" >! add_to_run.csh
+cat << "EndOfText" >! add_to_run.txt
# -------------------------------------------------------------------------
-# START OF DART STUFF:
-# See if CSM finishes correctly (pirated from ccsm_postrun.csh) and if so,
+# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
# perform an assimilation with DART.
# -------------------------------------------------------------------------
set CplLogFile = `ls -1t cpl.log* | head -1`
if ($CplLogFile == "") then
- echo "ERROR: Model did not complete - no cpl.log file present - exiting"
- echo "ERROR: Perfect_model run will not be attempted."
+ 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.ned.csh
+ ${CASEROOT}/assimilate.csh
if ( $status == 0 ) then
echo "`date` -- DART HAS FINISHED"
else
- echo "`date` -- DART PMO ERROR - ABANDON HOPE"
+ echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
exit -5
endif
endif
-# END OF DART STUFF
+# END OF DART BLOCK
# -------------------------------------------------------------------------
+"EndOfText"
-"EOF"
+# 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
-set len = `cat ${case}.${mach}.run.orig | wc -l`
-set lastlines = `grep -A 500 "CSM EXECUTION HAS FINISHED" ${case}.${mach}.run.orig | wc -l`
-@ lastlines -= 2
-@ keep = $len - $lastlines
-head -$keep ${case}.${mach}.run.orig > ${case}.${mach}.run
-cat ./add_to_run.csh >> ${case}.${mach}.run
+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
chmod 0755 ${case}.${mach}.run
-cd Tools
+# ====================================================================
+# IMPORTANT: All resubmits must be coldstarts.
+# Change Tools/ccsm_postrun.csh line 83 to CONTINUE_RUN -val FALSE'
+# ====================================================================
+
+echo 'Changing Tools/ccsm_postrun.csh:83 to CONTINUE_RUN -val FALSE'
+echo 'so all the resubmits are coldstarts.'
+
+cd ${caseroot}/Tools
cp ccsm_postrun.csh ccsm_postrun.orig
sed -e '/CONTINUE_RUN/s/TRUE/FALSE/' ccsm_postrun.orig >! ccsm_postrun.csh
chmod 0755 ccsm_postrun.csh
-cd ..
-echo 'Changed Change Tools/ccsm_postrun.csh:83 to CONTINUE_RUN -val FALSE'
-echo 'so all the resubmits are coldstarts.'
+# if run fails, you need to back up, or you want to check what
+# the current run time is, look here:
+# Buildconf/cpl.buildnml.csh: start_ymd, start_tod
+# ====================================================================
+# build
+# ====================================================================
-# if start date was not set above, set:
-# Buildconf/cpl.buildnml.csh: start_ymd, start_tod
+cd ${caseroot}
-#------------------
-# build
-#------------------
-
-echo
+echo ''
echo 'Building the case'
-echo
+echo ''
- cd $caseroot
- ./$case.$mach.build
+./$case.$mach.build
-#------------------
-# restarts - rundir does not exist until build runs
-#------------------
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be built."
+ exit 3
+endif
-echo
-echo 'Staging the restarts'
-echo
+# ====================================================================
+# Stage the restarts now that the run directory exists
+# ====================================================================
+set stagedir = ${my_scratch}/ned_datafiles
+
+echo ''
+echo "Staging the restarts from {$stagedir}"
+echo ''
+
@ n = 1
while ($n <= $num_instances)
echo "Staging restarts for instance $n of $num_instances"
- cp ${my_scratch}/ned_datafiles/CAM/caminput_${n}.nc ${rundir}/run/cam_initial_${n}.nc
- cp ${my_scratch}/ned_datafiles/CLM/clminput_${n}.nc ${rundir}/run/clm_restart_${n}.nc
- cp ${my_scratch}/ned_datafiles/ICE/iceinput_${n}.nc ${rundir}/run/ice_restart_${n}.nc
+ 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
-# no inflation in this experiment
-#cp ${my_scratch}/ned_datafiles/DART/p*inflate_restart.* ${rundir}/run/
+echo 'If inflation is being used ... '
+echo "must stage a ${rundir}/[prior,pos]_inflate_restart.YYYY-MM-DD-SSSSS"
-#------------------
-# Save another copy of the original 'initial' namelist so we
-# can tell if build changes anything?
-#------------------
-
-
# ====================================================================
-# Continue run
+# Edit the run script to reflect project, queue, and wallclock
# ====================================================================
-# if ($create_build_case == false) then
-# echo "Found:" {$lockroot}/{$case}.locked
-# echo "set parameters for continue run"
-# cd $caseroot
-# ./xmlchange -file env_run.xml -id RESUBMIT -val "$resubmit"
-# ./xmlchange -file env_run.xml -id STOP_OPTION -val $stop_option
-# ./xmlchange -file env_run.xml -id STOP_N -val $stop_n
-# ./xmlchange -file env_run.xml -id CONTINUE_RUN -val TRUE
-# endif
-# ====================================================================
-# Edit the run script if any vars are defined
-# ====================================================================
-
if ($?proj) then
set PROJ=`grep '^#PBS ' $case.$mach.run | grep -e '-P' `
sed -e s/$PROJ[3]/$proj/ < $case.$mach.run >! temp
/bin/mv temp $case.$mach.run
endif
-
+
if ($?timewall) then
set TIMEWALL=`grep '^#PBS ' $case.$mach.run | grep walltime `
- sed -e /${TIMEWALL}/s/=.\$/=$timewall/ < $case.$mach.run >! temp
+ sed -e /"${TIMEWALL}"/s/=.\$/=$timewall/ < $case.$mach.run >! temp
/bin/mv temp $case.$mach.run
endif
@@ -418,16 +444,23 @@
sed -e s/$QUEUE[3]/$queue/ < $case.$mach.run >! temp
/bin/mv temp $case.$mach.run
endif
+chmod 0744 $case.$mach.run
# ====================================================================
-# Submit job
+# Submit job
# ====================================================================
-echo
-echo 'Job ready to be submitted here'
-echo "cd into $caseroot and run: ./$case.$mach.submit"
-echo
+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 ''
+
+
# cd $caseroot
# ./$case.$mach.submit
Modified: DART/branches/development/models/cam/shell_scripts/setup_cesm_case.pmo.csh
===================================================================
--- DART/branches/development/models/cam/shell_scripts/setup_cesm_case.pmo.csh 2011-12-14 23:24:07 UTC (rev 5448)
+++ DART/branches/development/models/cam/shell_scripts/setup_cesm_case.pmo.csh 2011-12-14 23:28:55 UTC (rev 5449)
@@ -1,58 +1,66 @@
#!/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: setup_cesm_case.hopper.csh 5404 2011-11-16 15:30:00Z nancy $
-#
-# ====================================================================
-#
+# $Id: CESM_setup_zagar.csh 5444 2011-12-14 22:22:12Z thoar $
+
# ---------------------
# 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.
+# -- 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_$case.
+# If you don t have any source mods, the script creates an empty subdirectory mods_$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: ./$case.csh
-# The script creates your case, configure, compile and submit your job.
+# -- Now, you are ready to go. Save your script and submit your run with the command: ./$case.csh
+# The script creates your case, configure, compile and submit your job.
# -- The script also creates a subdirectory (nml_$case) that contains your namelists.
-#
+#
# ---------------------
# Important features
# ---------------------
-# -- If you want to change something in your case other than the runtime settings above,
-# you need to delete everything and start the run from scratch.
+#
+# If you want to change something in your case other than the runtime settings,
+# you need to delete everything and start the run from scratch.
+#
+# ./${CASENAME}.*.clean_build
+# ./configure -cleanall
# ====================================================================
# ==== Set case options
-# ====================================================================
+# ====================================================================
# ======================
-# case settings
+# case settings
# ======================
-# according to docs, F == F_2000
# beta05 is also available, but i'm still using 04 for now
# because i have a fixed copy in my home directory.
-setenv ccsmtag cesm1_1_beta04
-setenv case F_PMO_Z
-setenv compset F_2000
-setenv resolution f09_f09
+setenv ccsmtag cesm1_1_beta04
+setenv case F_PMO_Z
+setenv compset F_2000
+setenv resolution f09_f09
+setenv num_instances 1
+# 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
+# define machines and directories
# ================================
# my home, and temp/scratch space
@@ -60,7 +68,7 @@
setenv my_scratch $SCRATCH
setenv mach hopp2 ;# machine - must match cesm names
-setenv cesm_public /project/projectdirs/ccsm1
+setenv cesm_datadir /project/projectdirs/ccsm1/inputdata
setenv ccsmroot ${my_home}/${ccsmtag} ;# this is where the cesm code lives
#setenv ccsmroot ${cesm_public}/collections/${ccsmtag} ;# this is where the cesm code lives
@@ -69,6 +77,8 @@
setenv lockroot ${my_home}/locked_cases ;## locked cases
setenv rundir ${my_scratch}/${case}
+setenv DARTdir ${my_home}/devel
+
# for data files not in the public cems area
setenv my_datadir ${my_scratch}/cesm_datafiles
@@ -76,192 +86,207 @@
# clear out previous builds
# ======================
-echo removing old files from $caseroot and $rundir
-rm -fr $caseroot
-rm -fr $rundir
+echo "removing old files from ${caseroot} and ${rundir}"
+\rm -fr ${caseroot}
+\rm -fr ${rundir}
# ======================
# configure settings
# ======================
-setenv num_instances 1
-
setenv run_startdate 2008-08-01
-setenv sst_dataset $my_datadir/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
+setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
setenv year_start 1850
setenv year_end 2010
# ======================
-# job settings to alter in run script
+# runtime settings
# ======================
-setenv queue premium
-setenv timewall 00:40:00
+setenv resubmit 0
+setenv stop_n 12
+setenv stop_option nhours
# ======================
-# runtime settings
+# job settings
# ======================
-# each 'job' is 12 hours, so 8 resubmits should be 4 full days
-setenv resubmit 0
-setenv stop_n 12
-setenv stop_option nhours
+setenv timewall 00:40:00
+setenv queue premium
# ======================
# namelist variables
# ======================
-# We create namelist templates that get copied once the case has been configured.
+# Create namelist templates that get copied once the case has been configured.
setenv this_dir `pwd`
cat <<EOF >! user_nl_cam_${case}
&camexp
- inithist = 'ENDOFRUN'
- div24del2flag = 4
- bndtvghg = '${cesm_public}/inputdata/atm/cam/ggas/ghg_rcp45_1765-2500_c100405.nc'
- prescribed_ozone_datapath = '${cesm_public}/inputdata/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 = "$my_datadir"
- prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
- solar_data_file = '${cesm_public}/inputdata/atm/cam/solar/SOLAR_TSI_Lean_1610-2140_annual_c100301.nc'
- prescribed_aero_datapath = '${cesm_public}/inputdata/atm/cam/chem/trop_mozart_aero/aero'
- prescribed_aero_file = 'aero_rcp45_v1_1.9x2.5_L26_1995-2105_c100316.nc'
- aerodep_flx_datapath = "$my_datadir"
- aerodep_flx_file = 'aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+ inithist = 'ENDOFRUN'
+ div24del2flag = 4
+ aerodep_flx_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
+ aerodep_flx_file = 'aerosoldep_monthly_1849-2006_1.9x2.5_c090803.nc'
+ aerodep_flx_cycle_yr = 2000
+ aerodep_flx_type = 'CYCLICAL'
+ iradae = -12
+ empty_htapes = .true.
+ nhtfrq = -12
/
EOF
- #aerodep_flx_datapath = '${cesm_public}/inputdata/atm/cam/chem/trop_mozart_aero/aero'
- #prescribed_volcaero_file = 'CCSM4_volcanic_1850-2011_prototype1.nc'
-
cat <<EOF >! user_nl_clm_${case}
&clmexp
- fsurdat = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr1850_c091006.nc'
- fpftdyn = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_0.9x1.25_rcp2.6_simyr1850-2100_c100323.nc'
- faerdep = "$my_datadir/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc"
+ fatmgrid = '${cesm_datadir}/lnd/clm2/griddata/griddata_0.9x1.25_070212.nc'
+ faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
+ outnc_large_files = .true.
+ hist_nhtfrq = -12
+ hist_empty_htapes = .true.
/
EOF
- #fsurdat = '${cesm_public}/inputdata/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr2000_c100505.nc'
-
-
# ====================================================================
# ==== End of case options
-# ====================================================================
+# ====================================================================
# ====================================================================
-# Create a new case, configure, and build
-# for list of the cases: ./create_newcase -list
+# Create a new case, configure, and build.
+# For list of the cases: ./create_newcase -list
# ====================================================================
-cd $ccsmroot/scripts
-./create_newcase -case $caseroot -mach $mach -res $resolution -compset $compset -skip_rundb
+${ccsmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
+ -res ${resolution} -compset ${compset} -skip_rundb
-cd $caseroot
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be created."
+ exit 1
+endif
+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 ${my_scratch}/esmf-mpi
+#./xmlchange -file env_build.xml -id ESMF_LIBDIR -val ${nancy_scratch}/esmf-mpi
-# number of instances == ensemble size
-./xmlchange -file env_mach_pes.xml -id NINST_ATM -val $num_instances
-./xmlchange -file env_mach_pes.xml -id NINST_LND -val $num_instances
-./xmlchange -file env_mach_pes.xml -id NINST_ICE -val $num_instances
-
-# was 12 when nthreads was 1
-set num_tasks_per_instance = 8
+set num_tasks_per_instance = 12
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 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 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 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 startup
./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 DOCN_SSTDATA_FILENAME -val $sst_dataset
-./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 '-bgc cn -rtm off'
+./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_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
+./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
-# Have not sorted out the archiving just yet ... turning it off for now.
+# 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 -val 'TRUE'
-./xmlchange -file env_run.xml -id DOUT_L_MS -val 'TRUE'
-./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val 'TRUE'
+./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
-#------------------
+# ====================================================================
+# 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
-# FIXME: updated source files
+# ====================================================================
+# Update source files if need be
+# ====================================================================
cp ~/cesm_mods/seq*F90 $caseroot/SourceMods/src.drv
cp ~/cesm_mods/hist*F90 $caseroot/SourceMods/src.clm
-echo updated source files not in standard distribution:
-ls -l $caseroot/SourceMods/src.drv/*
-ls -l $caseroot/SourceMods/src.clm/*
-#------------------
-# configure
-#------------------
+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
- cd $caseroot
- ./configure -case
+# ====================================================================
+# Configure
+# ====================================================================
@@ Diff output truncated at 40000 characters. @@
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