[Dart-dev] [6079] DART/branches/development/models/POP/shell_scripts/CESM_setup_beta17 .csh: Removing an intermediate file for for an obsolete version of CESM.
nancy at ucar.edu
nancy at ucar.edu
Wed Apr 24 16:41:47 MDT 2013
Revision: 6079
Author: thoar
Date: 2013-04-24 16:41:46 -0600 (Wed, 24 Apr 2013)
Log Message:
-----------
Removing an intermediate file for for an obsolete version of CESM.
Use CESM1_1_setup_hybrid.csh
The ocean should (always) start with a hybrid start because it preserves
the velocity components. A 'cold' start only reads in the T,S fields.
Removed Paths:
-------------
DART/branches/development/models/POP/shell_scripts/CESM_setup_beta17.csh
-------------- next part --------------
Deleted: DART/branches/development/models/POP/shell_scripts/CESM_setup_beta17.csh
===================================================================
--- DART/branches/development/models/POP/shell_scripts/CESM_setup_beta17.csh 2013-04-24 22:29:27 UTC (rev 6078)
+++ DART/branches/development/models/POP/shell_scripts/CESM_setup_beta17.csh 2013-04-24 22:41:46 UTC (rev 6079)
@@ -1,569 +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 CAM, CLM, and CICE as active components over a single data ocean,
-# and will use DART to assimilate observations at regular intervals.
-# This script does not build DART.
-
-# ---------------------
-# How to set up the script
-# ---------------------
-# -- Either edit and run this script in the $DART/models/clm/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)
-# -- Examin the whole script to identify things to change for your experiments.
-# -- Provide any initial files needed by your run:
-# inflation
-# sampling error correction
-# CAM/CLM/CICE initial ensemble
-# ...
-# -- Run this script.
-# -- Edit the DART input.nml that appears in the $caseroot directory.
-# -- Submit the job using $caseroot/${case}.${mach}.submit
-# ($mach may not be needed for cesm releases after cesm1_1_beta04)
-#
-# ---------------------
-# Important features
-# ---------------------
-#
-# If you want to change something in your case other than the runtime
-# settings, you need to delete everything and start the run from scratch.
-#
-# ./${CASENAME}.*.clean_build
-# ./configure -cleanall
-#
-# ====================================================================
-# ==== Set case options
-# ====================================================================
-
-# case 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
-# reuse_existing_case:
-# false; Remove $caseroot and $exeroot and rebuild
-# true; configure -cleannamelist
-
-setenv case pop_beta17
-setenv compset CIAF
-setenv cesmtag cesm1_1_beta17
-setenv resolution T62_gx1v6
-setenv num_instances 4
-setenv reuse_existing_case false
-
-# ====================================================================
-# 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_beta04 on bluefire, MUST use 'thoar' value provided.
-# DARTroot Location of DART code tree.
-# Executables, scripts and input in $DARTroot/models/dev/...
-# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
-# Preferably not a frequently scrubbed location.
-# caseroot will be deleted if reuse_existing_case is false (below)
-# So this script, and other useful things should be kept elsewhere.
-# exeroot (Future) Run-time directory; scrubbable, large amount of space needed.
-# archdir (Future) Short-term archive directory
-# until the long-term archiver moves it to permanent storage.
-# ====================================================================
-
-setenv mach bluefire
-setenv cesm_datadir /glade/proj3/cseg/inputdata
-setenv cesmroot /glade/proj3/cseg/collections/$cesmtag
-
-setenv DARTroot /glade/home/${USER}/svn/DART/dev
-
-setenv caseroot /glade/user/${USER}/cases/${case}
-setenv exeroot /ptmp/${USER}/${case}
-setenv archdir /ptmp/${USER}/archive/${case}
-
-# ====================================================================
-# configure settings
-# ====================================================================
-
-setenv refyear 2000
-setenv stream_year_first 2000
-setenv stream_year_last 2006
-setenv stream_year_align 2000
-setenv refmon 01
-setenv refday 01
-setenv run_refdate $refyear-$refmon-$refday
-setenv run_reftod 00000
-
-# ====================================================================
-# runtime settings -- How many assimilation steps will be done after this one
-#
-# stop_option Units for determining the forecast length between assimilations
-# Changing stop_option requires changes to user_nl_clm below.
-# stop_n Number of time units in the forecast
-# ====================================================================
-
-setenv resubmit 4
-setenv stop_option ndays
-setenv stop_n 1
-
-# ====================================================================
-# job settings
-#
-# timewall can be changed during a series by changing the ${case}.run
-# queue can be changed during a series by changing the ${case}.run
-#
-# TJH How many f19_f19 CLM instances can fit on 1 'regular' node?
-# ====================================================================
-
-setenv proj 93300315
-setenv timewall 0:29
-setenv queue premium
-
-# ====================================================================
-# set these standard commands based on the machine you are running on.
-# ====================================================================
-
-switch ("`hostname`")
- case be*:
- # NCAR "bluefire"
- # The FORCE options are not optional.
- # the VERBOSE options are useful for debugging.
- set MOVE = '/usr/local/bin/mv -fv'
- set COPY = '/usr/local/bin/cp -fv --preserve=timestamps'
- set LINK = '/usr/local/bin/ln -fvs'
- set REMOVE = '/usr/local/bin/rm -fr'
-
- breaksw
- default:
- # NERSC "hopper"
- set MOVE = '/bin/mv -fv'
- set COPY = '/bin/cp -fv --preserve=timestamps'
- set LINK = '/bin/ln -fvs'
- set REMOVE = '/bin/rm -fr'
-
- breaksw
-endsw
-
-
-# ====================================================================
-# Create the case.
-#
-# For list of the pre-defined cases: ./create_newcase -list
-# To create a variant case, see the CESM documentation and carefully
-# incorporate any needed changes into this script.
-# ====================================================================
-
-if ("${reuse_existing_case}" == "false") then
- echo "removing old files from ${caseroot} and ${exeroot}"
- ${REMOVE} ${caseroot}
- ${REMOVE} ${exeroot}
- ${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
-else
- cd ${caseroot}
- ./configure -cleannamelist
- ./configure -cleanmach
-
-endif
-
-# ====================================================================
-# Configure the case.
-# ====================================================================
-
-cd ${caseroot}
-
-./xmlchange -file env_build.xml -id CALENDAR -val GREGORIAN
-./xmlchange -file env_build.xml -id EXEROOT -val ${exeroot}
-
-# with I compset ... CLM & DATM get num_instances, all else ninst == 1
-#
-# I really dont understand the logic of task layout.
-# "everything on 320 pes except land on 960.
-# cpl rootpe=0
-# lnd rootpe=320
-# ice rootpe=320
-# ocn rootpe=640
-# atm rootpe=960" -- Tony Craig
-
-if ($num_instances == 4) then
- # Tiny case - can fit on one node 64 tasks.
- # 1/8 cpl, 1/8 cice, 1/8 ocn, 5/8 lnd.
- @ total_nt = 64
- @ atm_pes = $total_nt
- @ cpl_pes = $total_nt / 8
- @ cice_pes = $total_nt / 8
- @ ocn_pes = $total_nt / 8
- @ lnd_pes = $total_nt - ($cpl_pes + $cice_pes + $ocn_pes)
-else if ($num_instances == 40) then
- @ total_nt = 640
- # 10 nodes
- # 2/8 cpl, 1/8 cice, 1/8 ocn, 5/8 lnd.
- @ atm_pes = $total_nt
- @ cpl_pes = $total_nt / 4
- @ cice_pes = $total_nt / 8
- @ ocn_pes = $total_nt / 8
- @ lnd_pes = $total_nt - ($cpl_pes + $cice_pes + $ocn_pes)
-else
- echo "Unsupported number of instances ... dying a horrible death."
- exit 4
-endif
-
-# first pe of each component (counted from 0)
-@ atm_rootpe = 0
-@ cpl_rootpe = 0
-
-@ cice_rootpe = $cpl_rootpe + $cpl_pes
-@ ocn_rootpe = $cice_rootpe + $cice_pes
-@ lnd_rootpe = $ocn_rootpe + $ocn_pes
-
-echo "check pe counting ..."
-@ last_pe = $atm_rootpe + $atm_pes
-echo "last pe => $last_pe =?= $total_nt <= total_nt"
-
-echo "task layout"
-echo "[$atm_rootpe .......................... ATM ..................... $total_nt]"
-echo "[$cpl_rootpe ... CPL ... $cice_rootpe ... ICE ... $ocn_rootpe ... OCN ... $lnd_rootpe ... LND ... $total_nt]"
-echo ""
-echo "ATM gets $atm_pes"
-echo "CPL gets $cpl_pes"
-echo "ICE gets $cice_pes"
-echo "OCN gets $ocn_pes"
-echo "LND gets $lnd_pes"
-echo ""
-
-./xmlchange -file env_pesetup.xml -id NTASKS_ATM -val $atm_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_ATM -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_ATM -val $atm_rootpe
-./xmlchange -file env_pesetup.xml -id NINST_ATM -val $num_instances
-
-./xmlchange -file env_pesetup.xml -id NTASKS_LND -val $lnd_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_LND -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_LND -val $lnd_rootpe
-./xmlchange -file env_pesetup.xml -id NINST_LND -val 1
-
-./xmlchange -file env_pesetup.xml -id NTASKS_ICE -val $cice_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_ICE -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_ICE -val $cice_rootpe
-./xmlchange -file env_pesetup.xml -id NINST_ICE -val 1
-
-./xmlchange -file env_pesetup.xml -id NTASKS_OCN -val $ocn_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_OCN -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_OCN -val $ocn_rootpe
-./xmlchange -file env_pesetup.xml -id NINST_OCN -val $num_instances
-
-./xmlchange -file env_pesetup.xml -id NTASKS_CPL -val $cpl_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_CPL -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_CPL -val $cpl_rootpe
-
-./xmlchange -file env_pesetup.xml -id NTASKS_GLC -val $ocn_pes
-./xmlchange -file env_pesetup.xml -id NTHRDS_GLC -val 1
-./xmlchange -file env_pesetup.xml -id ROOTPE_GLC -val $ocn_rootpe
-./xmlchange -file env_pesetup.xml -id NINST_GLC -val 1
-
-./xmlchange -file env_run.xml -id RUN_TYPE -val branch
-./xmlchange -file env_run.xml -id RUN_STARTDATE -val $run_refdate
-./xmlchange -file env_run.xml -id RUN_REFCASE -val c.da48
-./xmlchange -file env_run.xml -id RUN_REFDATE -val $run_refdate
-./xmlchange -file env_run.xml -id RUN_REFTOD -val $run_reftod
-./xmlchange -file env_run.xml -id BRNCH_RETAIN_CASENAME -val FALSE
-./xmlchange -file env_run.xml -id GET_REFCASE -val FALSE
-
-./xmlchange -file env_run.xml -id STOP_OPTION -val $stop_option
-./xmlchange -file env_run.xml -id STOP_N -val $stop_n
-./xmlchange -file env_run.xml -id CONTINUE_RUN -val FALSE
-./xmlchange -file env_run.xml -id RESUBMIT -val $resubmit
-
-./xmlchange -file env_run.xml -id DOUT_S -val TRUE
-./xmlchange -file env_run.xml -id DOUT_S_ROOT -val ${archdir}
-./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val FALSE
-./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE
-./xmlchange -file env_run.xml -id DOUT_L_MSROOT -val "csm/${case}"
-./xmlchange -file env_run.xml -id DOUT_L_HTAR -val FALSE
-
-./xmlchange -file env_run.xml -id DATM_MODE -val CPLHIST3HrWx
-./xmlchange -file env_run.xml -id DATM_CPLHIST_CASE -val $case
-./xmlchange -file env_run.xml -id DATM_CPLHIST_YR_ALIGN -val $refyear
-./xmlchange -file env_run.xml -id DATM_CPLHIST_YR_START -val $refyear
-./xmlchange -file env_run.xml -id DATM_CPLHIST_YR_END -val $refyear
-
-./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 $stop_n HOURS
-# hist_mfilt = 1, with precisely one day in it
-# hist_avgflag_pertape = 'I' use instantaneous values - no average
-#
-# The fincl2 history tape has the half-hourly flux tower observations.
-# The observation operators in obs_def_tower_mod.f90
-# are going to read from the .h1. history file for these values.
-# ====================================================================
-
-@ inst = 1
-while ($inst <= $num_instances)
-
- set instance = `printf %04d $inst`
-
- set fname = "user_nl_datm_$instance"
- 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'" >> $fname
- echo "streams = 'datm.streams.txt.CPLHIST3HrWx.Solar_"$instance $stream_year_align $stream_year_first $stream_year_last"'," >> $fname
- echo " 'datm.streams.txt.CPLHIST3HrWx.Precip_"$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 "taxmode = 'cycle','cycle','cycle'" >> $fname
- echo "tintalgo = 'coszen','coszen','coszen'" >> $fname
- echo "dataMode = 'CPLHIST'" >> $fname
-
- @ inst ++
-end
-
-set fname = "user_nl_dice"
-echo "streams = 'dice.streams.txt.SSMI_IAF" 1948 1948 2004"'" >> $fname
-echo "dataMode = 'SSTDATA'" >> $fname
-
-set fname = "user_nl_dlnd"
-echo "streams = 'dlnd.streams.txt.rof.diatren_iaf_rx1" 1 1 1"'" >> $fname
-echo "dataMode = 'DIATREN_IAF_RX1'" >> $fname
-
-# ====================================================================
-# to create custom streamfiles ...
-# ====================================================================
-
-./preview_namelists
-
-foreach FILE (CaseDocs/*streams*)
- set FNAME = $FILE:t
- cp -v $FILE user_$FNAME
-end
-
-echo "Change each of the user_ streams files"
-echo "Change each of the user_ streams files"
-echo "Change each of the user_ streams files"
-echo "Change each of the user_ streams files"
-
-exit
-
-./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.
-# ====================================================================
-
-# this one needs a recursive copy to get all the files in the subdirs
-${COPY} -r ~thoar/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
-if ( $status == 0) then
- echo "FYI - Local Source Modifications used for this case:"
- ls -lr ${caseroot}/SourceMods/*
-else
- echo "FYI - No SourceMods for this case"
-endif
-
-# ====================================================================
-# Stage the required parts of DART in the caseroot directory.
-# ====================================================================
-
-# if ("${reuse_existing_case}" == "false") then
-# ${MOVE} Tools/st_archive.sh Tools/st_archive.sh.orig
-# endif
-# ${COPY} ${DARTroot}/models/POP/shell_scripts/st_archive.sh Tools/
-# ${COPY} ${DARTroot}/models/POP/shell_scripts/datm.buildnml.csh Buildconf/
-#
-# ${COPY} ${DARTroot}/models/POP/shell_scripts/assimilate.csh assimilate.csh
-# ${COPY} ${DARTroot}/models/POP/work/input.nml .
-
-# ====================================================================
-# The *.run script must be modified to call the DART assimilate script.
-# The modifications are contained in a "here" document that MUST NOT
-# expand the wildcards etc., before it is run. This is achieved by
-# double-quoting the characters used to delineate the start/stop of
-# the "here" document. No kidding. It has to be "EndOfText",
-# not 'EndOfText' or EndOfText.
-# ====================================================================
-
-echo ''
-echo 'Adding the call to assimilate.csh to the *.run script.'
-echo ''
-
-cat << "EndOfText" >! add_to_run.txt
-
-# -------------------------------------------------------------------------
-# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
-# perform an assimilation with DART.
-# -------------------------------------------------------------------------
-
-set CplLogFile = `ls -1t cpl.log* | head -n 1`
-if ($CplLogFile == "") then
- echo 'ERROR: Model did not complete - no cpl.log file present - exiting'
- echo 'ERROR: Assimilation will not be attempted.'
- exit -4
-endif
-
-grep 'SUCCESSFUL TERMINATION' $CplLogFile
-if ( $status == 0 ) then
- ${CASEROOT}/assimilate.csh
-
- if ( $status == 0 ) then
- echo "`date` -- DART HAS FINISHED"
- else
- echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
- exit -5
- endif
-endif
-
-# END OF DART BLOCK
-# -------------------------------------------------------------------------
-
-"EndOfText"
-
-# Now that the "here" document is created,
-# determine WHERE to insert it -- 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
-
- mv ${case}.run ${case}.run.orig
-
- head -n $keep ${case}.run.orig >! ${case}.run
- cat add_to_run.txt >> ${case}.run
- tail -n $lastlines ${case}.run.orig >> ${case}.run
-
-endif
-
-# ====================================================================
-# Edit the run script to reflect project, queue, and wallclock
-# ====================================================================
-
-echo ''
-echo 'Updating the run script to set project number, wallclock, and queue.'
-echo ''
-
-set PROJ=`grep BSUB $case.run | grep -e '-P' `
-sed s/$PROJ[3]/$proj/ < $case.run >! temp
-${MOVE} temp $case.run
-
-set TIMEWALL=`grep BSUB $case.run | grep -e '-W' `
-sed s/$TIMEWALL[3]/$timewall/ < $case.run >! temp
-${MOVE} temp $case.run
-
-set QUEUE=`grep BSUB $case.run | grep -e '-q' `
-sed s/$QUEUE[3]/$queue/ < $case.run >! temp
-${MOVE} temp $case.run
-
-chmod 0744 $case.run
-
-# ====================================================================
-# build
-# ====================================================================
-
-echo ''
-echo 'Building the case'
-echo ''
-
-./$case.build
-
-if ( $status != 0 ) then
- echo "ERROR: Case could not be built."
- exit 3
-endif
-
-# ====================================================================
-# Stage the required parts of DART in the execution root directory,
-# now that EXEROOT exists.
-# ====================================================================
-
-foreach FILE ( filter clm_to_dart dart_to_clm )
- ${COPY} ${DARTroot}/models/clm/work/${FILE} ${exeroot}/
- if ( $status != 0 ) then
- echo "ERROR: ${DARTroot}/models/clm/work/${FILE} not copied to ${exeroot}"
- echo "ERROR: ${DARTroot}/models/clm/work/${FILE} not copied to ${exeroot}"
- exit 3
- endif
-end
-
-# ====================================================================
-# Stage the restarts now that the run directory exists
-# ====================================================================
-#
-# obs sequences files: /ptmp/yfzhang/Obs_seqs
-
-# 20000501 ... /ptmp/afox/MD_40_PME/run
-set stagedir = /ptmp/afox/MD_40_PME/run
-
-# 20021101 ... /ptmp/yfzhang/inputdata_cam/lnd/clm2/initdata
-# set stagedir = /ptmp/yfzhang/inputdata_cam/lnd/clm2/initdata
-
-echo ''
-echo "Copying the restart files from ${stagedir}"
-echo ''
-
-@ n = 1
-while ($n <= $num_instances)
-
- echo "Staging restarts for instance $n of $num_instances"
-
-# set LANDFILE = `printf ${stagedir}/init1998.clm2_%04d.r.2002-11-01-00000.nc $n`
- set LANDFILE = `printf ${stagedir}/MD_40_PME.clm2_%04d.r.2000-01-31-00000.nc $n`
- set LND_RESTART_FILENAME = `printf "${case}.clm2_%04d.r.%04d-%02d-%02d-%05d.nc" $n $refyear $refmon $refday $run_reftod`
-
- ${COPY} ${LANDFILE} ${exeroot}/run/${LND_RESTART_FILENAME}
-
- @ n++
-end
-
-# ====================================================================
-# What to do next
-# ====================================================================
-
-echo ''
-echo 'Time to check the case.'
-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 ''
-
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