[Dart-dev] [6487] DART/trunk/models/CESM/shell_scripts: The CESM setup scripts are working.
nancy at ucar.edu
nancy at ucar.edu
Fri Sep 20 16:53:23 MDT 2013
Revision: 6487
Author: thoar
Date: 2013-09-20 16:53:22 -0600 (Fri, 20 Sep 2013)
Log Message:
-----------
The CESM setup scripts are working.
CESM1_1_1_hybrid_initial pulls files from a collection of places
CESM1_1_1_hybrid pulls files from a single 'rest' directory
CESM_DART_config conditions a CASEROOT directory for DART
The assimilate scripts are very nearly identical to the individual model
component assimilate scripts.
The run_perfect_model_obs.csh script is fundamentally untested, only
removed unused whitespace.
Modified Paths:
--------------
DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid
DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial
DART/trunk/models/CESM/shell_scripts/CESM_DART_config
DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh
DART/trunk/models/CESM/shell_scripts/clm_assimilate.csh
DART/trunk/models/CESM/shell_scripts/pop_assimilate.csh
DART/trunk/models/CESM/shell_scripts/run_perfect_model_obs.csh
DART/trunk/models/CESM/shell_scripts/st_archive.sh
-------------- next part --------------
Modified: DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid
===================================================================
--- DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid 2013-09-20 22:26:31 UTC (rev 6486)
+++ DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid 2013-09-20 22:53:22 UTC (rev 6487)
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -f
#
# DART software - Copyright 2004 - 2013 UCAR. This open source software is
# provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -11,7 +11,7 @@
# ---------------------
#
# This script is designed to set up, stage, and build a multi-instance run of CESM
-# using a B compset where CAM, POP, and CLM are all active. The initial states
+# using a B compset where CAM, POP, and CLM are all active. The initial states
# come from a single multi-instance reference case so a CESM hybrid setup is used.
# While not required for CESM, POP is configured to write out netCDF restart files
# because they are required by DART (if you are going to assimilate ocean obs).
@@ -27,7 +27,7 @@
# capability to re-stage files in your RUN directory
#
# CASEROOT/CESM_DART_config will augment the CESM case with the required setup
-# and configuration to perform a DART assimilation. CASEROOT/CESM_DART_config
+# and configuration to perform a DART assimilation. CASEROOT/CESM_DART_config
# will insert a few dozen lines into the ${CASE}.run script after it makes a backup
# copy. This, and the required setup, can be run at a later date. e.g. you can
# advance an ensemble from 2004-01-01 to 2004-02-01 and then run
@@ -59,7 +59,7 @@
#
# -- Run this script.
#
-# -- If you want to run DART, read and understand ${CASEROOT}/CESM_DART_config
+# -- If you want to run DART; read, understand, and execute ${CASEROOT}/CESM_DART_config
#
# -- Submit the job using ${CASEROOT}/${CASE}.submit
#
@@ -83,12 +83,12 @@
# ==== Set case options
# ==============================================================================
-# case will be used many ways;
+# the value of "case" will be used many ways;
# directory and file names, both locally and on HPSS, and
# script names; so consider it's length and information content.
# num_instances: Number of ensemble members
-setenv case cesm_assim
+setenv case cesm_6h_hybrid
setenv compset B_2000_CAM5
setenv resolution 0.9x1.25_gx1v6
setenv cesmtag cesm1_1_1
@@ -99,7 +99,7 @@
#
# mach Computer name
# cesmroot Location of the cesm code base
-# For cesm1_1 on yellowstone
+# For cesm1_1_1 on yellowstone
# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
# Preferably not a frequently scrubbed location.
# This script will delete any existing caseroot, so this script,
@@ -121,7 +121,9 @@
setenv dartroot /glade/u/home/${USER}/svn/DART/trunk
# ==============================================================================
-# configure settings ... run_startdate format is yyyy-mm-dd
+# configure settings
+# The reference case has dates in it.
+# For a 'hybrid' start, these may be unrelated to the refyear, refmon, refday.
# ==============================================================================
setenv run_refcase cesm_hybrid
@@ -133,7 +135,7 @@
# THIS IS THE LOCATION of the 'reference case'.
-set stagedir = /glade/scratch/thoar/archive/${run_refcase}/rest/${run_refdate}-${run_reftod}
+set stagedir = /glade/p/image/CESM_initial_ensemble/rest/2004-01-10-00000
# ==============================================================================
# runtime settings -- How many assimilation steps will be done after this one
@@ -146,16 +148,16 @@
#
# If the long-term archiver is off, you get a chance to examine the files before
# they get moved to long-term storage. You can always submit $CASE.l_archive
-# whenever you want to free up space in the short-term archive directory.
+# whenever you want to free up space in the short-term archive directory.
#
# ==============================================================================
-setenv resubmit 8
+setenv short_term_archiver on
+setenv long_term_archiver off
+setenv resubmit 0
setenv stop_option nhours
-setenv stop_n 6
+setenv stop_n 12
setenv assim_n 6
-setenv short_term_archiver on
-setenv long_term_archiver off
# ==============================================================================
# job settings
@@ -169,7 +171,7 @@
setenv ACCOUNT P8685xxxx
setenv queue economy
-setenv timewall 0:20
+setenv timewall 0:30
# ==============================================================================
# set these standard commands based on the machine you are running on.
@@ -247,6 +249,10 @@
exit -1
endif
+# preserve a copy of this script as it was run
+set ThisFileName = $0:t
+${COPY} $ThisFileName ${caseroot}/${ThisFileName}.original
+
# ==============================================================================
# Record the DARTROOT directory and copy the DART setup script to CASEROOT.
# CESM_DART_config can be run at some later date if desired, but it presumes
@@ -259,7 +265,8 @@
endif
if ( -e CESM_DART_config ) then
- sed -e "s#BOGUS_DART_ROOT_STRING#$dartroot#" < CESM_DART_config >! temp.$$
+ sed -e "s#BOGUS_DART_ROOT_STRING#$dartroot#" \
+ -e "s#HISTORY_OUTPUT_INTERVAL#$assim_n#" < CESM_DART_config >! temp.$$
${MOVE} temp.$$ ${caseroot}/CESM_DART_config
chmod 755 ${caseroot}/CESM_DART_config
else
@@ -288,54 +295,54 @@
endif
end
-if ( $num_instances < 10) then
+if ($num_instances < 10) then
# This is only for the purpose of debugging the code.
@ atm_tasks = $ptile * $num_instances * 4
+ @ lnd_tasks = $ptile * $num_instances * 4
+ @ ice_tasks = $ptile * $num_instances
@ ocn_tasks = $ptile * $num_instances * 4
- @ lnd_tasks = $ptile * $num_instances * 4
- @ ice_tasks = $ptile * $num_instances * 1
+ @ cpl_tasks = $ptile * $num_instances
@ glc_tasks = $ptile * $num_instances
@ rof_tasks = $ptile * $num_instances
- @ cpl_tasks = $ptile * 4
else
# This works, but a more efficient layout should be used
@ atm_tasks = $ptile * $num_instances * 2
- @ ocn_tasks = $ptile * $num_instances * 2
@ lnd_tasks = $ptile * $num_instances * 2
@ ice_tasks = $ptile * $num_instances
+ @ ocn_tasks = $ptile * $num_instances * 2
+ @ cpl_tasks = $ptile * $num_instances
@ glc_tasks = $ptile * $num_instances
@ rof_tasks = $ptile * $num_instances
- @ cpl_tasks = $ptile * $num_instances
endif
# echo "task partitioning ... perhaps ... atm // ocn // lnd+ice+glc+rof"
# presently, all components run 'serially' - one after another.
echo ""
-echo "ATM gets $atm_tasks"
-echo "CPL gets $cpl_tasks"
-echo "ICE gets $ice_tasks"
-echo "LND gets $lnd_tasks"
-echo "GLC gets $glc_tasks"
-echo "DROF gets $rof_tasks"
-echo "OCN gets $ocn_tasks"
+echo "ATM gets $atm_tasks"
+echo "LND gets $lnd_tasks"
+echo "ICE gets $ice_tasks"
+echo "OCN gets $ocn_tasks"
+echo "CPL gets $cpl_tasks"
+echo "GLC gets $glc_tasks"
+echo "ROF gets $rof_tasks"
echo ""
-./xmlchange NTHRDS_CPL=$nthreads,NTASKS_CPL=$cpl_tasks
-./xmlchange NTHRDS_GLC=$nthreads,NTASKS_GLC=$glc_tasks,NINST_GLC=1
./xmlchange NTHRDS_ATM=$nthreads,NTASKS_ATM=$atm_tasks,NINST_ATM=$num_instances
./xmlchange NTHRDS_LND=$nthreads,NTASKS_LND=$lnd_tasks,NINST_LND=$num_instances
./xmlchange NTHRDS_ICE=$nthreads,NTASKS_ICE=$ice_tasks,NINST_ICE=$num_instances
+./xmlchange NTHRDS_OCN=$nthreads,NTASKS_OCN=$ocn_tasks,NINST_OCN=$num_instances
+./xmlchange NTHRDS_CPL=$nthreads,NTASKS_CPL=$cpl_tasks
+./xmlchange NTHRDS_GLC=$nthreads,NTASKS_GLC=$glc_tasks,NINST_GLC=1
./xmlchange NTHRDS_ROF=$nthreads,NTASKS_ROF=$rof_tasks,NINST_ROF=$num_instances
-./xmlchange NTHRDS_OCN=$nthreads,NTASKS_OCN=$ocn_tasks,NINST_OCN=$num_instances
./xmlchange ROOTPE_ATM=0
+./xmlchange ROOTPE_LND=0
+./xmlchange ROOTPE_ICE=0
./xmlchange ROOTPE_OCN=0
./xmlchange ROOTPE_CPL=0
-./xmlchange ROOTPE_LND=0
-./xmlchange ROOTPE_ICE=0
./xmlchange ROOTPE_GLC=0
./xmlchange ROOTPE_ROF=0
@@ -356,7 +363,14 @@
# TJH:
# DART's CAM implementation causes a bit more complexity. DART only uses CAM _initial_
# files, not RESTART files, so there are sourcemods to force a hybrid start for CAM to
-# read initial files - even when CONTINUE_RUN = TRUE.
+# read initial files - even when CONTINUE_RUN = TRUE. A hybrid start is better for POP
+# because the velocities are used rather than just T,S. A hybrid start is also more
+# desirable because initial values can be specified for ROF - as opposed to just zeros.
+#
+# The RUN_REFCASE/REFDATE/REFTOD are used by CLM & RTM to specify the namelist input
+# filenames - BUT - their buildnml scripts do not use the INSTANCE, so they all specify
+# the same (single) filename. This is remedied by using patched [clm,rtm].buildnml.csh
+# scripts that exist in the SourceMods directory.
./xmlchange RUN_TYPE=hybrid
./xmlchange RUN_STARTDATE=$run_refdate
@@ -373,12 +387,15 @@
./xmlchange STOP_N=$stop_n
./xmlchange CONTINUE_RUN=FALSE
./xmlchange RESUBMIT=$resubmit
+
./xmlchange PIO_TYPENAME=pnetcdf
# This sets the ocean coupling time to 6 hours.
# All related namelist settings are based on this value.
./xmlchange OCN_NCPL=4
+# There is no compset that has everything we want,
+# so we are also turning on the CLM biogeochemistry.
./xmlchange CLM_CONFIG_OPTS='-bgc cn'
if ($short_term_archiver == 'off') then
@@ -434,7 +451,7 @@
set QUEUE=`grep BSUB ${case}.run | grep -e '-q' `
sed -e "s/$TIMEWALL[3]/$timewall/" \
-e "s/ptile=[0-9][0-9]*/ptile=$ptile/" \
- -e "s/$QUEUE[3]/$queue/" < ${case}.run >> temp.$$
+ -e "s/$QUEUE[3]/$queue/" < ${case}.run >! temp.$$
${MOVE} temp.$$ ${case}.run
chmod 755 ${case}.run
breaksw
@@ -445,6 +462,56 @@
endsw
# ==============================================================================
+# Update source files.
+# Ideally, using DART would not require any modifications to the model source.
+# Until then, this script accesses sourcemods from a hardwired location.
+# If you have additional sourcemods, they will need to be merged into any DART
+# mods and put in the SourceMods subdirectory found in the 'case' directory.
+# ==============================================================================
+
+if ( -d ~/${cesmtag}/SourceMods ) then
+ ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
+else
+ echo "ERROR - No SourceMods for this case."
+ echo "ERROR - No SourceMods for this case."
+ echo "DART requires modifications to several src files."
+ echo "These files can be downloaded from:"
+ echo "http://www.image.ucar.edu/pub/DART/CESM/DART_SourceMods_cesm1_1_1.tar"
+ echo "untar these into your HOME directory - they will create a"
+ echo "~/cesm_1_1_1 directory with the appropriate SourceMods structure."
+ exit -4
+endif
+
+# The CESM multi-instance capability is relatively new and still has a few
+# implementation bugs. These are known problems and will be fixed soon.
+# this should be removed when the files are fixed:
+
+echo "REPLACING BROKEN CESM FILES HERE - SHOULD BE REMOVED WHEN FIXED"
+echo caseroot is ${caseroot}
+if ( -d ~/${cesmtag} ) then
+
+ # preserve the original version of the files
+ if ( ! -e ${caseroot}/Buildconf/clm.buildnml.csh.original ) then
+ ${MOVE} ${caseroot}/Buildconf/clm.buildnml.csh \
+ ${caseroot}/Buildconf/clm.buildnml.csh.original
+ endif
+ if ( ! -e ${caseroot}/Buildconf/rtm.buildnml.csh.original ) then
+ ${MOVE} ${caseroot}/Buildconf/rtm.buildnml.csh \
+ ${caseroot}/Buildconf/rtm.buildnml.csh.original
+ endif
+ if ( ! -e ${caseroot}/preview_namelists.original ) then
+ ${MOVE} ${caseroot}/preview_namelists \
+ ${caseroot}/preview_namelists.original
+ endif
+
+ # patch/replace the broken files
+ ${COPY} ~/${cesmtag}/clm.buildnml.csh ${caseroot}/Buildconf/.
+ ${COPY} ~/${cesmtag}/rtm.buildnml.csh ${caseroot}/Buildconf/.
+ ${COPY} ~/${cesmtag}/preview_namelists ${caseroot}/.
+
+endif
+
+# ==============================================================================
# Modify namelist templates for each instance. This is a bit of a nuisance in
# that we are pulling in restart and initial files from 'all over the place'
# and each model component has a different strategy.
@@ -466,25 +533,26 @@
@ inst = 1
while ($inst <= $num_instances)
- # instance now includes the leading underscore
- set instance = `printf _%04d $inst`
+ # following the CESM strategy for 'inst_string'
+ set inst_string = `printf _%04d $inst`
+
# ===========================================================================
- set fname = "user_nl_cam${instance}"
+ set fname = "user_nl_cam${inst_string}"
# ===========================================================================
# For a HOP TEST ... empty_htapes = .false.
# For a HOP TEST ... use a default fincl1
# FIXME ... add documentation for configuring CAM history files
echo " inithist = '6-HOURLY'" >> ${fname}
- echo " ncdata = 'cam_initial${instance}.nc'" >> ${fname}
+ echo " ncdata = 'cam_initial${inst_string}.nc'" >> ${fname}
echo " empty_htapes = .true. " >> ${fname}
echo " fincl1 = 'PHIS:I' " >> ${fname}
echo " nhtfrq = -$assim_n " >> ${fname}
echo " mfilt = 1 " >> ${fname}
# ===========================================================================
- set fname = "user_nl_clm${instance}"
+ set fname = "user_nl_clm${inst_string}"
# ===========================================================================
# Customize the land namelists
@@ -515,7 +583,7 @@
echo "hist_avgflag_pertape = 'A','A'" >> $fname
# ===========================================================================
- set fname = "user_nl_pop2${instance}"
+ set fname = "user_nl_pop2${inst_string}"
# ===========================================================================
# POP Namelists
@@ -530,78 +598,42 @@
#
# For a HOP TEST ... Would like to have restart files every day, not just for end.
# For a HOP TEST (untested)... tavg_file_freq_opt = 'nmonth' 'nday' 'once'"
+ #
+ # DEFAULT values for these are:
+ # tavg_file_freq_opt = 'nmonth' 'nmonth' 'once'
+ # tavg_freq_opt = 'nmonth' 'nday' 'once'
+ # The first entry indicates we get a monthly average once a month.
+ # The second entry indicates we get a monthly average as it is being created.
+ # The third entry indicates we get a daily timeslice
+ #
+ # IFF values for these are:
+ # tavg_file_freq_opt = 'nmonth' 'never' 'never'
+ # tavg_freq_opt = 'nmonth' 'never' 'never'
+ # The first entry indicates we get a monthly average once a month, and thats all we get..
+
+ echo "init_ts_suboption = 'data_assim'" >> $fname
+ echo "tavg_file_freq_opt = 'nmonth' 'never' 'never'" >> $fname
+ echo "tavg_freq_opt = 'nmonth' 'never' 'never'" >> $fname
- echo "init_ts_suboption = 'rest'" >> $fname
-
# ===========================================================================
- set fname = "user_nl_cice${instance}"
+ set fname = "user_nl_cice${inst_string}"
# ===========================================================================
# CICE Namelists
- echo "ice_ic = '${run_refcase}.cice${instance}.r.${run_refdate}-${run_reftod}.nc'" >> $fname
+ echo "ice_ic = '${run_refcase}.cice${inst_string}.r.${run_refdate}-${run_reftod}.nc'" >> $fname
# ===========================================================================
- set fname = "user_nl_rtm${instance}"
+ set fname = "user_nl_rtm${inst_string}"
# ===========================================================================
# RIVER RUNOFF CAN START FROM AN OLD CLM RESTART FILE
# you can specify the RTM filename here and override the settings from
# RUN_REFCASE/RUN_REFDATE/RUN_REFTOD (something you cannot do with CLM).
- echo "finidat_rtm = '${run_refcase}.rtm${instance}.r.${run_refdate}-${run_reftod}.nc'" >> $fname
+ echo "finidat_rtm = '${run_refcase}.rtm${inst_string}.r.${run_refdate}-${run_reftod}.nc'" >> $fname
@ inst ++
end
-# ==============================================================================
-# Update source files.
-# Ideally, using DART would not require any modifications to the model source.
-# Until then, this script accesses sourcemods from a hardwired location.
-# If you have additional sourcemods, they will need to be merged into any DART
-# mods and put in the SourceMods subdirectory found in the 'case' directory.
-# ==============================================================================
-
-if ( -d ~/${cesmtag}/SourceMods ) then
- ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
-else
- echo "ERROR - No SourceMods for this case."
- echo "ERROR - No SourceMods for this case."
- echo "DART requires modifications to several src files."
- echo "These files can be downloaded from:"
- echo "http://www.image.ucar.edu/pub/DART/CESM/DART_SourceMods_cesm1_1_1.tar"
- echo "untar these into your HOME directory - they will create a"
- echo "~/cesm_1_1_1 directory with the appropriate SourceMods structure."
- exit -4
-endif
-
-# The CESM multi-instance capability is relatively new and still has a few
-# implementation bugs. These are known problems and will be fixed soon.
-# this should be removed when the files are fixed:
-
-echo "REPLACING BROKEN CESM FILES HERE - SHOULD BE REMOVED WHEN FIXED"
-echo caseroot is ${caseroot}
-if ( -d ~/${cesmtag} ) then
-
- # preserve the original version of the files
- if ( ! -e ${caseroot}/Buildconf/clm.buildnml.csh.original ) then
- ${MOVE} ${caseroot}/Buildconf/clm.buildnml.csh \
- ${caseroot}/Buildconf/clm.buildnml.csh.original
- endif
- if ( ! -e ${caseroot}/Buildconf/rtm.buildnml.csh.original ) then
- ${MOVE} ${caseroot}/Buildconf/rtm.buildnml.csh \
- ${caseroot}/Buildconf/rtm.buildnml.csh.original
- endif
- if ( ! -e ${caseroot}/preview_namelists.original ) then
- ${MOVE} ${caseroot}/preview_namelists \
- ${caseroot}/preview_namelists.original
- endif
-
- # patch/replace the broken files
- ${COPY} ~/${cesmtag}/clm.buildnml.csh ${caseroot}/Buildconf/.
- ${COPY} ~/${cesmtag}/rtm.buildnml.csh ${caseroot}/Buildconf/.
- ${COPY} ~/${cesmtag}/preview_namelists ${caseroot}/.
-
-endif
-
./preview_namelists
# ==============================================================================
@@ -616,7 +648,8 @@
cd ${rundir}
echo ''
-echo 'Copying the restart files from the staging directory.'
+echo 'Copying the restart files from the staging directory'
+echo 'into the CESM run directory and relinking the CAM static names.'
echo ''
${COPY} ${stagedir}/* .
@@ -674,15 +707,18 @@
echo "3) Verify the contents of env_run.xml and submit the CESM job:"
echo " ./${case}.submit"
echo ""
-echo "4) After the job has run, make sure it worked and that "
-echo " POP is creating netCDF restart files."
+echo "4) After the job has run, check to make sure it worked and that"
+echo " a: POP is creating netCDF restart files,"
+echo " b: the right restart files exist in the run directory,"
+echo " c: (if you're running DART) the archive dart/hist directory has the DART output,"
+echo " d: everything is working correctly ..."
echo ""
echo "5) To extend the run in $assim_n '"$stop_option"' steps,"
echo " change the env_run.xml variables:"
echo ""
-echo " ./xmlchange CONTINUE_RUN=TRUE"
-echo " ./xmlchange RESUBMIT=<number_of_cycles_to_run>"
-echo " ./xmlchange STOP_N=$assim_n"
+echo " ./xmlchange CONTINUE_RUN=TRUE"
+echo " ./xmlchange RESUBMIT=<number_of_cycles_to_run>"
+echo " ./xmlchange STOP_N=$assim_n"
echo ""
exit 0
Modified: DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial
===================================================================
--- DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial 2013-09-20 22:26:31 UTC (rev 6486)
+++ DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial 2013-09-20 22:53:22 UTC (rev 6487)
@@ -1,4 +1,4 @@
-#!/bin/csh
+#!/bin/csh -f
#
# DART software - Copyright 2004 - 2013 UCAR. This open source software is
# provided by UCAR, "as is", without charge, subject to all terms of use at
@@ -51,7 +51,7 @@
# capability to re-stage files in your RUN directory
#
# CASEROOT/CESM_DART_config will augment the CESM case with the required setup
-# and configuration to perform a DART assimilation. CASEROOT/CESM_DART_config
+# and configuration to perform a DART assimilation. CASEROOT/CESM_DART_config
# will insert a few dozen lines into the ${CASE}.run script after it makes a backup
# copy. This, and the required setup, can be run at a later date. e.g. you can
# advance an ensemble from 2004-01-01 to 2004-02-01 and then run
@@ -83,7 +83,7 @@
#
# -- Run this script.
#
-# -- If you want to run DART, read and understand ${CASEROOT}/CESM_DART_config
+# -- If you want to run DART; read, understand, and execute ${CASEROOT}/CESM_DART_config
#
# -- Submit the job using ${CASEROOT}/${CASE}.submit
#
@@ -107,7 +107,7 @@
# ==== Set case options
# ==============================================================================
-# case will be used many ways;
+# the value of "case" will be used many ways;
# directory and file names, both locally and on HPSS, and
# script names; so consider it's length and information content.
# num_instances: Number of ensemble members
@@ -123,7 +123,7 @@
#
# mach Computer name
# cesmroot Location of the cesm code base
-# For cesm1_1 on yellowstone
+# For cesm1_1_1 on yellowstone
# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
# Preferably not a frequently scrubbed location.
# This script will delete any existing caseroot, so this script,
@@ -145,7 +145,7 @@
setenv dartroot /glade/u/home/${USER}/svn/DART/trunk
# ==============================================================================
-# configure settings ... run_startdate format is yyyy-mm-dd
+# configure settings
# ==============================================================================
setenv run_refcase cesm_test
@@ -161,8 +161,7 @@
set POP_stagedir = /glade/p/work/aliciak/DART_IC/CCSM4_ensembles/rest/2004-01-01-00000
# ==============================================================================
-# runtime settings -- How many assimilation steps will be done after this one
-# plus archiving options
+# runtime settings
#
# resubmit How many job steps to run on continue runs (will be 0 initially)
# stop_option Units for determining the forecast length between assimilations
@@ -171,16 +170,16 @@
#
# If the long-term archiver is off, you get a chance to examine the files before
# they get moved to long-term storage. You can always submit $CASE.l_archive
-# whenever you want to free up space in the short-term archive directory.
+# whenever you want to free up space in the short-term archive directory.
#
# ==============================================================================
+setenv short_term_archiver on
+setenv long_term_archiver off
setenv resubmit 0
setenv stop_option nhours
setenv stop_n 72
setenv assim_n 6
-setenv short_term_archiver on
-setenv long_term_archiver off
# ==============================================================================
# job settings
@@ -272,6 +271,10 @@
exit -1
endif
+# preserve a copy of this script as it was run
+set ThisFileName = $0:t
+${COPY} $ThisFileName ${caseroot}/${ThisFileName}.original
+
# ==============================================================================
# Record the DARTROOT directory and copy the DART setup script to CASEROOT.
# CESM_DART_config can be run at some later date if desired, but it presumes
@@ -284,7 +287,8 @@
endif
if ( -e CESM_DART_config ) then
- sed -e "s#BOGUS_DART_ROOT_STRING#$dartroot#" < CESM_DART_config >! temp.$$
+ sed -e "s#BOGUS_DART_ROOT_STRING#$dartroot#" \
+ -e "s#HISTORY_OUTPUT_INTERVAL#$assim_n#" < CESM_DART_config >! temp.$$
${MOVE} temp.$$ ${caseroot}/CESM_DART_config
chmod 755 ${caseroot}/CESM_DART_config
else
@@ -313,54 +317,54 @@
endif
end
-if ( $num_instances < 10) then
+if ($num_instances < 10) then
# This is only for the purpose of debugging the code.
@ atm_tasks = $ptile * $num_instances * 4
+ @ lnd_tasks = $ptile * $num_instances * 4
+ @ ice_tasks = $ptile * $num_instances
@ ocn_tasks = $ptile * $num_instances * 4
- @ lnd_tasks = $ptile * $num_instances * 4
- @ ice_tasks = $ptile * $num_instances * 1
+ @ cpl_tasks = $ptile * $num_instances
@ glc_tasks = $ptile * $num_instances
@ rof_tasks = $ptile * $num_instances
- @ cpl_tasks = $ptile * 4
else
# This works, but a more efficient layout should be used
@ atm_tasks = $ptile * $num_instances * 2
- @ ocn_tasks = $ptile * $num_instances * 2
@ lnd_tasks = $ptile * $num_instances * 2
@ ice_tasks = $ptile * $num_instances
+ @ ocn_tasks = $ptile * $num_instances * 2
+ @ cpl_tasks = $ptile * $num_instances
@ glc_tasks = $ptile * $num_instances
@ rof_tasks = $ptile * $num_instances
- @ cpl_tasks = $ptile * $num_instances
endif
# echo "task partitioning ... perhaps ... atm // ocn // lnd+ice+glc+rof"
# presently, all components run 'serially' - one after another.
echo ""
-echo "ATM gets $atm_tasks"
-echo "CPL gets $cpl_tasks"
-echo "ICE gets $ice_tasks"
-echo "LND gets $lnd_tasks"
-echo "GLC gets $glc_tasks"
-echo "DROF gets $rof_tasks"
-echo "OCN gets $ocn_tasks"
+echo "ATM gets $atm_tasks"
+echo "LND gets $lnd_tasks"
+echo "ICE gets $ice_tasks"
+echo "OCN gets $ocn_tasks"
+echo "CPL gets $cpl_tasks"
+echo "GLC gets $glc_tasks"
+echo "ROF gets $rof_tasks"
echo ""
-./xmlchange NTHRDS_CPL=$nthreads,NTASKS_CPL=$cpl_tasks
-./xmlchange NTHRDS_GLC=$nthreads,NTASKS_GLC=$glc_tasks,NINST_GLC=1
./xmlchange NTHRDS_ATM=$nthreads,NTASKS_ATM=$atm_tasks,NINST_ATM=$num_instances
./xmlchange NTHRDS_LND=$nthreads,NTASKS_LND=$lnd_tasks,NINST_LND=$num_instances
./xmlchange NTHRDS_ICE=$nthreads,NTASKS_ICE=$ice_tasks,NINST_ICE=$num_instances
+./xmlchange NTHRDS_OCN=$nthreads,NTASKS_OCN=$ocn_tasks,NINST_OCN=$num_instances
+./xmlchange NTHRDS_CPL=$nthreads,NTASKS_CPL=$cpl_tasks
+./xmlchange NTHRDS_GLC=$nthreads,NTASKS_GLC=$glc_tasks,NINST_GLC=1
./xmlchange NTHRDS_ROF=$nthreads,NTASKS_ROF=$rof_tasks,NINST_ROF=$num_instances
-./xmlchange NTHRDS_OCN=$nthreads,NTASKS_OCN=$ocn_tasks,NINST_OCN=$num_instances
./xmlchange ROOTPE_ATM=0
+./xmlchange ROOTPE_LND=0
+./xmlchange ROOTPE_ICE=0
./xmlchange ROOTPE_OCN=0
./xmlchange ROOTPE_CPL=0
-./xmlchange ROOTPE_LND=0
-./xmlchange ROOTPE_ICE=0
./xmlchange ROOTPE_GLC=0
./xmlchange ROOTPE_ROF=0
@@ -405,12 +409,15 @@
./xmlchange STOP_N=$stop_n
./xmlchange CONTINUE_RUN=FALSE
./xmlchange RESUBMIT=$resubmit
+
./xmlchange PIO_TYPENAME=pnetcdf
# This sets the ocean coupling time to 6 hours.
# All related namelist settings are based on this value.
./xmlchange OCN_NCPL=4
+# There is no compset that has everything we want,
+# so we are also turning on the CLM biogeochemistry.
./xmlchange CLM_CONFIG_OPTS='-bgc cn'
if ($short_term_archiver == 'off') then
@@ -466,7 +473,7 @@
set QUEUE=`grep BSUB ${case}.run | grep -e '-q' `
sed -e "s/$TIMEWALL[3]/$timewall/" \
-e "s/ptile=[0-9][0-9]*/ptile=$ptile/" \
- -e "s/$QUEUE[3]/$queue/" < ${case}.run >> temp.$$
+ -e "s/$QUEUE[3]/$queue/" < ${case}.run >! temp.$$
${MOVE} temp.$$ ${case}.run
chmod 755 ${case}.run
breaksw
@@ -477,6 +484,56 @@
endsw
# ==============================================================================
+# Update source files.
+# Ideally, using DART would not require any modifications to the model source.
+# Until then, this script accesses sourcemods from a hardwired location.
+# If you have additional sourcemods, they will need to be merged into any DART
+# mods and put in the SourceMods subdirectory found in the 'case' directory.
+# ==============================================================================
+
+if ( -d ~/${cesmtag}/SourceMods ) then
+ ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
+else
+ echo "ERROR - No SourceMods for this case."
+ echo "ERROR - No SourceMods for this case."
+ echo "DART requires modifications to several src files."
+ echo "These files can be downloaded from:"
+ echo "http://www.image.ucar.edu/pub/DART/CESM/DART_SourceMods_cesm1_1_1.tar"
+ echo "untar these into your HOME directory - they will create a"
+ echo "~/cesm_1_1_1 directory with the appropriate SourceMods structure."
+ exit -4
+endif
+
+# The CESM multi-instance capability is relatively new and still has a few
+# implementation bugs. These are known problems and will be fixed soon.
+# this should be removed when the files are fixed:
+
+echo "REPLACING BROKEN CESM FILES HERE - SHOULD BE REMOVED WHEN FIXED"
+echo caseroot is ${caseroot}
+if ( -d ~/${cesmtag} ) then
+
+ # preserve the original version of the files
+ if ( ! -e ${caseroot}/Buildconf/clm.buildnml.csh.original ) then
+ ${MOVE} ${caseroot}/Buildconf/clm.buildnml.csh \
+ ${caseroot}/Buildconf/clm.buildnml.csh.original
+ endif
+ if ( ! -e ${caseroot}/Buildconf/rtm.buildnml.csh.original ) then
+ ${MOVE} ${caseroot}/Buildconf/rtm.buildnml.csh \
+ ${caseroot}/Buildconf/rtm.buildnml.csh.original
+ endif
+ if ( ! -e ${caseroot}/preview_namelists.original ) then
+ ${MOVE} ${caseroot}/preview_namelists \
+ ${caseroot}/preview_namelists.original
+ endif
+
+ # patch/replace the broken files
+ ${COPY} ~/${cesmtag}/clm.buildnml.csh ${caseroot}/Buildconf/.
+ ${COPY} ~/${cesmtag}/rtm.buildnml.csh ${caseroot}/Buildconf/.
+ ${COPY} ~/${cesmtag}/preview_namelists ${caseroot}/.
+
+endif
+
+# ==============================================================================
# Modify namelist templates for each instance. This is a bit of a nuisance in
# that we are pulling in restart and initial files from 'all over the place'
# and each model component has a different strategy.
@@ -498,28 +555,28 @@
@ inst = 1
while ($inst <= $num_instances)
- # instance now includes the leading underscore
- set instance = `printf _%04d $inst`
+ # following the CESM strategy for 'inst_string'
+ set inst_string = `printf _%04d $inst`
# special for some files: no leading underscore, 2 digits
set instance2 = `printf %02d $inst`
# ===========================================================================
- set fname = "user_nl_cam${instance}"
+ set fname = "user_nl_cam${inst_string}"
# ===========================================================================
# For a HOP TEST ... empty_htapes = .false.
# For a HOP TEST ... use a default fincl1
# FIXME ... add documentation for configuring CAM history files
echo " inithist = '6-HOURLY'" >> ${fname}
- echo " ncdata = 'cam_initial${instance}.nc'" >> ${fname}
+ echo " ncdata = 'cam_initial${inst_string}.nc'" >> ${fname}
echo " empty_htapes = .true. " >> ${fname}
echo " fincl1 = 'PHIS:I' " >> ${fname}
echo " nhtfrq = -$assim_n " >> ${fname}
echo " mfilt = 1 " >> ${fname}
# ===========================================================================
- set fname = "user_nl_clm${instance}"
+ set fname = "user_nl_clm${inst_string}"
# ===========================================================================
# Customize the land namelists
@@ -550,7 +607,7 @@
echo "hist_avgflag_pertape = 'A','A'" >> $fname
# ===========================================================================
- set fname = "user_nl_pop2${instance}"
+ set fname = "user_nl_pop2${inst_string}"
# ===========================================================================
# POP Namelists
@@ -565,18 +622,32 @@
#
# For a HOP TEST ... Would like to have restart files every day, not just for end.
# For a HOP TEST (untested)... tavg_file_freq_opt = 'nmonth' 'nday' 'once'"
+ #
+ # DEFAULT values for these are:
+ # tavg_file_freq_opt = 'nmonth' 'nmonth' 'once'
+ # tavg_freq_opt = 'nmonth' 'nday' 'once'
+ # The first entry indicates we get a monthly average once a month.
+ # The second entry indicates we get a monthly average as it is being created.
+ # The third entry indicates we get a daily timeslice
+ #
+ # IFF values for these are:
+ # tavg_file_freq_opt = 'nmonth' 'never' 'never'
+ # tavg_freq_opt = 'nmonth' 'never' 'never'
+ # The first entry indicates we get a monthly average once a month, and thats all we get..
+
+ echo "init_ts_suboption = 'data_assim'" >> $fname
+ echo "tavg_file_freq_opt = 'nmonth' 'never' 'never'" >> $fname
+ echo "tavg_freq_opt = 'nmonth' 'never' 'never'" >> $fname
- echo "init_ts_suboption = 'rest'" >> $fname
-
# ===========================================================================
- set fname = "user_nl_cice${instance}"
+ set fname = "user_nl_cice${inst_string}"
# ===========================================================================
# CICE Namelists
echo "ice_ic = 'b40.20th.005_ens${instance2}.cice.r.2004-01-01-00000.nc'" >> $fname
# ===========================================================================
- set fname = "user_nl_rtm${instance}"
+ set fname = "user_nl_rtm${inst_string}"
# ===========================================================================
# RIVER RUNOFF CAN START FROM AN OLD CLM RESTART FILE
# you can specify the RTM filename here and override the settings from
@@ -587,56 +658,6 @@
@ inst ++
end
-# ==============================================================================
-# Update source files.
-# Ideally, using DART would not require any modifications to the model source.
-# Until then, this script accesses sourcemods from a hardwired location.
-# If you have additional sourcemods, they will need to be merged into any DART
-# mods and put in the SourceMods subdirectory found in the 'case' directory.
-# ==============================================================================
-
-if ( -d ~/${cesmtag}/SourceMods ) then
- ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
-else
- echo "ERROR - No SourceMods for this case."
- echo "ERROR - No SourceMods for this case."
- echo "DART requires modifications to several src files."
- echo "These files can be downloaded from:"
- echo "http://www.image.ucar.edu/pub/DART/CESM/DART_SourceMods_cesm1_1_1.tar"
- echo "untar these into your HOME directory - they will create a"
- echo "~/cesm_1_1_1 directory with the appropriate SourceMods structure."
- exit -4
-endif
-
-# The CESM multi-instance capability is relatively new and still has a few
-# implementation bugs. These are known problems and will be fixed soon.
-# this should be removed when the files are fixed:
-
-echo "REPLACING BROKEN CESM FILES HERE - SHOULD BE REMOVED WHEN FIXED"
-echo caseroot is ${caseroot}
-if ( -d ~/${cesmtag} ) then
-
- # preserve the original version of the files
- if ( ! -e ${caseroot}/Buildconf/clm.buildnml.csh.original ) then
- ${MOVE} ${caseroot}/Buildconf/clm.buildnml.csh \
- ${caseroot}/Buildconf/clm.buildnml.csh.original
- endif
- if ( ! -e ${caseroot}/Buildconf/rtm.buildnml.csh.original ) then
- ${MOVE} ${caseroot}/Buildconf/rtm.buildnml.csh \
- ${caseroot}/Buildconf/rtm.buildnml.csh.original
- endif
- if ( ! -e ${caseroot}/preview_namelists.original ) then
- ${MOVE} ${caseroot}/preview_namelists \
- ${caseroot}/preview_namelists.original
- endif
-
- # patch/replace the broken files
- ${COPY} ~/${cesmtag}/clm.buildnml.csh ${caseroot}/Buildconf/.
- ${COPY} ~/${cesmtag}/rtm.buildnml.csh ${caseroot}/Buildconf/.
- ${COPY} ~/${cesmtag}/preview_namelists ${caseroot}/.
-
-endif
-
./preview_namelists
# ==============================================================================
@@ -726,15 +747,18 @@
echo "3) Verify the contents of env_run.xml and submit the CESM job:"
echo " ./${case}.submit"
echo ""
-echo "4) After the job has run, make sure it worked and that "
-echo " POP is creating netCDF restart files."
+echo "4) After the job has run, check to make sure it worked and that"
+echo " a: POP is creating netCDF restart files,"
+echo " b: the right restart files exist in the run directory,"
+echo " c: (if you're running DART) the archive dart/hist directory has the DART output,"
+echo " d: everything is working correctly ..."
echo ""
echo "5) To extend the run in $assim_n '"$stop_option"' steps,"
echo " change the env_run.xml variables:"
echo ""
-echo " ./xmlchange CONTINUE_RUN=TRUE"
-echo " ./xmlchange RESUBMIT=<number_of_cycles_to_run>"
-echo " ./xmlchange STOP_N=$assim_n"
+echo " ./xmlchange CONTINUE_RUN=TRUE"
+echo " ./xmlchange RESUBMIT=<number_of_cycles_to_run>"
+echo " ./xmlchange STOP_N=$assim_n"
echo ""
exit 0
Modified: DART/trunk/models/CESM/shell_scripts/CESM_DART_config
===================================================================
--- DART/trunk/models/CESM/shell_scripts/CESM_DART_config 2013-09-20 22:26:31 UTC (rev 6486)
+++ DART/trunk/models/CESM/shell_scripts/CESM_DART_config 2013-09-20 22:53:22 UTC (rev 6487)
@@ -167,6 +167,16 @@
# this script was autogenerated by $0
# using the variables set in that script
+for FILE in cam_input.nml clm_input.nml pop_input.nml input.nml; do
+ if [[ -e \$FILE ]]; then
+ if [[ -e \$FILE.original ]]; then
+ echo "\$FILE.original already exists - not making another"
+ else
+ ${COPY} \$FILE \$FILE.original
+ fi
+ fi
+done
+
${COPY} ${DARTROOT}/models/cam/work/cam_to_dart ${EXEROOT}/.
${COPY} ${DARTROOT}/models/cam/work/dart_to_cam ${EXEROOT}/.
${COPY} ${DARTROOT}/models/cam/work/filter ${EXEROOT}/filter_cam
@@ -190,7 +200,7 @@
# The first time this is executed, the update namlist script does not exist.
if [[ -x update_dart_namelists ]]; then
- ./update_dart_namelists
+ ./update_dart_namelists
fi
exit 0
@@ -238,6 +248,7 @@
g;num_output_state_members ;s;= .*;= ${NINST_LND};
g;num_output_obs_members ;s;= .*;= ${NINST_LND};
g;casename ;s;= .*;= "../${CASE}",;
+g;hist_nhtfrq ;s;= .*;= -HISTORY_OUTPUT_INTERVAL,;
wq
ex_end
@@ -257,11 +268,13 @@
./update_dart_namelists
#=========================================================================
-# Stage the files needed for SAMPLING ERROR CORRECTION
+# Stage the files needed for SAMPLING ERROR CORRECTION - even if not
+# initially requested. The file is static, small, and may be needed later.
#
-# The sampling error correction is a lookup table.
-# Each ensemble size has its own (static) file.
-# It is only needed if any
+# If it is requested and is not present ... it is an error.
+#
+# The sampling error correction is a lookup table. Each ensemble size
+# has its own (static) file. It is only needed if any
# input.nml:&assim_tools_nml:sampling_error_correction = .true.,
#
# If any of the SECs in any namelist are true, force the final_full.nn
@@ -287,7 +300,7 @@
echo "ERROR: no sampling error correction file for this ensemble size."
echo "ERROR: looking for ${SAMP_ERR_FILE} in"
echo "ERROR: ${DARTROOT}/system_simulation/final_full_precomputed_tables"
- echo "ERROR: one can be generated for any ensemble size; see docs"
+ echo "ERROR: one can be generated for any ensemble size; see docs."
exit -3
endif
endif
@@ -325,8 +338,8 @@
# it is useful to specify an initial file of inflation values for the first
# assimilation step. However, I can think of no general way to do this. The
@@ Diff output truncated at 40000 characters. @@
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