[Dart-dev] [5980] DART/branches/development/models/cam/shell_scripts/ CESM_setup_startup.csh: This ran for one timestep on yellowstone and got to the assimilate part of the game .
nancy at ucar.edu
nancy at ucar.edu
Thu Feb 28 12:14:34 MST 2013
Revision: 5980
Author: thoar
Date: 2013-02-28 12:14:33 -0700 (Thu, 28 Feb 2013)
Log Message:
-----------
This ran for one timestep on yellowstone and got to the assimilate part of the game.
There is a lot of 'customization' needed to run for 2008 because most of the default files
end in 2005.
Modified Paths:
--------------
DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh
-------------- next part --------------
Modified: DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh
===================================================================
--- DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh 2013-02-27 18:23:08 UTC (rev 5979)
+++ DART/branches/development/models/cam/shell_scripts/CESM_setup_startup.csh 2013-02-28 19:14:33 UTC (rev 5980)
@@ -14,7 +14,10 @@
# 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.
-
+#
+# 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
# ---------------------
@@ -25,30 +28,29 @@
# 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.
+# -- Examine 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)
+# -- 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, you need to delete everything and start the run from scratch.
+# settings, it is safest to delete everything and start the run from scratch.
+# For the brave, read
#
-# ./${CASENAME}.*.clean_build
-# ./configure -cleanall
+# http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/x1142.html
#
-# ====================================================================
+# ==============================================================================
# === IMPORTANT modifications to the distribution code before ANYTHING
-# ====================================================================
+# ==============================================================================
# Had to edit the following to remove the LSB_PJL_... word too long error
# cesm1_1_beta04/scripts/ccsm_utils/Machines/mkbatch.bluefire .
@@ -62,88 +64,87 @@
#
# The cesm1_1_beta04 lt_archive script did not create parent dirs
# if they did not already exist. To fix the script, edit:
-# ${cesmroot}/scripts/ccsm_utils/Tools/lt_archive.csh
+# ${cesmroot}/scripts/ccsm_utils/Tools/lt_archive.csh
# and change 'mkdir' to 'mkdir -p'. This is fixed in more recent
# versions of the code.
#
# For these reasons, it is required that you use ~thoar/cesm1_1_beta04
# as the source of the CESM code.
-# ====================================================================
+# ==============================================================================
# ==== 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 Exp1
-setenv compset F_2000
-setenv cesmtag cesm1_1_beta04
+setenv case cam_test_1
+setenv compset F_AMIP_CAM5
+setenv cesmtag cesm1_1_1
setenv resolution f09_f09
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.
+# For cesm1_1 on yellowstone
# DARTroot Location of DART code tree.
# Executables, scripts and input in $DARTroot/models/cam/...
# caseroot Your (future) cesm case directory, where this CESM+DART will be built.
# Preferably not a frequently scrubbed location.
-# caseroot will be deleted if reuse_existing_case is false (below)
-# So this script, and other useful things should be kept elsewhere.
-# exeroot (Future) Run-time directory; scrubbable, large amount of space needed.
+# This script will delete any existing caseroot, so this script,
+# and other useful things should be kept elsewhere.
+# rundir (Future) Run-time directory; scrubbable, large amount of space needed.
+# exeroot (Future) directory for executables - scrubbable, large amount of space needed.
# archdir (Future) Short-term archive directory
# until the long-term archiver moves it to permanent storage.
-# ====================================================================
+# ==============================================================================
-setenv mach bluefire
-setenv cesm_datadir /glade/proj3/cseg/inputdata
-setenv cesmroot /glade/home/thoar/${cesmtag}
+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/${case}
-setenv DARTroot /glade/home/${USER}/svn/DART/dev
+setenv DARTroot /glade/u/home/${USER}/svn/DART/dev
-setenv caseroot /glade/user/${USER}/cases/${case}
-setenv exeroot /glade/scratch/${USER}/${case}
-setenv archdir /glade/scratch/${USER}/archive/${case}
-
-# ====================================================================
+# ==============================================================================
# configure settings
-# ====================================================================
-
+# ==============================================================================
# yyyy-mm-dd
setenv run_startdate 2008-10-31
-setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
+setenv sst_dataset ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2008_c100127.nc
setenv year_start 1850
setenv year_end 2010
-# ====================================================================
+# TJH FIXME ... the sst_dataset above does not appear in that directory._CAM5
+# Try this: ${cesm_datadir}/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2011_c110307.nc
+
+# ==============================================================================
# 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_cam below.
# stop_n Number of time units in the forecast
-# ====================================================================
+# ==============================================================================
setenv resubmit 0
setenv stop_option nhours
setenv stop_n 6
-# ====================================================================
+# ==============================================================================
# job settings
#
-# timewall can be changed during a series by changing the ${case}.${mach}.run
-# queue can be changed during a series by changing the ${case}.${mach}.run
+# timewall can be changed during a series by changing the ${case}.run
+# queue can be changed during a series by changing the ${case}.run
# lrg_ queues are used in order to fit more instances on each node.
# FV 1-degree can comfortably fit 4 instances on 1 lrg_ node (~60 gbyte)
# On bluefire the regular queue (or higher) is probably necessary,
@@ -151,15 +152,16 @@
# and the regular memory nodes. So economy jobs requesting smaller numbers
# of processors seem to prevent this lrg_economy job (20 nodes for 1-degree)
# from running for long periods.
-# ====================================================================
+# ==============================================================================
-setenv proj 12345678
-setenv timewall 2:00
-setenv queue lrg_regular
+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*:
@@ -172,72 +174,62 @@
set REMOVE = '/usr/local/bin/rm -fr'
breaksw
- case hopp*:
- # NERSC "hopper"
+ 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
- default:
- # make this work for your system
- set MOVE = 'mv -fv'
- set COPY = 'cp -fv --preserve=timestamps'
- set LINK = 'ln -fvs'
- set REMOVE = 'rm -fr'
+endsw
- 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}"
+ 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} -skip_rundb
+ -res ${resolution} -compset ${compset}
if ( $status != 0 ) then
echo "ERROR: Case could not be created."
- exit 1
+ exit -1
endif
-else
- cd ${caseroot}
- ./configure -cleannamelist
-endif
-# ====================================================================
-# Configure the case.
-# ====================================================================
+# ==============================================================================
+# Configure the case - this creates the CASEROOT directory.
+# ==============================================================================
cd ${caseroot}
-./xmlchange -file env_build.xml -id EXEROOT -val ${exeroot}
-./xmlchange -file env_build.xml -id USE_ESMF_LIB -val TRUE
-#./xmlchange -file env_build.xml -id ESMF_LIBDIR -val ${nancy_scratch}/esmf-mpi
+# Save a copy for debug purposes
+foreach FILE ( *xml )
+ ${COPY} $FILE ${FILE}.original
+end
# num_tasks_per_instance = #tasks_node / #instances_node
# Bluefire: #tasks_node = 64 using SMT
# #instances_node = 1-degree: 4 on lrg_ nodes, 2 on standard.
# 2-degree: 16 on lrg_ nodes, 8 on standard
# CAM5; to be determined, but no more than listed for CAM4
-set num_tasks_per_node = 64
-set num_tasks_per_instance = 16
+set num_tasks_per_node = 15
+set num_tasks_per_instance = 8
set num_threads = 1
# This is hard-wiring for the current (1/17/2011) multi-instance CESM restriction
# that all instances must be advanced simultaneously. Work is underway to relax that.
-@ total_nt = $num_instances * $num_tasks_per_instance
-echo "total MPI tasks requested = $total_nt"
+# @ total_nt = $num_instances * $num_tasks_per_instance
+# echo "total MPI tasks requested = $total_nt"
# Atm gets all the nodes and runs.
# The other components divide them up.
@@ -246,234 +238,318 @@
# to run each component on whole nodes, or the components need to share some nodes.
# The hard-coded numbers (and ratios between them) are estimates; change them if you
# know better.
-@ atm_pes = $total_nt
-@ large_small = $total_nt / (8 * $num_tasks_per_node)
-if ($large_small > 0) then
- # Large_small > 0 means there are at least 8 nodes requested.
- # Allot whole nodes to the major components.
- @ cpl_pes = ( $total_nt / (3 * $num_tasks_per_node) ) * $num_tasks_per_node
- @ cice_pes = ( $total_nt / (3 * $num_tasks_per_node) ) * $num_tasks_per_node
- @ docn_pes = $num_tasks_per_node
- @ lnd_pes = $total_nt - ($cpl_pes + $cice_pes + $docn_pes)
-else
- # 1/4 cpl, 1/4 cice, 1/8 docn, 3/8 lnd. These will occupy fractions of nodes.
- @ cpl_pes = $total_nt / 4
- @ cice_pes = $total_nt / 4
- @ docn_pes = $total_nt / 8
- @ lnd_pes = $total_nt - ($cpl_pes + $cice_pes + $docn_pes)
-endif
+#@ atm_pes = $total_nt
+#@ large_small = $total_nt / (8 * $num_tasks_per_node)
+#if ($large_small > 0) then
+# # Large_small > 0 means there are at least 8 nodes requested.
+# # Allot whole nodes to the major components.
+# @ cpl_pes = ( $total_nt / (3 * $num_tasks_per_node) ) * $num_tasks_per_node
+# @ ice_pes = ( $total_nt / (3 * $num_tasks_per_node) ) * $num_tasks_per_node
+# @ glc_pes = ( $total_nt / (3 * $num_tasks_per_node) ) * $num_tasks_per_node
+# @ ocn_pes = $num_tasks_per_node
+# @ rof_pes = $num_tasks_per_node
+# @ lnd_pes = $total_nt - ($cpl_pes + $ice_pes + $ocn_pes + $glc_pes + $rof_pes)
+#else
+ # dummy layout
+ @ cpl_pes = 8
+ @ glc_pes = 8
+ @ ocn_pes = 8
+ @ ice_pes = 32
+ @ rof_pes = 32
+ @ lnd_pes = 32
+ @ atm_pes = 32
+#endif
-# first pe of each component (counted from 0)
-@ atm_rootpe = 0
-@ cpl_rootpe = 0
-@ cice_rootpe = $cpl_rootpe + $cpl_pes
-@ docn_rootpe = $cice_rootpe + $cice_pes
-@ lnd_rootpe = $docn_rootpe + $docn_pes
-
-# echo "check pe counting; last_pe should = total_nt - 1"
-# @ last_pe = ( $lnd_rootpe + $lnd_pes ) - 1
-# echo $last_pe
-
echo "task layout"
-echo "[$atm_rootpe ......................... ATM ............................. $atm_pes]"
-echo "[$cpl_rootpe ... CPL ... $cice_rootpe ... ICE ... $docn_rootpe ... OCN ... $lnd_rootpe ... LND ... $total_nt]"
echo ""
+echo "CPL gets $cpl_pes"
echo "ATM gets $atm_pes"
-echo "ICE gets $cice_pes"
+echo "ICE gets $ice_pes"
echo "LND gets $lnd_pes"
-echo "CPL gets $cpl_pes"
-echo "OCN gets $docn_pes"
+echo "ROF gets $rof_pes"
+echo "GLC gets $glc_pes"
+echo "OCN gets $ocn_pes"
echo ""
-./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val $atm_pes
-./xmlchange -file env_mach_pes.xml -id NTHRDS_ATM -val $num_threads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_ATM -val $atm_rootpe
-./xmlchange -file env_mach_pes.xml -id NINST_ATM -val $num_instances
+./xmlchange NTHRDS_CPL=$num_threads,NTASKS_CPL=$cpl_pes
+./xmlchange NTHRDS_ATM=$num_threads,NTASKS_ATM=$atm_pes,NINST_ATM=$num_instances
+./xmlchange NTHRDS_ICE=$num_threads,NTASKS_ICE=$ice_pes,NINST_ICE=$num_instances
+./xmlchange NTHRDS_LND=$num_threads,NTASKS_LND=$lnd_pes,NINST_LND=$num_instances
+./xmlchange NTHRDS_ROF=$num_threads,NTASKS_ROF=$rof_pes,NINST_ROF=$num_instances
+./xmlchange NTHRDS_GLC=$num_threads,NTASKS_GLC=$glc_pes,NINST_GLC=1
+./xmlchange NTHRDS_OCN=$num_threads,NTASKS_OCN=$ocn_pes,NINST_OCN=1
+./xmlchange ROOTPE_OCN=$ice_pes
-./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val $cpl_pes
-./xmlchange -file env_mach_pes.xml -id NTHRDS_CPL -val $num_threads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_CPL -val $cpl_rootpe
+./xmlchange RUN_TYPE=startup
+./xmlchange RUN_STARTDATE=$run_startdate
+./xmlchange EXEROOT=${exeroot}
-./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val $cice_pes
-./xmlchange -file env_mach_pes.xml -id NTHRDS_ICE -val $num_threads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_ICE -val $cice_rootpe
-./xmlchange -file env_mach_pes.xml -id NINST_ICE -val $num_instances
+./xmlchange DOUT_S_ROOT=${archdir}
+./xmlchange DOUT_S=FALSE
+./xmlchange DOUT_S_SAVE_INT_REST_FILES=TRUE
+./xmlchange DOUT_L_MS=FALSE
+./xmlchange DOUT_L_MSROOT="csm/${case}"
+./xmlchange DOUT_L_HTAR=FALSE
-./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val $docn_pes
-./xmlchange -file env_mach_pes.xml -id NTHRDS_OCN -val $num_threads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_OCN -val $docn_rootpe
+./xmlchange SSTICE_DATA_FILENAME=$sst_dataset
+./xmlchange SSTICE_YEAR_ALIGN=$year_start
+./xmlchange SSTICE_YEAR_START=$year_start
+./xmlchange SSTICE_YEAR_END=$year_end
-./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val $lnd_pes
-./xmlchange -file env_mach_pes.xml -id NTHRDS_LND -val $num_threads
-./xmlchange -file env_mach_pes.xml -id ROOTPE_LND -val $lnd_rootpe
-./xmlchange -file env_mach_pes.xml -id NINST_LND -val $num_instances
-
-./xmlchange -file env_conf.xml -id RUN_TYPE -val startup
-./xmlchange -file env_conf.xml -id RUN_STARTDATE -val $run_startdate
-./xmlchange -file env_conf.xml -id DOCN_SSTDATA_FILENAME -val $sst_dataset
-./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_START -val $year_start
-./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_END -val $year_end
-./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val '-rtm off'
-# The river transport model ON is useful only when using an active ocean or
-# land surface diagnostics.
-
-# Substantial archiving changes exist in the Tools/st_archive.sh script.
# Do not change the CALENDAR or the CONTINUE_RUN
# DOUT_S is to turn on/off the short-term archiving
# DOUT_L_MS is to store to the HPSS (formerly "MSS")
-./xmlchange -file env_run.xml -id CONTINUE_RUN -val FALSE
-./xmlchange -file env_run.xml -id RESUBMIT -val $resubmit
-./xmlchange -file env_run.xml -id STOP_OPTION -val $stop_option
-./xmlchange -file env_run.xml -id STOP_N -val $stop_n
-./xmlchange -file env_run.xml -id CALENDAR -val GREGORIAN
-./xmlchange -file env_run.xml -id DOUT_S_ROOT -val ${archdir}
-./xmlchange -file env_run.xml -id DOUT_S -val TRUE
-./xmlchange -file env_run.xml -id DOUT_S_SAVE_INT_REST_FILES -val TRUE
-./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE
-./xmlchange -file env_run.xml -id DOUT_L_MSROOT -val "csm/${case}"
-./xmlchange -file env_run.xml -id DOUT_L_HTAR -val FALSE
+./xmlchange CALENDAR=GREGORIAN
+./xmlchange STOP_OPTION=$stop_option
+./xmlchange STOP_N=$stop_n
+./xmlchange CONTINUE_RUN=FALSE
+./xmlchange RESUBMIT=$resubmit
+./xmlchange PIO_TYPENAME=pnetcdf
-# ====================================================================
-# Create namelist template: user_nl_cam, user_nl_clm
-# ====================================================================
+# 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.
-cd ${caseroot}
+./xmlchange ROF_GRID='r05'
-cat <<EOF >! user_nl_cam
-&camexp
- inithist = 'ENDOFRUN'
- div24del2flag = 4
- empty_htapes = .true.
- fincl1 = 'PHIS:I'
- nhtfrq = -$stop_n
- iradae = -$stop_n
- aerodep_flx_datapath = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero'
- aerodep_flx_file = 'aerosoldep_monthly_1849-2006_1.9x2.5_c090803.nc'
- aerodep_flx_cycle_yr = 2000
- aerodep_flx_type = 'CYCLICAL'
-/
-EOF
+# level of debug output, 0=minimum, 1=normal, 2=more, 3=too much, valid values: 0,1,2,3 (integer)
-cat <<EOF >! user_nl_clm
-&clmexp
- fatmgrid = '${cesm_datadir}/lnd/clm2/griddata/griddata_0.9x1.25_070212.nc'
- faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc'
- outnc_large_files = .true.
- hist_empty_htapes = .true.
-/
-EOF
+./xmlchange DEBUG=TRUE
+./xmlchange INFO_DBUG=2
-# ====================================================================
+# ==============================================================================
+# 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 $stop_n HOURS
+# hist_mfilt = 1, with precisely one day in it
+# hist_avgflag_pertape = 'I' use instantaneous values - no average
+#
+# ==============================================================================
+
+set chem_datapath = "${cesm_datadir}/atm/cam/chem/trop_mozart_aero"
+
+@ inst = 1
+while ($inst <= $num_instances)
+
+ set instance = `printf %04d $inst`
+
+ # ===========================================================================
+ set fname = "user_nl_cam_$instance"
+ # ===========================================================================
+ # A lot of the files specified here are because the 'default' files only
+ # contain data through 2005 and we are interested in timeframes after that.
+
+# echo " iradae = -$stop_n " >> ${fname}
+
+ echo " inithist = 'ENDOFRUN' " >> ${fname}
+ echo " ncdata = 'cam_initial_${instance}.nc' " >> ${fname}
+ echo " avgflag_pertape = 'A','A' " >> ${fname}
+ echo " div24del2flag = 4 " >> ${fname}
+ echo " empty_htapes = .true. " >> ${fname}
+ echo " fincl1 = 'PHIS:I' " >> ${fname}
+ echo " fincl2 = 'PS', 'Z3', 'T', 'U', 'V', 'FLNT', 'PSL', 'OMEGA' " >> ${fname}
+ echo " nhtfrq = -$stop_n,-1 " >> ${fname}
+ echo " mfilt = 1,1 " >> ${fname}
+
+ echo " aerodep_flx_datapath = '${chem_datapath}/aero' " >> ${fname}
+ echo " aerodep_flx_file = 'aerosoldep_monthly_1849-2006_1.9x2.5_c090803.nc' " >> ${fname}
+ echo " aerodep_flx_cycle_yr = 2000 " >> ${fname}
+ echo " aerodep_flx_type = 'CYCLICAL' " >> ${fname}
+ echo " bndtvghg = '${cesm_datadir}/atm/cam/ggas/ghg_hist_1765-2009_c100902.nc' " >> ${fname}
+ echo " prescribed_ozone_file = 'ozone_1.9x2.5_L26_1850-2015_rcp45_c101108.nc' " >> ${fname}
+ echo " tracer_cnst_file = 'oxid_1.9x2.5_L26_1850-2015_rcp45_c101108.nc' " >> ${fname}
+
+ echo " ext_frc_specifier = " >> ${fname}
+ echo " 'SO2 -> ${chem_datapath}/emis/ar5_mam3_so2_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'bc_a1 -> ${chem_datapath}/emis/ar5_mam3_bc_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'num_a1 -> ${chem_datapath}/emis/ar5_mam3_num_a1_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'num_a2 -> ${chem_datapath}/emis/ar5_mam3_num_a2_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'pom_a1 -> ${chem_datapath}/emis/ar5_mam3_oc_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'so4_a1 -> ${chem_datapath}/emis/ar5_mam3_so4_a1_elev_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'so4_a2 -> ${chem_datapath}/emis/ar5_mam3_so4_a2_elev_1850-2010_c20100902_v12.nc' " >> ${fname}
+
+ echo " srf_emis_specifier = " >> ${fname}
+ echo " 'DMS -> ${chem_datapath}/emis/aerocom_mam3_dms_surf_1849-2010_c20100902.nc'," >> ${fname}
+ echo " 'SO2 -> ${chem_datapath}/emis/ar5_mam3_so2_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'SOAG -> ${chem_datapath}/emis/ar5_mam3_soag_1.5_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'bc_a1 -> ${chem_datapath}/emis/ar5_mam3_bc_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'num_a1 -> ${chem_datapath}/emis/ar5_mam3_num_a1_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'num_a2 -> ${chem_datapath}/emis/ar5_mam3_num_a2_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'pom_a1 -> ${chem_datapath}/emis/ar5_mam3_oc_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'so4_a1 -> ${chem_datapath}/emis/ar5_mam3_so4_a1_surf_1850-2010_c20100902_v12.nc'," >> ${fname}
+ echo " 'so4_a2 -> ${chem_datapath}/emis/ar5_mam3_so4_a2_surf_1850-2010_c20100902_v12.nc' " >> ${fname}
+
+ echo " solar_data_file = '${cesm_datadir}/atm/cam/solar/spectral_irradiance_Lean_1610-2009_ann_c100405.nc' " >> ${fname}
+
+
+ # ===========================================================================
+ set fname = "user_nl_clm_$instance"
+ # ===========================================================================
+ # faerdep does not make its way to the final namelist in the F_AMIP_CAM5 case:
+
+# echo "faerdep = '${cesm_datadir}/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1849-2104_0.9x1.25_c100407.nc' " >> ${fname}
+ echo "hist_empty_htapes = .true. " >> ${fname}
+ echo "finidat = 'clm_restart_${instance}.nc' " >> ${fname}
+
+
+ # ===========================================================================
+ set fname = "user_nl_cice_$instance"
+ # ===========================================================================
+
+ echo " ice_ic = 'ice_restart_${instance}.nc' " >> ${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
+# $DARTroot/models/POP/shell_scripts directory and modify one for each instance.
+#
+# ==============================================================================
+
+# none needed for CAM
+
+# ==============================================================================
# Update source files if need be
# Ideally, using DART will not require any source mods.
# Until then, this script accesses source mods from a hard-wired location below.
# Those may eventually be packaged into the DART repository.
# If you have additional source mods, they will need to be merged into any DART
# mods and put in the SourceMods subdirectory found in the 'case' directory.
-# ====================================================================
+# ==============================================================================
-# this one needs a recursive copy to get all the files in the subdirs
-${COPY} -r ~thoar/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
-if ( $status == 0) then
- echo "FYI - Local Source Modifications used for this case:"
- ls -lr ${caseroot}/SourceMods/*
+if ( -d ~/${cesmtag}/SourceMods ) then
+ ${COPY} -r ~/${cesmtag}/SourceMods/* ${caseroot}/SourceMods/
else
- echo "FYI - No SourceMods for this case"
+ 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 -3
endif
-# ====================================================================
-# Configure
-# ====================================================================
+# ==============================================================================
+# build
+# ==============================================================================
-cd ${caseroot}
+echo ''
+echo 'Building the case'
+echo ''
-./configure -case
+./${case}.build
if ( $status != 0 ) then
- echo "ERROR: Case could not be configured."
- exit 2
+ echo "ERROR: Case could not be built."
+ exit -4
endif
-# ====================================================================
-# Stage the required parts of DART in the caseroot directory.
-# ====================================================================
+# ==============================================================================
+# Stage the restarts now that the run directory exists
+# ==============================================================================
-cd ${caseroot}
+# CAM5 ... /glade/p/work/raeder/Exp/Pincus_Cam5/archive/Exp3/rest/2008-11-01-00000
-if ("${reuse_existing_case}" == "false") then
- ${MOVE} Tools/st_archive.sh Tools/st_archive.sh.orig
-endif
-${COPY} ${DARTroot}/models/cam/shell_scripts/st_archive.sh Tools/
+set stagedir = /glade/p/work/raeder/Exp/Pincus_Cam5/archive/Exp3/rest/2008-11-01-00000
-# The cesm1_1_beta04 release had an error in that it did not
-# provide the lt_archive.csh script, and the one in the repos
-# did not have the -p flag, which is a good idea. So, for now ...
-${COPY} ${cesmroot}/scripts/ccsm_utils/Tools/lt_archive.csh Tools/
+echo ''
+echo "Copying the restart files from ${stagedir}"
+echo 'into the CESM run directory.'
+echo ''
-${COPY} ${DARTroot}/models/cam/shell_scripts/assimilate.csh .
-${COPY} ${DARTroot}/models/cam/work/input.nml .
+@ n = 1
+while ($n <= $num_instances)
+ set instance = `printf %04d $n`
+ echo "Staging restarts for instance $n of $num_instances"
+ ${COPY} ${stagedir}/cam_initial_${n}.nc ${rundir}/cam_initial_${instance}.nc
+ ${COPY} ${stagedir}/clm_restart_${n}.nc ${rundir}/clm_restart_${instance}.nc
+ ${COPY} ${stagedir}/ice_restart_${n}.nc ${rundir}/ice_restart_${instance}.nc
+ @ n++
+end
-# ====================================================================
-# Update the scripts that build the namelists.
-# The active components scripts need to support the multi-instance naming.
-# ====================================================================
+if ( -e ${stagedir}/prior_inflate_restart* ) then
+ ${COPY} ${stagedir}/prior_inflate_restart* ${rundir}/.
+endif
+# ==============================================================================
+# IMPORTANT: All resubmits must be type 'startup'.
+# Change Tools/ccsm_postrun.csh line 83 to CONTINUE_RUN -val FALSE'
+# ==============================================================================
+
echo ''
-echo 'Editing the Buildconf/{cam,cice,clm}.buildnml.csh files'
+echo 'Changing Tools/ccsm_postrun.csh such that all the resubmits are "startup",'
+echo 'which means CONTINUE_RUN should be FALSE in ccsm_postrun.csh'
echo ''
-cd ${caseroot}/Buildconf
+ex Tools/ccsm_postrun.csh <<ex_end
+/use COMP_RUN_BARRIERS as surrogate for timing run logical/
+/CONTINUE_RUN/
+s;TRUE;FALSE;
+wq
+ex_end
-${COPY} cam.buildnml.csh cam.buildnml.csh.orig
-${COPY} cice.buildnml.csh cice.buildnml.csh.orig
-${COPY} clm.buildnml.csh clm.buildnml.csh.orig
+# ==============================================================================
+# Edit the run script to reflect project, queue, and wallclock
+# ==============================================================================
-# The CAM buildnml script only needs changing in one place.
+echo ''
+echo 'Updating the run script to set wallclock and queue.'
+echo ''
-ex cam.buildnml.csh <<ex_end
-/cam_inparm/
-/ncdata/
-s;= '.*';= "cam_initial_\${atm_inst_counter}.nc";
-wq
-ex_end
+${COPY} ${case}.run ${case}.run.orig
-# The CICE buildnml script only needs changing in one place.
+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.$$
+ ${MOVE} temp.$$ ${case}.run
+ breaksw
-ex cice.buildnml.csh <<ex_end
-/setup_nml/
-/ice_ic/
-s;= '.*';= "ice_restart_\${ice_inst_counter}.nc";
-wq
-ex_end
+ default:
-# The CLM buildnml script needs changing in MULTIPLE places.
+ breaksw
+endsw
-@ n = 1
-while ($n <= $num_instances)
- set inst = `printf "%04d" $n`
- ex clm.buildnml.csh <<ex_end
-/lnd_in_$inst/
-/finidat/
-s;= '.*';= "clm_restart_${n}.nc";
-wq
-ex_end
- @ n++
-end
+chmod 0755 ${case}.run
-chmod 0755 clm.buildnml.csh
-
-# ====================================================================
+# ==============================================================================
# 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.
-# ====================================================================
+# ==============================================================================
-cd ${caseroot}
-
echo ''
echo 'Adding the call to assimilate.csh to the *.run script.'
echo ''
@@ -483,163 +559,96 @@
# -------------------------------------------------------------------------
# START OF DART: if CESM finishes correctly (pirated from ccsm_postrun.csh);
# perform an assimilation with DART.
-# -------------------------------------------------------------------------
set CplLogFile = `ls -1t cpl.log* | head -n 1`
if ($CplLogFile == "") then
- echo 'ERROR: Model did not complete - no cpl.log file present - exiting'
- echo 'ERROR: Assimilation will not be attempted.'
- exit -4
+ 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
+ ${CASEROOT}/assimilate.csh
- if ( $status == 0 ) then
- echo "`date` -- DART HAS FINISHED"
- else
- echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
- exit -5
- endif
+ if ( $status == 0 ) then
+ echo "`date` -- DART HAS FINISHED"
+ else
+ echo "`date` -- DART FILTER ERROR - ABANDON HOPE"
+ exit -3
+ endif
+else
+ echo 'ERROR: Model did not complete successfully - exiting.'
+ echo 'ERROR: Assimilation will not be attempted.'
+ 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" ${case}.${mach}.run
+grep "ABANDON HOPE" ${case}.run
set STATUSCHECK = $status
if ( ${STATUSCHECK} == 0 ) then
- echo "DART block already present in ${case}.${mach}.run"
+ echo "DART block already present in ${case}.run"
else if ( ${STATUSCHECK} == 1 ) then
- set MYSTRING = `grep --line-number "CSM EXECUTION HAS FINISHED" ${case}.${mach}.run`
+ set MYSTRING = `grep --line-number "CSM EXECUTION HAS FINISHED" ${case}.run`
set MYSTRING = `echo $MYSTRING | sed -e "s#:# #g"`
- @ origlen = `cat ${case}.${mach}.run | wc -l`
+ @ origlen = `cat ${case}.run | wc -l`
@ keep = $MYSTRING[1]
@ lastlines = $origlen - $keep
- mv ${case}.${mach}.run ${case}.${mach}.run.orig
+ head -n $keep ${case}.run >! temp.$$
+ cat add_to_run.txt >> temp.$$
+ tail -n $lastlines ${case}.run >> temp.$$
- head -n $keep ${case}.${mach}.run.orig >! ${case}.${mach}.run
- cat add_to_run.txt >> ${case}.${mach}.run
- tail -n $lastlines ${case}.${mach}.run.orig >> ${case}.${mach}.run
+ ${MOVE} temp.$$ ${case}.run
+ ${REMOVE} add_to_run.txt
else
- echo "ERROR in grep of ${case}.${mach}.run: aborting"
+ echo "ERROR in grep of ${case}.run: aborting"
echo "status was ${STATUSCHECK}"
- exit 10
+ exit -5
endif
-# ====================================================================
-# Edit the run script to reflect project, queue, and wallclock
-# ====================================================================
+# ==============================================================================
+# Stage the required parts of DART in the CASEROOT directory.
+# ==============================================================================
-echo ''
-echo 'Updating the run script to set the project number, wallclock time'
-echo 'and queue name.'
-echo ''
+# The cesm1_1_beta04 release had an error in that it did not
+# provide the lt_archive.sh script, and the one in the repos
+# did not have the -p flag, which is a good idea. So, for now ...
-if ($?proj) then
- set PROJ=`grep BSUB $case.$mach.run | grep -e '-P' `
- sed s/$PROJ[3]/$proj/ < $case.$mach.run >! temp
- ${MOVE} temp $case.$mach.run
+if ( ~ -e Tools/st_archive.sh.orig ) then
+ ${COPY} Tools/st_archive.sh Tools/st_archive.sh.orig
+else
+ echo "a Tools/st_archive.sh backup copy already exists"
endif
-
-if ($?timewall) then
- set TIMEWALL=`grep BSUB $case.$mach.run | grep -e '-W' `
- sed s/$TIMEWALL[3]/$timewall/ < $case.$mach.run >! temp
- ${MOVE} temp $case.$mach.run
-endif
-
-if ($?queue) then
- set QUEUE=`grep BSUB $case.$mach.run | grep -e '-q' `
- sed s/$QUEUE[3]/$queue/ < $case.$mach.run >! temp
- ${MOVE} temp $case.$mach.run
-endif
-chmod 0755 ${case}.${mach}.run
+# ${COPY} ${DARTroot}/models/cam/shell_scripts/st_archive.sh Tools/
-# ====================================================================
-# IMPORTANT: All resubmits must be type 'startup'.
-# Change Tools/ccsm_postrun.csh line 83 to CONTINUE_RUN -val FALSE'
-# ====================================================================
+${COPY} ${DARTroot}/models/cam/shell_scripts/assimilate.csh .
+${COPY} ${DARTroot}/models/cam/work/input.nml .
-cd ${caseroot}/Tools
+# ==============================================================================
+# Stage the DART executables in the CESM execution root directory: EXEROOT
+# ==============================================================================
-echo ''
-echo 'Changing Tools/ccsm_postrun.csh such that all the resubmits are "startup",'
-echo 'which means CONTINUE_RUN should be FALSE in ccsm_postrun.csh'
-echo ''
-
-ex ccsm_postrun.csh <<ex_end
-/use COMP_RUN_BARRIERS as surrogate for timing run logical/
@@ Diff output truncated at 40000 characters. @@
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