[Dart-dev] [6486] DART/trunk/models/clm/shell_scripts: Renaming the perfect model setup script to be same at that in the POP directory .
nancy at ucar.edu
nancy at ucar.edu
Fri Sep 20 16:26:32 MDT 2013
Revision: 6486
Author: thoar
Date: 2013-09-20 16:26:31 -0600 (Fri, 20 Sep 2013)
Log Message:
-----------
Renaming the perfect model setup script to be same at that in the POP directory.
Hoping for some consistency, ultimately.
The CESM_DART_config:refresh_dart_files script now preserves a copy of the
existing input.nml before copying a new one into the caseroot directory.
Modified Paths:
--------------
DART/trunk/models/clm/shell_scripts/CESM_DART_config
Added Paths:
-----------
DART/trunk/models/clm/shell_scripts/CESM1_1_1_setup_pmo
Removed Paths:
-------------
DART/trunk/models/clm/shell_scripts/CESM1_1_1_pmo_setup
-------------- next part --------------
Deleted: DART/trunk/models/clm/shell_scripts/CESM1_1_1_pmo_setup
===================================================================
--- DART/trunk/models/clm/shell_scripts/CESM1_1_1_pmo_setup 2013-09-19 19:26:53 UTC (rev 6485)
+++ DART/trunk/models/clm/shell_scripts/CESM1_1_1_pmo_setup 2013-09-20 22:26:31 UTC (rev 6486)
@@ -1,779 +0,0 @@
-#!/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
-# http://www.image.ucar.edu/DAReS/DART/DART_download
-#
-# DART $Id$
-
-# ---------------------
-# Purpose
-# ---------------------
-#
-# This script is designed to set up, stage, and build a single-instance run of CESM
-# using an I compset where only CLM is active and the ocean and land states are
-# specified by data files. CESM is set up with a 'hybrid' start.
-#
-# CLM: The initial state is set by specifying the 'finidat' variable in
-# user_nl_clm. Under a hybrid start, CESM uses the REFCASE and REFDATE
-# information to construct the finidat value. This script makes an effort
-# to coordinate the staging of the file so it is consistent with CESM
-#
-# DATM: We are using an ensemble of data atmospheres. This requires modification of
-# the stream text files (and the stream files) for each CESM instance.
-#
-# DOCN: We are using a single data ocean.
-#
-# This script has a counterpart that is a multi-instance setup for either a free
-# run or an assimilation experiment. To make it easy to maintain (and hopefully
-# understand), the two scripts are intended to parallel each other. That means this
-# script performs a lot of manipulation of the 'instance' portion of the
-# filenames, which seems unnecessary initially.
-#
-# This script results in a viable setup for a CESM single instance experiment. You
-# are STRONGLY encouraged to run the single instance CESM a few times and experiment
-# with different settings BEFORE you try to generate 'perfect' observations.
-# You should become comfortable using CESM's restart 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 use DART to harvest synthetic observations. 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
-# CESM_DART_config to augment the existing run script, modify STOP_N to 6 hours,
-# and start harvesting synthetic observations when CESM stops at 2004-02-01 06Z ...
-#
-# This script relies heavily on the information in:
-# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/book1.html
-#
-# ---------------------
-# How to use this script.
-# ---------------------
-#
-# -- You will have to read and understand the script in its entirety.
-# You will have to modify things outside this script.
-# This script sets up a CESM single instance run as we understand them and
-# it has almost nothing to do with DART. This is intentional.
-#
-# -- Edit and run this script in the $DART/models/CESM/shell_scripts directory
-# or copy it to somewhere that it will be preserved and run it there.
-# It will create a CESM 'CASE' directory, where the model will be built,
-# and an execution directory, where each forecast 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 the CESM initial file needed by your run.
-#
-# -- Run this script.
-#
-# -- If you want to run DART; read, understand, and execute ${CASEROOT}/CESM_DART_config
-#
-# -- 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
-# ==============================================================================
-
-# 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.
-
-setenv case clm_pmo
-setenv compset I_2000_CN
-setenv resolution f09_f09
-setenv cesmtag cesm1_1_1
-
-# ==============================================================================
-# define machines and directories
-#
-# mach Computer name
-# cesmroot Location of the cesm code base
-# 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,
-# 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.
-# dartroot Location of _your_ DART installation
-# This is passed on to the CESM_DART_config script.
-# ==============================================================================
-
-setenv mach yellowstone
-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/trunk
-
-# ==============================================================================
-# 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 80_member_freerun_one_degree
-setenv refyear 2004
-setenv refmon 01
-setenv refday 01
-setenv run_reftod 00000
-setenv run_refdate $refyear-$refmon-$refday
-
-setenv stream_year_first 2004
-setenv stream_year_last 2004
-setenv stream_year_align 2004
-
-# SingleInstanceRefcase: the filenames are fundamentally different for
-# a multi-instance CESM run or a single-instance CESM run. A correct setting
-# of this variable makes staging the required files easier - that's all.
-# 1 means 'true' ... the restart file has a single-instance-like name.
-# 0 means 'false' .. the restart file has a multi-instance-like name.
-#
-# TRUTHinstance: specifies the specific instance you want to define as the TRUTH.
-# If you have an initial ensemble size of 80, 1<= instance <= 80.
-# If you only have one CLM state ... use 1. This value is also
-# used to specify _which_ DATM streamfile to use to force the
-# TRUTH run.
-#
-# CLM_stagedir: specifies the location of the CLM restart file you are defining as
-# the truth. As this state evolves in time, it will be used as the
-# input to the exact same forward observation operator code that
-# will be used during a subsequent assimilation.
-
-setenv SingleInstanceRefcase 0
-setenv TRUTHinstance 23
-setenv CLM_stagedir /glade/scratch/afox/archive/$run_refcase/rest/$refyear-$refmon-$refday-$run_reftod
-
-# ==============================================================================
-# runtime settings
-#
-# resubmit How many job steps to run on continue runs (will be 0 initially)
-# stop_option DART REQUIRES this to be 'nhours' ... DO NOT CHANGE
-# stop_n Specifies number of hours to advance the model in a single execution.
-# assim_n Specifies number of hours between desired observation files.
-# clm_dtime dynamical timestep (in seconds) ... 1800 is the default for CLM
-# h1nsteps is the number of time steps to put in a single .h1. file
-# DART needs to know this and the only time it is known is during
-# this configuration step. The run-time settings can lie.
-#
-# 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.
-#
-# ==============================================================================
-
-setenv short_term_archiver on
-setenv long_term_archiver off
-setenv resubmit 0
-setenv stop_option nhours
-setenv stop_n 72
-setenv assim_n 24
-
-# This specifies the number of time steps available to the forward obs. operator.
-
-@ clm_dtime = 1800
-@ h1nsteps = $assim_n * 3600 / $clm_dtime
-
-# ==============================================================================
-# job settings
-#
-# queue can be changed during a series by changing the ${case}.run
-# timewall can be changed during a series by changing the ${case}.run
-#
-# TJH: Advancing 1 instance for 72 hours with 60 pes (4 nodes)
-# took less than 2 minutes on yellowstone.
-# ==============================================================================
-
-setenv ACCOUNT P8685xxxx
-setenv queue economy
-setenv timewall 0:10
-
-# ==============================================================================
-# set these standard commands based on the machine you are running on.
-# ==============================================================================
-
-set nonomatch # suppress "rm" warnings if wildcard does not match anything
-
-# The FORCE options are not optional.
-# The VERBOSE options are useful for debugging though
-# some systems don't like the -v option to any of the following
-switch ("`hostname`")
- case be*:
- # NCAR "bluefire"
- set MOVE = '/usr/local/bin/mv -fv'
- set COPY = '/usr/local/bin/cp -fv --preserve=timestamps'
- set LINK = '/usr/local/bin/ln -fvs'
- set REMOVE = '/usr/local/bin/rm -fr'
-
- breaksw
- default:
- # NERSC "hopper", NWSC "yellowstone"
- set MOVE = '/bin/mv -fv'
- set COPY = '/bin/cp -fv --preserve=timestamps'
- set LINK = '/bin/ln -fvs'
- set REMOVE = '/bin/rm -fr'
-
- breaksw
-endsw
-
-# ==============================================================================
-# Make sure the CESM directories exist.
-# VAR is the shell variable name, DIR is the value
-# ==============================================================================
-
-foreach VAR ( cesmroot dartroot CLM_stagedir )
- set DIR = `eval echo \${$VAR}`
- if ( ! -d $DIR ) then
- echo "ERROR: directory '$DIR' not found"
- echo " In the setup script check the setting of: $VAR "
- exit -1
- endif
-end
-
-# ==============================================================================
-# Create the case - this creates the CASEROOT directory.
-#
-# 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.
-# ==============================================================================
-
-# fatal idea to make caseroot the same dir as where this setup script is
-# since the build process removes all files in the caseroot dir before
-# populating it. try to prevent shooting yourself in the foot.
-
-if ( $caseroot == `dirname $0` ) then
- echo "ERROR: the setup script should not be located in the caseroot"
- echo "directory, because all files in the caseroot dir will be removed"
- echo "before creating the new case. move the script to a safer place."
- exit -1
-endif
-
-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
-
-# 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
-# to be run from a CASEROOT directory. If CESM_DART_config does not exist locally,
-# then it better exist in the expected part of the DARTROOT tree.
-# ==============================================================================
-
-if ( ! -e CESM_DART_config ) then
- ${COPY} ${dartroot}/models/clm/shell_scripts/CESM_DART_config .
-endif
-
-if ( -e CESM_DART_config ) then
- sed -e "s#BOGUS_DART_ROOT_STRING#$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
- echo "WARNING: the script to configure for data assimilation is not available."
- echo " CESM_DART_config should be present locally or in"
- echo " ${dartroot}/models/clm/shell_scripts/"
- echo " You can stage this script later, but you must manually edit it"
- echo " to reflect the location of the DART code tree."
-endif
-
-# ==============================================================================
-# Configure the case.
-# ==============================================================================
-
-cd ${caseroot}
-
-source ./Tools/ccsm_getenv || exit -2
-
-@ ptile = $MAX_TASKS_PER_NODE / 2
-@ nthreads = 1
-
-# Save a copy for debug purposes
-foreach FILE ( *xml )
- if ( ! -e ${FILE}.original ) then
- ${COPY} $FILE ${FILE}.original
- endif
-end
-
- # This is only for the purpose of debugging the code.
- @ atm_tasks = $ptile * 4
- @ lnd_tasks = $ptile * 4
- @ ice_tasks = $ptile
- @ ocn_tasks = $ptile
- @ cpl_tasks = $ptile
- @ glc_tasks = $ptile
- @ rof_tasks = $ptile * 4
-
-# 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 "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 $rof_tasks"
-echo ""
-
-./xmlchange NTHRDS_ATM=$nthreads,NTASKS_ATM=$atm_tasks,NINST_ATM=1
-./xmlchange NTHRDS_LND=$nthreads,NTASKS_LND=$lnd_tasks,NINST_LND=1
-./xmlchange NTHRDS_ICE=$nthreads,NTASKS_ICE=$ice_tasks,NINST_ICE=1
-./xmlchange NTHRDS_OCN=$nthreads,NTASKS_OCN=$ocn_tasks,NINST_OCN=1
-./xmlchange NTHRDS_CPL=$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=1
-./xmlchange ROOTPE_ATM=0
-./xmlchange ROOTPE_LND=0
-./xmlchange ROOTPE_ICE=0
-./xmlchange ROOTPE_OCN=0
-./xmlchange ROOTPE_CPL=0
-./xmlchange ROOTPE_GLC=0
-./xmlchange ROOTPE_ROF=0
-
-# 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 $RUN_STARTDATE)
-# can be modified relative to the reference case. In a hybrid run, the model does not
-# continue in a bit-for-bit fashion with respect to the reference case. The resulting
-# climate, however, should be continuous provided that no model source code or
-# namelists are changed in the hybrid run. In a hybrid initialization, the ocean
-# model does not start until the second ocean coupling (normally the second day),
-# and the coupler does a "cold start" without a restart file."
-
-# The RUN_REFCASE/REFDATE/REFTOD are used by CLM & RTM to specify the namelist input
-# filenames - BUT - their buildnml scripts do not use the INSTANCE, so they all specify
-# the same (single) filename. This is remedied by using patched [clm,rtm].buildnml.csh
-# scripts that exist in the SourceMods directory.
-
-./xmlchange RUN_TYPE=hybrid
-./xmlchange RUN_STARTDATE=$run_refdate
-./xmlchange START_TOD=$run_reftod
-./xmlchange RUN_REFCASE=$run_refcase
-./xmlchange RUN_REFDATE=$run_refdate
-./xmlchange RUN_REFTOD=$run_reftod
-./xmlchange GET_REFCASE=FALSE
-./xmlchange EXEROOT=${exeroot}
-
-./xmlchange DATM_MODE=CPLHIST3HrWx
-./xmlchange DATM_CPLHIST_CASE=$case
-./xmlchange DATM_CPLHIST_YR_ALIGN=$refyear
-./xmlchange DATM_CPLHIST_YR_START=$refyear
-./xmlchange DATM_CPLHIST_YR_END=$refyear
-
-./xmlchange CALENDAR=GREGORIAN
-./xmlchange STOP_OPTION=$stop_option
-./xmlchange STOP_N=$stop_n
-./xmlchange CONTINUE_RUN=FALSE
-./xmlchange RESUBMIT=$resubmit
-
-./xmlchange PIO_TYPENAME=pnetcdf
-
-# The river transport model ON is useful only when using an active ocean or
-# land surface diagnostics. Setting ROF_GRID to 'null' turns off the RTM.
-# so we are also turning on the CLM biogeochemistry.
-
-./xmlchange ROF_GRID='null'
-./xmlchange CLM_CONFIG_OPTS='-bgc cn'
-
-if ($short_term_archiver == 'off') then
- ./xmlchange DOUT_S=FALSE
-else
- ./xmlchange DOUT_S=TRUE
- ./xmlchange DOUT_S_ROOT=${archdir}
- ./xmlchange DOUT_S_SAVE_INT_REST_FILES=FALSE
-endif
-if ($long_term_archiver == 'off') then
- ./xmlchange DOUT_L_MS=FALSE
-else
- ./xmlchange DOUT_L_MS=TRUE
- ./xmlchange DOUT_L_MSROOT="csm/${case}"
- ./xmlchange DOUT_L_HTAR=FALSE
-endif
-
-# 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
-
-# ==============================================================================
-# Edit the run script to reflect queue and wallclock
-# ==============================================================================
-
-echo ''
-echo 'Updating the run script to set wallclock and queue.'
-echo ''
-
-if ( ! -e ${case}.run.original ) then
- ${COPY} ${case}.run ${case}.run.original
-endif
-
-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 ${case}.run | grep -e '-q' `
- sed -e "s/$TIMEWALL[3]/$timewall/" \
- -e "s/ptile=[0-9][0-9]*/ptile=$ptile/" \
- -e "s/$QUEUE[3]/$queue/" < ${case}.run >! temp.$$
- ${MOVE} temp.$$ ${case}.run
- chmod 755 ${case}.run
- breaksw
-
- default:
-
- breaksw
-endsw
-
-# ==============================================================================
-# Update source files.
-# Ideally, using DART would not require any modifications to the model source.
-# Until then, this script accesses sourcemods from a hardwired location.
-# If you have additional sourcemods, they will need to be merged into any DART
-# mods and put in the SourceMods subdirectory found in the 'case' directory.
-# ==============================================================================
-
-if ( -d ~/${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}/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}/preview_namelists ${caseroot}/.
-
-endif
-
-# ==============================================================================
-# Modify namelist templates for each instance. This is a bit of a nuisance in
-# that we are pulling in restart and initial files from 'all over the place'
-# and each model component has a different strategy.
-#
-# In a hybrid run with CONTINUE_RUN = FALSE (i.e. just starting up):
-#
-# CLM builds its own 'finidat' value from the REFCASE variables but in CESM1_1_1
-# it does not use the instance string. There is a patch for clm.buildnml.csh
-#
-# All of these must later on be staged with these same filenames.
-# OR - all these namelists can be changed to match whatever has been staged.
-# MAKE SURE THE STAGING SECTION OF THIS SCRIPT MATCHES THESE VALUES.
-# ==============================================================================
-
-@ inst = 1
-while ($inst <= 1)
-
- # following the CESM strategy for 'inst_string'
- set inst_string = ''
-
- # ===========================================================================
- set fname = "user_nl_datm${inst_string}"
- # ===========================================================================
-
- echo "dtlimit = 1.5, 1.5, 1.5" >> $fname
- echo "fillalgo = 'nn', 'nn', 'nn'" >> $fname
- echo "fillmask = 'nomask','nomask','nomask'" >> $fname
- echo "mapalgo = 'bilinear','bilinear','bilinear'" >> $fname
- echo "mapmask = 'nomask','nomask','nomask'" >> $fname
- echo "streams = 'datm.streams.txt.CPLHIST3HrWx.Solar$inst_string $stream_year_align $stream_year_first $stream_year_last'," >> $fname
- echo " 'datm.streams.txt.CPLHIST3HrWx.Precip$inst_string $stream_year_align $stream_year_first $stream_year_last'," >> $fname
- echo " 'datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip$inst_string $stream_year_align $stream_year_first $stream_year_last'" >> $fname
- echo "taxmode = 'cycle','cycle','cycle'" >> $fname
- echo "tintalgo = 'coszen','nearest','linear'" >> $fname
- echo "restfils = 'unset'" >> $fname
- echo "restfilm = 'unset'" >> $fname
-
- # ===========================================================================
- set fname = "user_nl_clm${inst_string}"
- # ===========================================================================
-
- # Customize the land namelists
- # The filename is built using the REFCASE/REFDATE/REFTOD information. i.e.
- # finidat = ${CLM_stagedir}/${case}.clm2${inst_string}.r.${run_refdate}-${run_reftod}.nc
- #
- # This is the time to consider how DART and CESM will interact. If you intend
- # on assimilating flux tower observations (nominally at 30min intervals),
- # then it is required to create a .h1. file with the instantaneous flux
- # variables every 30 minutes. Despite being in a namelist, these values
- # HAVE NO EFFECT once CONTINUE_RUN = TRUE so now is the time to set these.
- #
- # See page 65 of:
- # http://www.cesm.ucar.edu/models/cesm1.1/clm/models/lnd/clm/doc/UsersGuide/clm_ug.pdf
- #
- # DART's forward observation operators for these fluxes just reads them
- # from the .h1. file rather than trying to create them from the subset of
- # CLM variables that are available in the DART state vector. We have a terrible
- # time trying to predict the .h1. filename given only current model time.
- # DART does not read the clm namelist input that has this information, and
- # since it is in a namelist - it can change during the course of a run - BUT
- # as discussed above, only the first settings are important. Tricky.
- #
- # For a HOP TEST ... hist_empty_htapes = .false.
- # For a HOP TEST ... use a default hist_fincl1
- #
- # Customize the land namelists:
- # The initial ensemble can be set by specifying the 'finidat' variable in the
- # user_nl_clm${inst_string}. A FULL pathname to the file is required. This is nice
- # for two reasons - one is that you don't need to copy the files and rename them
- # (tedious), the second is that the full pathname provides a means of tracking
- # the origin of the initial ensemble.
-
- echo "dtime = $clm_dtime," >> $fname
- echo "hist_empty_htapes = .false.," >> $fname
- echo "hist_fincl1 = 'NEP'," >> $fname
- echo "hist_fincl2 = 'NEP','FSH','EFLX_LH_TOT_R'," >> $fname
- echo "hist_nhtfrq = -$assim_n,1," >> $fname
- echo "hist_mfilt = 1,$h1nsteps," >> $fname
- echo "hist_avgflag_pertape = 'A','A'" >> $fname
-
- @ inst ++
-end
-
-# ==============================================================================
-# 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/clm/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
- 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.
-# In a PMO setting, the stream text file 'instance' must refer to an
-# existing instance in the set of available forcing files.
-# The $TRUTHinstance specifies which DATM forcing file is used to
-# drive the TRUTH.
-
-foreach FNAME (user*streams*)
- set name_parse = `echo $FNAME | sed 's/\_/ /g'`
- @ filename_index = $#name_parse
- set streamname = $name_parse[$filename_index]
- set instance = `printf %04d $TRUTHinstance`
-
- if (-e $dartroot/models/clm/shell_scripts/user_$streamname*template) then
-
- echo "Copying DART template for $FNAME and changing instance, refyear"
-
- ${COPY} $dartroot/models/clm/shell_scripts/user_$streamname*template $FNAME
-
- sed s/NINST/$instance/g $FNAME >! out.$$
- sed s/REFYEAR/$refyear/g out.$$ >! $FNAME
- \rm -f out.$$
-
- 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
-
-# ==============================================================================
-# Stage the restarts now that the run directory exists
-# THIS IS THE STAGING SECTION - MAKE SURE THIS MATCHES THE NAMELISTS.
-# POP/CAM/CICE read from pointer files. The others use namelist values initially.
-# ==============================================================================
-
-cat << EndOfText >! stage_initial_cesm_files
-#!/bin/sh
-
-cd ${rundir}
-
-echo ''
-echo 'Copying the required restart file from the staging directory.'
-echo 'With CONTINUE_RUN=FALSE, only a single file is required.'
-echo ''
-
-if (( $SingleInstanceRefcase ))
-then
- ${COPY} ${CLM_stagedir}/${run_refcase}.clm2.r.${run_refdate}-${run_reftod}.nc .
-else
-
- let inst=$TRUTHinstance
-
- inst_string=\`printf _%04d \$inst\`
-
- echo ''
- echo "Staging restart for instance \$inst"
-
- ${COPY} ${CLM_stagedir}/${run_refcase}.clm2\${inst_string}.r.${run_refdate}-${run_reftod}.nc \
- ${run_refcase}.clm2.r.${run_refdate}-${run_reftod}.nc
-fi
-
-exit 0
-
-EndOfText
-chmod 0755 stage_initial_cesm_files
-
-./stage_initial_cesm_files
-
-# ==============================================================================
-# build
-# ==============================================================================
-
-echo ''
-echo 'Building the case'
-echo ''
-
-./${case}.build
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be built."
- exit -5
-endif
-
-# ==============================================================================
-# What to do next
-# ==============================================================================
-
-echo ""
-echo "Time to check the case."
-echo ""
-echo "1) cd ${rundir}"
-echo " check the compatibility between the namelists and the files that were staged."
-echo ""
-echo "2) cd ${caseroot}"
-echo " (on yellowstone) If the ${case}.run script still contains:"
-echo ' #BSUB -R "select[scratch_ok > 0]"'
-echo " around line 9, delete it."
-echo ""
-echo "3) If you want to create 'perfect obs' 'right away', configure and execute"
-echo " the ${caseroot}/CESM_DART_config script."
-echo ""
-echo "3) Verify the contents of env_run.xml and submit the CESM job:"
-echo " ./${case}.submit"
-echo ""
-echo "4) After the run finishes ... check the contents of the DART observation sequence file"
-echo " ${archdir}/dart/hist/obs_seq.YYYY-MM-DD-SSSSS"
-echo " to make sure there are good values in the file. (not -888888.)"
-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 ""
-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 ""
-
-exit 0
-
-# <next few lines under version control, do not edit>
-# $URL$
-# $Revision$
-# $Date$
-
Copied: DART/trunk/models/clm/shell_scripts/CESM1_1_1_setup_pmo (from rev 6485, DART/trunk/models/clm/shell_scripts/CESM1_1_1_pmo_setup)
===================================================================
--- DART/trunk/models/clm/shell_scripts/CESM1_1_1_setup_pmo (rev 0)
+++ DART/trunk/models/clm/shell_scripts/CESM1_1_1_setup_pmo 2013-09-20 22:26:31 UTC (rev 6486)
@@ -0,0 +1,779 @@
+#!/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
+# http://www.image.ucar.edu/DAReS/DART/DART_download
+#
+# DART $Id$
+
+# ---------------------
+# Purpose
+# ---------------------
+#
+# This script is designed to set up, stage, and build a single-instance run of CESM
+# using an I compset where only CLM is active and the ocean and land states are
+# specified by data files. CESM is set up with a 'hybrid' start.
+#
+# CLM: The initial state is set by specifying the 'finidat' variable in
+# user_nl_clm. Under a hybrid start, CESM uses the REFCASE and REFDATE
+# information to construct the finidat value. This script makes an effort
+# to coordinate the staging of the file so it is consistent with CESM
+#
+# DATM: We are using an ensemble of data atmospheres. This requires modification of
+# the stream text files (and the stream files) for each CESM instance.
+#
+# DOCN: We are using a single data ocean.
+#
+# This script has a counterpart that is a multi-instance setup for either a free
+# run or an assimilation experiment. To make it easy to maintain (and hopefully
+# understand), the two scripts are intended to parallel each other. That means this
+# script performs a lot of manipulation of the 'instance' portion of the
+# filenames, which seems unnecessary initially.
+#
+# This script results in a viable setup for a CESM single instance experiment. You
+# are STRONGLY encouraged to run the single instance CESM a few times and experiment
+# with different settings BEFORE you try to generate 'perfect' observations.
+# You should become comfortable using CESM's restart 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 use DART to harvest synthetic observations. 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
+# CESM_DART_config to augment the existing run script, modify STOP_N to 6 hours,
+# and start harvesting synthetic observations when CESM stops at 2004-02-01 06Z ...
+#
+# This script relies heavily on the information in:
+# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/book1.html
+#
+# ---------------------
+# How to use this script.
+# ---------------------
+#
+# -- You will have to read and understand the script in its entirety.
+# You will have to modify things outside this script.
+# This script sets up a CESM single instance run as we understand them and
+# it has almost nothing to do with DART. This is intentional.
+#
+# -- Edit and run this script in the $DART/models/CESM/shell_scripts directory
+# or copy it to somewhere that it will be preserved and run it there.
+# It will create a CESM 'CASE' directory, where the model will be built,
+# and an execution directory, where each forecast 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 the CESM initial file needed by your run.
+#
+# -- Run this script.
+#
+# -- If you want to run DART; read, understand, and execute ${CASEROOT}/CESM_DART_config
+#
+# -- 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
+# ==============================================================================
+
+# 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.
+
+setenv case clm_pmo
+setenv compset I_2000_CN
+setenv resolution f09_f09
+setenv cesmtag cesm1_1_1
+
+# ==============================================================================
+# define machines and directories
+#
+# mach Computer name
+# cesmroot Location of the cesm code base
+# 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,
+# 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.
+# dartroot Location of _your_ DART installation
+# This is passed on to the CESM_DART_config script.
+# ==============================================================================
+
+setenv mach yellowstone
+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/trunk
+
+# ==============================================================================
+# 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 80_member_freerun_one_degree
+setenv refyear 2004
+setenv refmon 01
+setenv refday 01
+setenv run_reftod 00000
+setenv run_refdate $refyear-$refmon-$refday
+
+setenv stream_year_first 2004
+setenv stream_year_last 2004
+setenv stream_year_align 2004
+
+# SingleInstanceRefcase: the filenames are fundamentally different for
+# a multi-instance CESM run or a single-instance CESM run. A correct setting
+# of this variable makes staging the required files easier - that's all.
+# 1 means 'true' ... the restart file has a single-instance-like name.
+# 0 means 'false' .. the restart file has a multi-instance-like name.
+#
+# TRUTHinstance: specifies the specific instance you want to define as the TRUTH.
+# If you have an initial ensemble size of 80, 1<= instance <= 80.
+# If you only have one CLM state ... use 1. This value is also
+# used to specify _which_ DATM streamfile to use to force the
+# TRUTH run.
+#
+# CLM_stagedir: specifies the location of the CLM restart file you are defining as
+# the truth. As this state evolves in time, it will be used as the
+# input to the exact same forward observation operator code that
+# will be used during a subsequent assimilation.
+
+setenv SingleInstanceRefcase 0
+setenv TRUTHinstance 23
+setenv CLM_stagedir /glade/scratch/afox/archive/$run_refcase/rest/$refyear-$refmon-$refday-$run_reftod
+
+# ==============================================================================
+# runtime settings
+#
+# resubmit How many job steps to run on continue runs (will be 0 initially)
@@ Diff output truncated at 40000 characters. @@
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