[Dart-dev] [6036] DART/branches/development/models/CESM/shell_scripts: The setup for beta17 is not applicable.
nancy at ucar.edu
nancy at ucar.edu
Wed Apr 3 09:22:48 MDT 2013
Revision: 6036
Author: thoar
Date: 2013-04-03 09:22:47 -0600 (Wed, 03 Apr 2013)
Log Message:
-----------
The setup for beta17 is not applicable.
The shell scripts were renamed with extensions that our
subversion configuration files know how to handle.
Added Paths:
-----------
DART/branches/development/models/CESM/shell_scripts/CESM1_1_1_setup.csh
DART/branches/development/models/CESM/shell_scripts/run_filter.csh
DART/branches/development/models/CESM/shell_scripts/run_perfect_model_obs.csh
Removed Paths:
-------------
DART/branches/development/models/CESM/shell_scripts/CESM1_1_setup_hybrid.csh
DART/branches/development/models/CESM/shell_scripts/CESM_setup_beta17.csh
DART/branches/development/models/CESM/shell_scripts/run_filter.batch
DART/branches/development/models/CESM/shell_scripts/run_perfect_model_obs.batch
-------------- next part --------------
Copied: DART/branches/development/models/CESM/shell_scripts/CESM1_1_1_setup.csh (from rev 6035, DART/branches/development/models/CESM/shell_scripts/CESM1_1_setup_hybrid.csh)
===================================================================
--- DART/branches/development/models/CESM/shell_scripts/CESM1_1_1_setup.csh (rev 0)
+++ DART/branches/development/models/CESM/shell_scripts/CESM1_1_1_setup.csh 2013-04-03 15:22:47 UTC (rev 6036)
@@ -0,0 +1,661 @@
+#!/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
+# ---------------------
+#
+# This script is designed to configure and build a multi-instance CESM model
+# that has POP as active components
+# and will use DART to assimilate observations at regular intervals.
+# This script does not build DART.
+#
+# This script relies heavily on the information in:
+# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/book1.html
+#
+# ---------------------
+# How to set up the script
+# ---------------------
+# -- Either edit and run this script in the $DART/models/POP/shell_scripts
+# directory where it first appears,
+# or copy it to somewhere that it will be preserved and run it there.
+# It will create a 'case' directory, where the model will be built,
+# and an execution directory, where each forecast and assimilation will
+# take place. The short term archiver will use a third directory for
+# storage of model output until it can be moved to long term storage (HPSS)
+# -- Examine the whole script to identify things to change for your experiments.
+# -- Provide any initial files needed by your run:
+# inflation
+# sampling error correction
+# POP initial ensemble
+# ...
+# -- Run this script.
+# -- Edit the DART input.nml that appears in the $CASEROOT directory.
+# -- Submit the job using $CASEROOT/${case}.submit
+#
+# ---------------------
+# Important features
+# ---------------------
+#
+# If you want to change something in your case other than the runtime
+# settings, it is safest to delete everything and start the run from scratch.
+# For the brave, read
+#
+# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/x1142.html
+#
+# and you may be able to salvage something with
+# ./cesm_setup -clean
+# ./cesm_setup
+# ./${case}.clean_build
+# ./${case}.build
+#
+# ==============================================================================
+# ==== Set case options
+# ==============================================================================
+
+# 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 pop_hybrid_opt
+setenv compset GIAF
+setenv cesmtag cesm1_1_1
+setenv resolution T62_gx1v6
+setenv num_instances 30
+
+# ==============================================================================
+# define machines and directories
+#
+# mach Computer name
+# cesm_datadir Root path of the public CESM data files
+# cesmroot Location of the cesm code base
+# For cesm1_1 on yellowstone
+# DARTroot Location of DART code tree.
+# Executables, scripts and input in $DARTroot/models/dev/...
+# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
+# Preferably not a frequently scrubbed location.
+# This script will delete any existing caseroot, so this script,
+# and other useful things should be kept elsewhere.
+# rundir (Future) Run-time directory; scrubbable, large amount of space needed.
+# exeroot (Future) directory for executables - scrubbable, large amount of space needed.
+# archdir (Future) Short-term archive directory
+# until the long-term archiver moves it to permanent storage.
+# ==============================================================================
+
+setenv mach yellowstone
+setenv cesm_datadir /glade/p/cesm/cseg/inputdata
+setenv cesmroot /glade/p/cesm/cseg/collections/$cesmtag
+setenv caseroot /glade/p/work/${USER}/cases/${case}
+setenv exeroot /glade/scratch/${USER}/${case}/bld
+setenv rundir /glade/scratch/${USER}/${case}/run
+setenv archdir /glade/scratch/${USER}/archive/${case}
+
+setenv DARTroot /glade/u/home/${USER}/svn/DART/dev
+
+# ==============================================================================
+# configure settings
+# ==============================================================================
+
+setenv stream_year_first 2004
+setenv stream_year_last 2004
+setenv stream_year_align 2004
+setenv refyear 2004
+setenv refmon 01
+setenv refday 01
+setenv run_reftod 00000
+setenv run_refdate $refyear-$refmon-$refday
+
+# ==============================================================================
+# runtime settings -- How many assimilation steps will be done after this one
+#
+# stop_option Units for determining the forecast length between assimilations
+# stop_n Number of time units in the forecast
+# ==============================================================================
+
+setenv resubmit 0
+setenv stop_option ndays
+setenv stop_n 2
+
+# ==============================================================================
+# job settings
+#
+# timewall can be changed during a series by changing the ${case}.run
+# queue can be changed during a series by changing the ${case}.run
+#
+# TJH: How many T62_gx1v6 POP instances can fit on 1 node?
+# ==============================================================================
+
+setenv ACCOUNT P86850054
+setenv timewall 0:30
+setenv queue regular
+setenv ptile 15
+
+# ==============================================================================
+# set these standard commands based on the machine you are running on.
+# ==============================================================================
+
+switch ("`hostname`")
+ case be*:
+ # NCAR "bluefire"
+ # The FORCE options are not optional.
+ # the VERBOSE options are useful for debugging.
+ set MOVE = '/usr/local/bin/mv -fv'
+ set COPY = '/usr/local/bin/cp -fv --preserve=timestamps'
+ set LINK = '/usr/local/bin/ln -fvs'
+ set REMOVE = '/usr/local/bin/rm -fr'
+
+ breaksw
+ default:
+ # NERSC "hopper", NWSC "yellowstone"
+ set MOVE = '/bin/mv -fv'
+ set COPY = '/bin/cp -fv --preserve=timestamps'
+ set LINK = '/bin/ln -fvs'
+ set REMOVE = '/bin/rm -fr'
+
+ breaksw
+endsw
+
+# ==============================================================================
+# Create the case.
+#
+# For list of the pre-defined cases: ./create_newcase -list
+# To create a variant case, see the CESM documentation and carefully
+# incorporate any needed changes into this script.
+# ==============================================================================
+
+ echo "removing old files from ${caseroot}"
+ echo "removing old files from ${exeroot}"
+ echo "removing old files from ${rundir}"
+ ${REMOVE} ${caseroot}
+ ${REMOVE} ${exeroot}
+ ${REMOVE} ${rundir}
+ ${cesmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
+ -res ${resolution} -compset ${compset}
+
+ if ( $status != 0 ) then
+ echo "ERROR: Case could not be created."
+ exit -1
+ endif
+
+# ==============================================================================
+# Configure the case - this creates the CASEROOT directory.
+# ==============================================================================
+
+cd ${caseroot}
+
+# Save a copy for debug purposes
+foreach FILE ( *xml )
+ ${COPY} $FILE ${FILE}.original
+end
+
+# Try to lay out the tasks in some sort of reasonable way.
+# The ocean root pe is the only one that is not zero.
+
+if ($num_instances == 4) then
+
+ # This is only for the purpose of debugging the code.
+ # A more efficient layout must be done when running a full assimilation.
+
+ @ atm_pes = $ptile
+ @ cpl_pes = $ptile
+ @ ice_pes = $ptile
+ @ lnd_pes = $ptile
+ @ glc_pes = $ptile
+ @ rof_pes = $ptile
+ @ ocn_pes = $ptile * 4
+
+else
+
+ # layout for 30 members.
+ # Made in conjunction with Mike Levy, David Bailey and Jim Edwards.
+
+ @ atm_pes = 450
+ @ cpl_pes = 450
+ @ ice_pes = 450
+ @ lnd_pes = 450
+ @ glc_pes = 450
+ @ rof_pes = 450
+ @ ocn_pes = 1800
+
+endif
+
+echo "task partitioning ... ice and ocean run at the same time."
+echo ""
+echo "ATM gets $atm_pes"
+echo "CPL gets $cpl_pes"
+echo "ICE gets $ice_pes"
+echo "LND gets $lnd_pes"
+echo "GLC gets $glc_pes"
+echo "DROF gets $rof_pes"
+echo "OCN gets $ocn_pes"
+echo ""
+
+./xmlchange ROOTPE_ATM=0,NTHRDS_ATM=1,NTASKS_ATM=$atm_pes,NINST_ATM=$num_instances
+./xmlchange ROOTPE_ICE=0,NTHRDS_ICE=1,NTASKS_ICE=$ice_pes,NINST_ICE=$num_instances
+./xmlchange ROOTPE_GLC=0,NTHRDS_GLC=1,NTASKS_GLC=$glc_pes,NINST_GLC=1
+./xmlchange ROOTPE_LND=0,NTHRDS_LND=1,NTASKS_LND=$lnd_pes,NINST_LND=1
+./xmlchange ROOTPE_ROF=0,NTHRDS_ROF=1,NTASKS_ROF=$rof_pes,NINST_ROF=1
+./xmlchange ROOTPE_CPL=0,NTHRDS_CPL=1,NTASKS_CPL=$cpl_pes
+./xmlchange NTHRDS_OCN=1,NTASKS_OCN=$ocn_pes,NINST_OCN=$num_instances
+./xmlchange ROOTPE_OCN=$ice_pes
+
+# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/c1158.html#run_start_stop
+# "A hybrid run indicates that CESM is initialized more like a startup, but uses
+# initialization datasets from a previous case. This is somewhat analogous to a
+# branch run with relaxed restart constraints. A hybrid run allows users to bring
+# together combinations of initial/restart files from a previous case (specified
+# by $RUN_REFCASE) at a given model output date (specified by $RUN_REFDATE).
+# Unlike a branch run, the starting date of a hybrid run (specified by $RUN_STARTDATE)
+# can be modified relative to the reference case. In a hybrid run, the model does not
+# continue in a bit-for-bit fashion with respect to the reference case. The resulting
+# climate, however, should be continuous provided that no model source code or
+# namelists are changed in the hybrid run. In a hybrid initialization, the ocean
+# model does not start until the second ocean coupling (normally the second day),
+# and the coupler does a "cold start" without a restart file.
+
+./xmlchange RUN_TYPE=hybrid
+./xmlchange RUN_STARTDATE=$run_refdate
+./xmlchange RUN_REFCASE=b40.20th.005
+./xmlchange RUN_REFDATE=$run_refdate
+./xmlchange RUN_REFTOD=$run_reftod
+./xmlchange BRNCH_RETAIN_CASENAME=FALSE
+./xmlchange GET_REFCASE=FALSE
+./xmlchange EXEROOT=${exeroot}
+
+# The streams files were generated with a NO_LEAP calendar in mind.
+# We need to test these with a GREGORIAN calendar.
+
+./xmlchange CALENDAR=GREGORIAN
+
+./xmlchange STOP_OPTION=$stop_option
+./xmlchange STOP_N=$stop_n
+./xmlchange CONTINUE_RUN=FALSE
+./xmlchange RESUBMIT=$resubmit
+./xmlchange PIO_TYPENAME=pnetcdf
+
+./xmlchange DOUT_S=TRUE
+./xmlchange DOUT_S_ROOT=${archdir}
+./xmlchange DOUT_S_SAVE_INT_REST_FILES=FALSE
+./xmlchange DOUT_L_MS=FALSE
+./xmlchange DOUT_L_MSROOT="csm/${case}"
+./xmlchange DOUT_L_HTAR=FALSE
+
+./xmlchange DATM_MODE=CPLHIST3HrWx
+./xmlchange DATM_CPLHIST_CASE=$case
+./xmlchange DATM_CPLHIST_YR_ALIGN=$refyear
+./xmlchange DATM_CPLHIST_YR_START=$refyear
+./xmlchange DATM_CPLHIST_YR_END=$refyear
+
+# level of debug output, 0=minimum, 1=normal, 2=more, 3=too much, valid values: 0,1,2,3 (integer)
+
+./xmlchange DEBUG=FALSE
+./xmlchange INFO_DBUG=0
+
+# ==============================================================================
+# Set up the case.
+# This creates the EXEROOT and RUNDIR directories.
+# ==============================================================================
+
+./cesm_setup
+
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be set up."
+ exit -2
+endif
+
+# ==============================================================================
+# Modify namelist templates for each instance.
+#
+# hist_empty_htapes = .true. suppresses the creation of all history files
+# hist_fincl1 = 'TG', except the first one, which will have one variable
+# hist_nhtfrq = -$stop_n, create one every $stop_n HOURS
+# hist_mfilt = 1, with precisely one day in it
+# hist_avgflag_pertape = 'I' use instantaneous values - no average
+#
+# ==============================================================================
+
+@ inst = 1
+while ($inst <= $num_instances)
+
+ set instance = `printf %04d $inst`
+ set instance2 = `printf %02d $inst`
+
+ set fname = "user_nl_datm_$instance"
+
+ echo "streams = 'datm.streams.txt.CPLHIST3HrWx.Solar_$instance $stream_year_align $stream_year_first $stream_year_last'," >> $fname
+ echo " 'datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_$instance $stream_year_align $stream_year_first $stream_year_last'" >> $fname
+ echo "dtlimit = 1.5, 1.5" >> $fname
+ echo "fillalgo = 'nn', 'nn'" >> $fname
+ echo "fillmask = 'nomask','nomask'" >> $fname
+ echo "mapalgo = 'bilinear','bilinear'" >> $fname
+ echo "mapmask = 'nomask','nomask'" >> $fname
+ echo "taxmode = 'cycle','cycle'" >> $fname
+ echo "tintalgo = 'linear','linear'" >> $fname
+ echo "restfils = 'unset'" >> $fname
+ echo "restfilm = 'unset'" >> $fname
+
+ # CICE Namelists
+ # this is only used for a hybrid start, else rpointers are used.
+ echo "ice_ic = 'b40.20th.005_ens"$instance2".cice.r.2004-01-01-00000.nc'" >> user_nl_cice_$instance
+
+ # POP Namelists
+ # init_ts_suboption = 'data_assim' for non bit-for-bit restarting (assimilation mode)
+ # init_ts_suboption = 'null' for 'perfect' restarting/forecasting
+
+ echo "init_ts_suboption = 'data_assim'" >> user_nl_pop2_$instance
+
+ @ inst ++
+end
+
+# DLND
+
+echo "streams = 'drof.streams.txt.rof.diatren_iaf_rx1" 1 1948 2009"'" >> user_nl_drof
+
+# ==============================================================================
+# to create custom streamfiles ...
+# "To modify the contents of a stream txt file, first use preview_namelists to
+# obtain the contents of the stream txt files in CaseDocs, and then place a copy
+# of the modified stream txt file in $CASEROOT with the string user_ prepended."
+#
+# -or-
+#
+# we copy a template stream txt file from the
+# $DARTroot/models/POP/shell_scripts directory and modify one for each instance.
+#
+# ==============================================================================
+
+./preview_namelists
+
+# This gives us a stream txt file for each instance that we can
+# modify for our own purpose.
+
+foreach FILE (CaseDocs/*streams*)
+ set FNAME = $FILE:t
+
+ switch ( ${FNAME} )
+ case *presaero*:
+ echo "Using default prescribed aerosol stream.txt file ${FNAME}"
+ breaksw
+ case *diatren*:
+ echo "Using default runoff stream.txt file ${FNAME}"
+ breaksw
+ case *\.Precip_*:
+ echo "Precipitation in nonSolarNonPrecip stream.txt file - not ${FNAME}"
+ breaksw
+ default:
+ ${COPY} $FILE user_$FNAME
+ chmod 644 user_$FNAME
+ breaksw
+ endsw
+
+end
+
+# Replace each default stream txt file with one that uses the CAM DATM
+# conditions for a default year and modify the instance number.
+
+foreach FNAME (user*streams*)
+ set name_parse = `echo $FNAME | sed 's/\_/ /g'`
+ @ filename_index = $#name_parse - 1
+ @ instance_index = $#name_parse
+ set streamname = $name_parse[$filename_index]
+ set n = `echo $name_parse[$instance_index] | sed 's/0*//'`
+
+ if (-e $DARTroot/models/POP/shell_scripts/user_$streamname*template) then
+
+ echo "Copying DART template for $FNAME and changing instances."
+
+ ${COPY} $DARTroot/models/POP/shell_scripts/user_$streamname*template $FNAME
+
+ sed s/NINST/$n/g $FNAME >! out.$$
+ ${MOVE} out.$$ $FNAME
+
+ else
+ echo "DIED Looking for a DART stream txt template for $FNAME"
+ echo "DIED Looking for a DART stream txt template for $FNAME"
+ exit -3
+ endif
+
+end
+
+./preview_namelists
+
+# ==============================================================================
+# Update source files if need be
+# Ideally, using DART will not require any source mods.
+# Until then, this script accesses source mods from a hard-wired location below.
+# Those may eventually be packaged into the DART repository.
+# If you have additional source mods, they will need to be merged into any DART
+# mods and put in the SourceMods subdirectory found in the 'case' directory.
+# ==============================================================================
+
+if ( -d ~/${cesmtag}/SourceMods ) then
+ ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
+else
+ echo "ERROR - No SourceMods for this case."
+ echo "ERROR - No SourceMods for this case."
+ echo "DART requires modifications to several src.pop2/ files."
+ echo "These files can be downloaded from:"
+ echo "http://www.image.ucar.edu/pub/DART/CESM/DART_SourceMods_cesm1_1_1.tar"
+ echo "untar these into your HOME directory - they will create a"
+ echo "~/cesm_1_1_1 directory with the appropriate SourceMods structure."
+ exit -4
+endif
+
+# ==============================================================================
+# build
+# ==============================================================================
+
+echo ''
+echo 'Building the case'
+echo ''
+
+./${case}.build
+
+if ( $status != 0 ) then
+ echo "ERROR: Case could not be built."
+ exit -5
+endif
+
+# ==============================================================================
+# Stage the restarts now that the run directory exists
+#
+# set stagedir = /glade/scratch/thoar/DART_POP_RESTARTS/2004-01-01-00000
+# ==============================================================================
+
+set stagedir = /glade/p/work/aliciak/DART_IC/CCSM4_ensembles/rest/2004-01-01-00000
+
+echo "Copying the restart files from ${stagedir}"
+
+@ i = 1
+while ($i <= $num_instances)
+ set n4 = `printf %04d $i`
+ set n2 = `printf %02d $i`
+
+ echo ''
+ echo "Staging restarts for instance $i of $num_instances"
+ #AK: Note that the pop ocean must have the .hdr file to describe the
+ # metadata for binary restarts.
+ ${COPY} ${stagedir}/rpointer.ocn_${n4}.restart ${rundir}
+ ${COPY} ${stagedir}/rpointer.ocn_${n4}.ovf ${rundir}
+ ${COPY} ${stagedir}/rpointer.ice_${n4} ${rundir}
+ ${COPY} ${stagedir}/b40.20th.005_ens${n2}.pop.r.2004-01-01-00000 ${rundir}
+ ${COPY} ${stagedir}/b40.20th.005_ens${n2}.pop.r.2004-01-01-00000.hdr ${rundir}
+ ${COPY} ${stagedir}/b40.20th.005_ens${n2}.pop.ro.2004-01-01-00000 ${rundir}
+ ${COPY} ${stagedir}/b40.20th.005_ens${n2}.cice.r.2004-01-01-00000.nc ${rundir}
+
+ @ i ++
+
+end
+
+# ==============================================================================
+# Edit the run script to reflect project, queue, and wallclock
+# ==============================================================================
+
+echo ''
+echo 'Updating the run script to set wallclock and queue.'
+echo ''
+
+${COPY} ${case}.run ${case}.run.orig
+
+source Tools/ccsm_getenv
+set BATCH = `echo $BATCHSUBMIT | sed 's/ .*$//'`
+switch ( $BATCH )
+ case bsub*:
+ # NCAR "bluefire", "yellowstone"
+ set TIMEWALL=`grep BSUB ${case}.run | grep -e '-W' `
+ set QUEUE=`grep BSUB ${case}.run | grep -e '-q' `
+ sed -e "s/ptile=32/ptile=$ptile/" \
+ -e "s/$TIMEWALL[3]/$timewall/" \
+ -e "s/$QUEUE[3]/$queue/" < ${case}.run >! temp.$$
+ ${MOVE} temp.$$ ${case}.run
+ breaksw
+
+ default:
+
+ breaksw
+endsw
+
+# ==============================================================================
+# The *.run script must be modified to call the DART assimilate script.
+# The modifications are contained in a "here" document that MUST NOT
+# expand the wildcards etc., before it is run. This is achieved by
+# double-quoting the characters used to delineate the start/stop of
+# the "here" document. No kidding. It has to be "EndOfText",
+# not 'EndOfText' or EndOfText.
+# ==============================================================================
+
+echo ''
+echo 'Adding the call to assimilate.csh to the *.run script.'
+echo ''
+
+cat << "EndOfText" >! add_to_run.txt
+
+# -------------------------------------------------------------------------
+# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
+# perform an assimilation with DART.
+
+set CplLogFile = `ls -1t cpl.log* | head -n 1`
+if ($CplLogFile == "") then
+ echo 'ERROR: Model did not complete - no cpl.log file present - exiting.'
+ echo 'ERROR: Assimilation will not be attempted.'
+ exit -1
+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"
+ setenv LSB_PJL_TASK_GEOMETRY "{(0)}"
+ mpirun.lsf "exit -3"
+ endif
+else
+ echo 'ERROR: Model did not complete successfully - exiting.'
+ echo 'ERROR: Assimilation will not be attempted.'
+ setenv LSB_PJL_TASK_GEOMETRY "{(0)}"
+ mpirun.lsf "exit -2"
+endif
+
+# END OF DART BLOCK
+# -------------------------------------------------------------------------
+"EndOfText"
+
+# Now that the "here" document is created,
+# determine WHERE to insert it -- ONLY IF it is not already there.
+
+grep "ABANDON HOPE" ${case}.run
+set STATUSCHECK = $status
+
+if ( ${STATUSCHECK} == 0 ) then
+ echo "DART block already present in ${case}.run"
+else if ( ${STATUSCHECK} == 1 ) then
+
+ set MYSTRING = `grep --line-number "CSM EXECUTION HAS FINISHED" ${case}.run`
+ set MYSTRING = `echo $MYSTRING | sed -e "s#:# #g"`
+
+ @ origlen = `cat ${case}.run | wc -l`
+ @ keep = $MYSTRING[1]
+ @ lastlines = $origlen - $keep
+
+ head -n $keep ${case}.run >! temp.$$
+ cat add_to_run.txt >> temp.$$
+ tail -n $lastlines ${case}.run >> temp.$$
+
+ ${MOVE} temp.$$ ${case}.run
+
+endif
+
+chmod 0744 ${case}.run
+
+# ==============================================================================
+# Stage the required parts of DART in the CASEROOT directory.
+# ==============================================================================
+
+# AK: the standard CESM short-term archiving script may need to be altered
+# to archive addtional or subsets of things, or to reduce the amount of
+# data that is sent to the long-term archive. Put a version of st_archive.sh
+# in ${DARTroot}/models/POP/shell_scripts when/if necessary
+#
+if ( ~ -e Tools/st_archive.sh.orig ) then
+ ${MOVE} Tools/st_archive.sh Tools/st_archive.sh.orig
+else
+ echo "a Tools/st_archive.sh backup copy already exists"
+endif
+
+# AK note: you must use this assimilate.csh script.
+# It has hardcoded variables that point to the location of
+# the observations sequence files and the DART working
+# directory and the PE layout for DART.
+
+# ${COPY} ${DARTroot}/models/POP/shell_scripts/st_archive.sh Tools/ TJH DEBUG
+${COPY} ${DARTroot}/models/POP/shell_scripts/assimilate.csh assimilate.csh
+${COPY} ${DARTroot}/models/POP/work/input.nml input.nml
+
+# ==============================================================================
+# Stage the DART executables in the CESM execution root directory: EXEROOT
+# ==============================================================================
+
+foreach FILE ( filter pop_to_dart dart_to_pop )
+ ${COPY} ${DARTroot}/models/POP/work/${FILE} ${exeroot}/
+ if ( $status != 0 ) then
+ echo "ERROR: ${DARTroot}/models/POP/work/${FILE} not copied to ${exeroot}"
+ echo "ERROR: ${DARTroot}/models/POP/work/${FILE} not copied to ${exeroot}"
+ exit -3
+ endif
+end
+
+# ==============================================================================
+# What to do next
+# ==============================================================================
+
+echo ''
+echo "Time to check the case."
+echo ''
+echo "cd into ${caseroot}"
+echo "Modify what you like in input.nml, make sure the observation directory"
+echo "names set in assimilate.csh match those on your system, and submit"
+echo "the CESM job by running:"
+echo "./${case}.submit"
+echo ''
+echo "For continued submissions after the initial (hybrid) startup,"
+echo "make the following changes to the env_run variables:"
+echo ''
+echo " ./xmlchange -file env_run.xml -id STOP_N -val 1"
+echo " ./xmlchange -file env_run.xml -id CONTINUE_RUN -val TRUE"
+echo " ./xmlchange -file env_run.xml -id RESUBMIT -val <your_favorite_number>"
+echo ''
+echo "Check the streams listed in the streams text files. If more or different"
+echo 'dates need to be added, then do this in the $CASEROOT/user_*files*'
+echo "then invoke 'preview_namelists' so you can check the information in the"
+echo "CaseDocs or ${rundir} directories."
+echo ''
+
Deleted: DART/branches/development/models/CESM/shell_scripts/CESM1_1_setup_hybrid.csh
===================================================================
--- DART/branches/development/models/CESM/shell_scripts/CESM1_1_setup_hybrid.csh 2013-04-02 22:34:35 UTC (rev 6035)
+++ DART/branches/development/models/CESM/shell_scripts/CESM1_1_setup_hybrid.csh 2013-04-03 15:22:47 UTC (rev 6036)
@@ -1,661 +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
-# ---------------------
-#
-# This script is designed to configure and build a multi-instance CESM model
-# that has POP as active components
-# and will use DART to assimilate observations at regular intervals.
-# This script does not build DART.
-#
-# This script relies heavily on the information in:
-# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/book1.html
-#
-# ---------------------
-# How to set up the script
-# ---------------------
-# -- Either edit and run this script in the $DART/models/POP/shell_scripts
-# directory where it first appears,
-# or copy it to somewhere that it will be preserved and run it there.
-# It will create a 'case' directory, where the model will be built,
-# and an execution directory, where each forecast and assimilation will
-# take place. The short term archiver will use a third directory for
-# storage of model output until it can be moved to long term storage (HPSS)
-# -- Examine the whole script to identify things to change for your experiments.
-# -- Provide any initial files needed by your run:
-# inflation
-# sampling error correction
-# POP initial ensemble
-# ...
-# -- Run this script.
-# -- Edit the DART input.nml that appears in the $CASEROOT directory.
-# -- Submit the job using $CASEROOT/${case}.submit
-#
-# ---------------------
-# Important features
-# ---------------------
-#
-# If you want to change something in your case other than the runtime
-# settings, it is safest to delete everything and start the run from scratch.
-# For the brave, read
-#
-# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/x1142.html
-#
-# and you may be able to salvage something with
-# ./cesm_setup -clean
-# ./cesm_setup
-# ./${case}.clean_build
-# ./${case}.build
-#
-# ==============================================================================
-# ==== Set case options
-# ==============================================================================
-
-# 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 pop_hybrid_opt
-setenv compset GIAF
-setenv cesmtag cesm1_1_1
-setenv resolution T62_gx1v6
-setenv num_instances 30
-
-# ==============================================================================
-# define machines and directories
-#
-# mach Computer name
-# cesm_datadir Root path of the public CESM data files
-# cesmroot Location of the cesm code base
-# For cesm1_1 on yellowstone
-# DARTroot Location of DART code tree.
-# Executables, scripts and input in $DARTroot/models/dev/...
-# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
-# Preferably not a frequently scrubbed location.
-# This script will delete any existing caseroot, so this script,
-# and other useful things should be kept elsewhere.
-# rundir (Future) Run-time directory; scrubbable, large amount of space needed.
-# exeroot (Future) directory for executables - scrubbable, large amount of space needed.
-# archdir (Future) Short-term archive directory
-# until the long-term archiver moves it to permanent storage.
-# ==============================================================================
-
-setenv mach yellowstone
-setenv cesm_datadir /glade/p/cesm/cseg/inputdata
-setenv cesmroot /glade/p/cesm/cseg/collections/$cesmtag
-setenv caseroot /glade/p/work/${USER}/cases/${case}
-setenv exeroot /glade/scratch/${USER}/${case}/bld
-setenv rundir /glade/scratch/${USER}/${case}/run
-setenv archdir /glade/scratch/${USER}/archive/${case}
-
-setenv DARTroot /glade/u/home/${USER}/svn/DART/dev
-
-# ==============================================================================
-# configure settings
-# ==============================================================================
-
-setenv stream_year_first 2004
-setenv stream_year_last 2004
-setenv stream_year_align 2004
-setenv refyear 2004
-setenv refmon 01
-setenv refday 01
-setenv run_reftod 00000
-setenv run_refdate $refyear-$refmon-$refday
-
-# ==============================================================================
-# runtime settings -- How many assimilation steps will be done after this one
-#
-# stop_option Units for determining the forecast length between assimilations
-# stop_n Number of time units in the forecast
-# ==============================================================================
-
-setenv resubmit 0
-setenv stop_option ndays
-setenv stop_n 2
-
-# ==============================================================================
-# job settings
-#
-# timewall can be changed during a series by changing the ${case}.run
-# queue can be changed during a series by changing the ${case}.run
-#
-# TJH: How many T62_gx1v6 POP instances can fit on 1 node?
-# ==============================================================================
-
-setenv ACCOUNT P86850054
-setenv timewall 0:30
-setenv queue regular
-setenv ptile 15
-
-# ==============================================================================
-# set these standard commands based on the machine you are running on.
-# ==============================================================================
-
-switch ("`hostname`")
- case be*:
- # NCAR "bluefire"
- # The FORCE options are not optional.
- # the VERBOSE options are useful for debugging.
- set MOVE = '/usr/local/bin/mv -fv'
- set COPY = '/usr/local/bin/cp -fv --preserve=timestamps'
- set LINK = '/usr/local/bin/ln -fvs'
- set REMOVE = '/usr/local/bin/rm -fr'
-
- breaksw
- default:
- # NERSC "hopper", NWSC "yellowstone"
- set MOVE = '/bin/mv -fv'
- set COPY = '/bin/cp -fv --preserve=timestamps'
- set LINK = '/bin/ln -fvs'
- set REMOVE = '/bin/rm -fr'
-
- breaksw
-endsw
-
-# ==============================================================================
-# Create the case.
-#
-# For list of the pre-defined cases: ./create_newcase -list
-# To create a variant case, see the CESM documentation and carefully
-# incorporate any needed changes into this script.
-# ==============================================================================
-
- echo "removing old files from ${caseroot}"
- echo "removing old files from ${exeroot}"
- echo "removing old files from ${rundir}"
- ${REMOVE} ${caseroot}
- ${REMOVE} ${exeroot}
- ${REMOVE} ${rundir}
- ${cesmroot}/scripts/create_newcase -case ${caseroot} -mach ${mach} \
- -res ${resolution} -compset ${compset}
-
- if ( $status != 0 ) then
- echo "ERROR: Case could not be created."
- exit -1
- endif
-
-# ==============================================================================
-# Configure the case - this creates the CASEROOT directory.
-# ==============================================================================
-
-cd ${caseroot}
-
-# Save a copy for debug purposes
-foreach FILE ( *xml )
- ${COPY} $FILE ${FILE}.original
-end
-
-# Try to lay out the tasks in some sort of reasonable way.
-# The ocean root pe is the only one that is not zero.
-
-if ($num_instances == 4) then
-
- # This is only for the purpose of debugging the code.
- # A more efficient layout must be done when running a full assimilation.
-
- @ atm_pes = $ptile
- @ cpl_pes = $ptile
- @ ice_pes = $ptile
- @ lnd_pes = $ptile
- @ glc_pes = $ptile
- @ rof_pes = $ptile
- @ ocn_pes = $ptile * 4
-
-else
-
- # layout for 30 members.
- # Made in conjunction with Mike Levy, David Bailey and Jim Edwards.
-
- @ atm_pes = 450
- @ cpl_pes = 450
- @ ice_pes = 450
- @ lnd_pes = 450
- @ glc_pes = 450
- @ rof_pes = 450
- @ ocn_pes = 1800
-
-endif
-
-echo "task partitioning ... ice and ocean run at the same time."
-echo ""
-echo "ATM gets $atm_pes"
-echo "CPL gets $cpl_pes"
-echo "ICE gets $ice_pes"
-echo "LND gets $lnd_pes"
-echo "GLC gets $glc_pes"
-echo "DROF gets $rof_pes"
-echo "OCN gets $ocn_pes"
-echo ""
-
-./xmlchange ROOTPE_ATM=0,NTHRDS_ATM=1,NTASKS_ATM=$atm_pes,NINST_ATM=$num_instances
-./xmlchange ROOTPE_ICE=0,NTHRDS_ICE=1,NTASKS_ICE=$ice_pes,NINST_ICE=$num_instances
-./xmlchange ROOTPE_GLC=0,NTHRDS_GLC=1,NTASKS_GLC=$glc_pes,NINST_GLC=1
-./xmlchange ROOTPE_LND=0,NTHRDS_LND=1,NTASKS_LND=$lnd_pes,NINST_LND=1
-./xmlchange ROOTPE_ROF=0,NTHRDS_ROF=1,NTASKS_ROF=$rof_pes,NINST_ROF=1
-./xmlchange ROOTPE_CPL=0,NTHRDS_CPL=1,NTASKS_CPL=$cpl_pes
-./xmlchange NTHRDS_OCN=1,NTASKS_OCN=$ocn_pes,NINST_OCN=$num_instances
-./xmlchange ROOTPE_OCN=$ice_pes
-
-# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/c1158.html#run_start_stop
-# "A hybrid run indicates that CESM is initialized more like a startup, but uses
-# initialization datasets from a previous case. This is somewhat analogous to a
-# branch run with relaxed restart constraints. A hybrid run allows users to bring
-# together combinations of initial/restart files from a previous case (specified
-# by $RUN_REFCASE) at a given model output date (specified by $RUN_REFDATE).
-# Unlike a branch run, the starting date of a hybrid run (specified by $RUN_STARTDATE)
-# can be modified relative to the reference case. In a hybrid run, the model does not
-# continue in a bit-for-bit fashion with respect to the reference case. The resulting
-# climate, however, should be continuous provided that no model source code or
-# namelists are changed in the hybrid run. In a hybrid initialization, the ocean
-# model does not start until the second ocean coupling (normally the second day),
-# and the coupler does a "cold start" without a restart file.
-
-./xmlchange RUN_TYPE=hybrid
-./xmlchange RUN_STARTDATE=$run_refdate
-./xmlchange RUN_REFCASE=b40.20th.005
-./xmlchange RUN_REFDATE=$run_refdate
-./xmlchange RUN_REFTOD=$run_reftod
-./xmlchange BRNCH_RETAIN_CASENAME=FALSE
-./xmlchange GET_REFCASE=FALSE
-./xmlchange EXEROOT=${exeroot}
-
-# The streams files were generated with a NO_LEAP calendar in mind.
-# We need to test these with a GREGORIAN calendar.
-
-./xmlchange CALENDAR=GREGORIAN
-
-./xmlchange STOP_OPTION=$stop_option
-./xmlchange STOP_N=$stop_n
-./xmlchange CONTINUE_RUN=FALSE
-./xmlchange RESUBMIT=$resubmit
-./xmlchange PIO_TYPENAME=pnetcdf
-
-./xmlchange DOUT_S=TRUE
-./xmlchange DOUT_S_ROOT=${archdir}
-./xmlchange DOUT_S_SAVE_INT_REST_FILES=FALSE
-./xmlchange DOUT_L_MS=FALSE
-./xmlchange DOUT_L_MSROOT="csm/${case}"
-./xmlchange DOUT_L_HTAR=FALSE
-
-./xmlchange DATM_MODE=CPLHIST3HrWx
-./xmlchange DATM_CPLHIST_CASE=$case
-./xmlchange DATM_CPLHIST_YR_ALIGN=$refyear
-./xmlchange DATM_CPLHIST_YR_START=$refyear
-./xmlchange DATM_CPLHIST_YR_END=$refyear
-
-# level of debug output, 0=minimum, 1=normal, 2=more, 3=too much, valid values: 0,1,2,3 (integer)
-
-./xmlchange DEBUG=FALSE
-./xmlchange INFO_DBUG=0
-
-# ==============================================================================
-# Set up the case.
-# This creates the EXEROOT and RUNDIR directories.
-# ==============================================================================
-
-./cesm_setup
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be set up."
- exit -2
-endif
-
-# ==============================================================================
-# Modify namelist templates for each instance.
-#
-# hist_empty_htapes = .true. suppresses the creation of all history files
-# hist_fincl1 = 'TG', except the first one, which will have one variable
-# hist_nhtfrq = -$stop_n, create one every $stop_n HOURS
-# hist_mfilt = 1, with precisely one day in it
-# hist_avgflag_pertape = 'I' use instantaneous values - no average
-#
-# ==============================================================================
-
-@ inst = 1
-while ($inst <= $num_instances)
-
- set instance = `printf %04d $inst`
- set instance2 = `printf %02d $inst`
-
- set fname = "user_nl_datm_$instance"
-
- echo "streams = 'datm.streams.txt.CPLHIST3HrWx.Solar_$instance $stream_year_align $stream_year_first $stream_year_last'," >> $fname
- echo " 'datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_$instance $stream_year_align $stream_year_first $stream_year_last'" >> $fname
- echo "dtlimit = 1.5, 1.5" >> $fname
- echo "fillalgo = 'nn', 'nn'" >> $fname
- echo "fillmask = 'nomask','nomask'" >> $fname
- echo "mapalgo = 'bilinear','bilinear'" >> $fname
- echo "mapmask = 'nomask','nomask'" >> $fname
- echo "taxmode = 'cycle','cycle'" >> $fname
- echo "tintalgo = 'linear','linear'" >> $fname
- echo "restfils = 'unset'" >> $fname
- echo "restfilm = 'unset'" >> $fname
-
- # CICE Namelists
- # this is only used for a hybrid start, else rpointers are used.
- echo "ice_ic = 'b40.20th.005_ens"$instance2".cice.r.2004-01-01-00000.nc'" >> user_nl_cice_$instance
-
- # POP Namelists
- # init_ts_suboption = 'data_assim' for non bit-for-bit restarting (assimilation mode)
- # init_ts_suboption = 'null' for 'perfect' restarting/forecasting
-
- echo "init_ts_suboption = 'data_assim'" >> user_nl_pop2_$instance
-
- @ inst ++
-end
-
-# DLND
-
-echo "streams = 'drof.streams.txt.rof.diatren_iaf_rx1" 1 1948 2009"'" >> user_nl_drof
-
-# ==============================================================================
-# to create custom streamfiles ...
-# "To modify the contents of a stream txt file, first use preview_namelists to
-# obtain the contents of the stream txt files in CaseDocs, and then place a copy
-# of the modified stream txt file in $CASEROOT with the string user_ prepended."
-#
-# -or-
-#
-# we copy a template stream txt file from the
-# $DARTroot/models/POP/shell_scripts directory and modify one for each instance.
-#
-# ==============================================================================
-
-./preview_namelists
-
-# This gives us a stream txt file for each instance that we can
-# modify for our own purpose.
-
-foreach FILE (CaseDocs/*streams*)
- set FNAME = $FILE:t
-
- switch ( ${FNAME} )
- case *presaero*:
- echo "Using default prescribed aerosol stream.txt file ${FNAME}"
- breaksw
- case *diatren*:
- echo "Using default runoff stream.txt file ${FNAME}"
- breaksw
- case *\.Precip_*:
@@ Diff output truncated at 40000 characters. @@
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