[Dart-dev] [5447] DART/branches/development/models/cam/shell_scripts/assimilate.ned. csh: The assimilate script i was using for the Zagar test
nancy at ucar.edu
nancy at ucar.edu
Wed Dec 14 15:40:42 MST 2011
Revision: 5447
Author: nancy
Date: 2011-12-14 15:40:41 -0700 (Wed, 14 Dec 2011)
Log Message:
-----------
The assimilate script i was using for the Zagar test
on hopper with cam.
Added Paths:
-----------
DART/branches/development/models/cam/shell_scripts/assimilate.ned.csh
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Added: DART/branches/development/models/cam/shell_scripts/assimilate.ned.csh
===================================================================
--- DART/branches/development/models/cam/shell_scripts/assimilate.ned.csh (rev 0)
+++ DART/branches/development/models/cam/shell_scripts/assimilate.ned.csh 2011-12-14 22:40:41 UTC (rev 5447)
@@ -0,0 +1,441 @@
+#!/usr/bin/tcsh
+# FIXME: where it might be on bluefire but not hopper:
+#!/usr/local/bin/tcsh
+# 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: assimilate.hopper.csh 5403 2011-11-16 15:20:05Z nancy $
+
+# The FORCE options are not optional.
+# the VERBOSE options are useful for debugging.
+set MOVE = 'mv -fv'
+set COPY = 'cp -fv --preserve=timestamps'
+set LINK = 'ln -fvs'
+set REMOVE = 'rm -fr'
+# FIXME: not on hopper:
+#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'
+
+set ensemble_size = ${NINST_ATM}
+
+# Create temporary working directory for the assimilation
+set temp_dir = assimilate_dir
+echo "temp_dir is $temp_dir"
+mkdir -p $temp_dir
+cd $temp_dir
+
+#-------------------------------------------------------------------------
+# Determine time of model state ... from file name of first member
+# of the form "./${CASE}.cam_${ensemble_member}.r.2000-01-06-00000.nc"
+#-------------------------------------------------------------------------
+
+set FILE = `head -1 ../rpointer.atm_0001`
+set FILE = $FILE:t
+set FILE = $FILE:r
+set MYCASE = $FILE:ar
+set MODEL_DATE_EXT = `echo $FILE:e`
+set MODEL_DATE = `echo $FILE:e | sed -e "s#-# #g"`
+set MODEL_YEAR = $MODEL_DATE[1]
+set MODEL_MONTH = $MODEL_DATE[2]
+set MODEL_DAY = $MODEL_DATE[3]
+set MODEL_SECONDS = $MODEL_DATE[4]
+set MODEL_HOUR = `echo $MODEL_DATE[4] / 3600 | bc`
+
+echo "valid time of model is $MODEL_YEAR $MODEL_MONTH $MODEL_DAY $MODEL_SECONDS (seconds)"
+echo "valid time of model is $MODEL_YEAR $MODEL_MONTH $MODEL_DAY $MODEL_HOUR (hours)"
+
+#-----------------------------------------------------------------------------
+# Set variables containing various directory names where we will GET things
+#-----------------------------------------------------------------------------
+
+# FIXME: different for everyone
+set DARTROOT = ${HOME}/devel
+set DARTDIR = ${DARTROOT}/models/cam/work
+
+# FIXME: different on hopper
+set DART_OBS_DIR = UVT_Set1_12H
+set OBSDIR = /scratch/scratchdirs/nscollin/Synthetic/${DART_OBS_DIR}
+
+#-------------------------------------------------------------------------
+# DART COPY BLOCK
+# Populate a run-time directory with the bits needed to run DART
+#-------------------------------------------------------------------------
+
+foreach FILE ( input_1.nml input_n.nml filter cam_to_dart dart_to_cam )
+ if ( -e ${DARTDIR}/${FILE} ) then
+ ${COPY} ${DARTDIR}/${FILE} .
+ else
+ echo "DART required file ${DARTDIR}/${FILE} not found ... ERROR"
+ exit 1
+ endif
+end
+
+# special: input_1.nml for first step, input_n.nml after.
+# FIXME: this should sed the few lines which are special for run 1
+# so we only have a single input.nml file running around.
+#${COPY} input_1.nml input.nml
+${COPY} input_n.nml input.nml
+
+# FIXME: doesn't exist on hopper
+#${COPY} /glade/proj3/DART/raeder/FV1deg_4.0/cam_phis.nc .
+${COPY} $HOME/cam_phis.nc .
+
+# Modify the DART input.nml such that
+# the DART ensemble size matches the CESM number of instances
+# WARNING: the output files contain ALL enemble members ==> BIG
+
+ex input.nml <<ex_end
+g;ens_size ;s;= .*;= $ensemble_size;
+g;num_output_state_members ;s;= .*;= $ensemble_size;
+wq
+ex_end
+
+# we do not need all 80 obs values
+#g;num_output_obs_members ;s;= .*;= $ensemble_size;
+
+#-------------------------------------------------------------------------
+# DART SAMPLING ERROR CORRECTION BLOCK
+# This stages the files needed for the sampling error correction.
+# Each ensemble size has its own (static) file which does not need to be archived.
+# It is only needed if
+# input.nml:&assim_tools_nml:sampling_error_correction = .true.,
+#-------------------------------------------------------------------------
+
+set MYSTRING = `grep -A 50 \&assim_tools_nml input.nml | grep sampling_error_correction | head -1`
+set SECSTRING = `echo $MYSTRING | sed -e "s#.*= *\.\(.*\)\..*#.\1.#" | tr 'A-Z' 'a-z'`
+
+if ( $SECSTRING == ".true." ) then
+ set SAMP_ERR_FILE = ${DARTROOT}/system_simulation/final_full_precomputed_tables/final_full.${ensemble_size}
+ if ( -e ${SAMP_ERR_FILE} ) then
+ ${COPY} ${SAMP_ERR_FILE} .
+ else
+ echo "ERROR: no sampling error correction file for this ensemble size."
+ echo "ERROR: looking for ${SAMP_ERR_FILE}"
+ exit 2
+ endif
+else
+ echo "Sampling Error Correction not requested for this assimilation."
+endif
+
+#-------------------------------------------------------------------------
+# DART INFLATION BLOCK
+# This stages the files that contain the inflation values.
+# The inflation values change through time and should be archived.
+#
+# This file is only relevant if 'inflation' is turned on -
+# i.e. if inf_flavor(1) /= 0 AND inf_initial_from_restart = .TRUE.
+#
+# filter_nml
+# inf_flavor = 2, 0,
+# inf_initial_from_restart = .true., .false.,
+# inf_in_file_name = 'prior_inflate_ics', 'post_inflate_ics',
+# inf_out_file_name = 'prior_inflate_restart', 'post_inflate_restart',
+# inf_diag_file_name = 'prior_inflate_diag', 'post_inflate_diag',
+#
+# NOTICE: the archiving scripts more or less require the names of these
+# files to be as listed above. When being archived, the filenames get a
+# unique extension (describing the assimilation time) appended to them.
+#
+# The inflation file is essentially a duplicate of the model state ...
+# it is slaved to a specific geometry. The initial files are created
+# offline with values of unity. For the purpose of this script, they are
+# thought to be the output of a previous assimilation, so they should be
+# named something like prior_inflate_restart.YYYY-MM-DD-SSSSS
+#
+# The first inflation file can be created with 'fill_inflation_restart'
+# which can be built in the usual DART manner.
+#
+# The strategy is to use the LATEST inflation file from the CESM 'rundir'.
+# After an assimilation, the new inflation values/files will be moved to
+# the CESM rundir to be used for subsequent assimilations. If the short-term
+# archiver has worked correctly, only the LATEST files will available. Of
+# course, it is not required to have short-term archiving turned on, so ...
+#-------------------------------------------------------------------------
+
+set MYSTRING = `grep inf_flavor input.nml`
+set MYSTRING = `echo $MYSTRING | sed -e "s#[=,]# #g"`
+set PRIOR_INF = $MYSTRING[2]
+set POSTE_INF = $MYSTRING[3]
+
+set MYSTRING = `grep inf_initial_from_restart input.nml`
+set MYSTRING = `echo $MYSTRING | sed -e "s#[=,]# #g"`
+set PRIOR_TF = `echo $MYSTRING[2] | tr 'A-Z' 'a-z'`
+set POSTE_TF = `echo $MYSTRING[3] | tr 'A-Z' 'a-z'`
+
+# its a little tricky to remove both styles of quotes from the string.
+# (only in the cshell. bash/ksh variants have better quoting styles)
+
+set MYSTRING = `grep inf_in_file_name input.nml`
+set MYSTRING = `echo $MYSTRING | sed -e "s#[=,']# #g"`
+set MYSTRING = `echo $MYSTRING | sed -e 's#"# #g'`
+set PRIOR_INF_IFNAME = $MYSTRING[2]
+set POSTE_INF_IFNAME = $MYSTRING[3]
+
+set MYSTRING = `grep inf_out_file_name input.nml`
+set MYSTRING = `echo $MYSTRING | sed -e "s#[=,']# #g"`
+set MYSTRING = `echo $MYSTRING | sed -e 's#"# #g'`
+set PRIOR_INF_OFNAME = $MYSTRING[2]
+set POSTE_INF_OFNAME = $MYSTRING[3]
+
+set MYSTRING = `grep inf_diag_file_name input.nml`
+set MYSTRING = `echo $MYSTRING | sed -e "s#[=,']# #g"`
+set MYSTRING = `echo $MYSTRING | sed -e 's#"# #g'`
+set PRIOR_INF_DIAG = $MYSTRING[2]
+set POSTE_INF_DIAG = $MYSTRING[3]
+
+# IFF we want PRIOR inflation:
+
+if ( $PRIOR_INF > 0 ) then
+
+ if ($PRIOR_TF == ".false.") then
+ echo "ERROR: inf_flavor(1) = $PRIOR_INF, yet inf_initial_from_restart = $PRIOR_TF"
+ echo "ERROR: fix input.nml to reflect whether you want prior inflation or not."
+ exit 3
+ endif
+
+ # Look for the output from the previous assimilation
+ (ls -rt1 ../${PRIOR_INF_OFNAME}.* | tail -1 >! latestfile) > & /dev/null
+ set nfiles = `cat latestfile | wc -l`
+
+ # If one exists, use it as input for this assimilation
+ if ( $nfiles > 0 ) then
+ set latest = `cat latestfile`
+ ${LINK} $latest ${PRIOR_INF_IFNAME}
+ else
+ echo "ERROR: Requested prior inflation but specified no incoming prior inflation file."
+ echo "ERROR: expected something like ../${PRIOR_INF_OFNAME}.YYYY-MM-DD-SSSSS"
+ exit 4
+ endif
+else
+ echo "Prior Inflation not requested for this assimilation."
+endif
+
+# POSTERIOR: We look for the 'newest' and use it - IFF we need it.
+
+if ( $POSTE_INF > 0 ) then
+
+ if ($POSTE_TF == ".false.") then
+ echo "ERROR: inf_flavor(2) = $POSTE_INF, yet inf_initial_from_restart = $POSTE_TF"
+ echo "ERROR: fix input.nml to reflect whether you want posterior inflation or not."
+ exit 5
+ endif
+
+ # Look for the output from the previous assimilation
+ (ls -rt1 ../${POSTE_INF_OFNAME}.* | tail -1 >! latestfile) > & /dev/null
+ set nfiles = `cat latestfile | wc -l`
+
+ # If one exists, use it as input for this assimilation
+ if ( $nfiles > 0 ) then
+ set latest = `cat latestfile`
+ ${LINK} $latest ${POSTE_INF_IFNAME}
+ else
+ echo "ERROR: Requested POSTERIOR inflation but specified no incoming POSTERIOR inflation file."
+ echo "ERROR: expected something like ../${POSTE_INF_OFNAME}.YYYY-MM-DD-SSSSS"
+ exit 6
+ endif
+else
+ echo "Posterior Inflation not requested for this assimilation."
+endif
+
+#-------------------------------------------------------------------------
+# Block 1: convert N cam restart files to DART initial conditions file(s)
+# cam_to_dart is serial code, we can do all of these at the same time
+# and just wait for them to finish IFF it were not for the fact we'd have
+# to have unique namelists for all of them.
+#
+# At the end of the block, we have DART restart files filter_ic_old.[1-N]
+# that came from pointer files ../rpointer.atm_[1-N]
+#
+# DART namelist settings appropriate/required:
+# &filter_nml: restart_in_file_name = 'filter_ic_old'
+# &ensemble_manager_nml: single_restart_file_in = '.false.'
+# &cam_to_dart_nml: cam_to_dart_output_file = 'dart_ics',
+#-------------------------------------------------------------------------
+
+set member = 1
+while ( ${member} <= ${ensemble_size} )
+
+ # Each member will do its job in its own directory.
+ # That way, we can do N of them simultaneously -
+ # they all read their OWN 'input.nml' ... the output
+ # filenames must inserted into the appropriate input.nml
+
+ set MYTEMPDIR = member_${member}
+ mkdir -p $MYTEMPDIR
+ cd $MYTEMPDIR
+
+ set POINTER_FILENAME = `printf rpointer.atm_%04d ${member}`
+ set MODEL_RESTART_FILENAME = `head -1 ../../${POINTER_FILENAME}`
+ set MODEL_INITIAL_FILENAME = `echo ${MODEL_RESTART_FILENAME} | sed "s#\.r\.#\.i\.#"`
+ ${LINK} ../../$MODEL_INITIAL_FILENAME caminput.nc
+ ${LINK} ../cam_phis.nc .
+
+ # TJH can we use a .h0. file instead of some arbitrary cam_phis.nc
+
+ set DART_IC_FILE = `printf ../filter_ic_old.%04d ${member}`
+
+ sed -e "s#dart_ics#${DART_IC_FILE}#" < ../input.nml >! input.nml
+
+ echo "starting cam_to_dart for member ${member} at "`date`
+ ../cam_to_dart >! output.${member}.cam_to_dart &
+ echo "finished cam_to_dart for member ${member} at "`date`
+
+ cd ..
+
+ @ member++
+end
+
+wait
+
+#-------------------------------------------------------------------------
+# Block 2: Actually run the assimilation.
+# Will result in a set of files : 'filter_restart.xxxx'
+#
+# DART namelist settings required:
+# &filter_nml: async = 0,
+# &filter_nml: adv_ens_command = "./no_model_advance.csh",
+# &filter_nml: restart_in_file_name = 'filter_ic_old'
+# &filter_nml: restart_out_file_name = 'filter_ic_new'
+# &filter_nml: obs_sequence_in_name = 'obs_seq.out'
+# &filter_nml: obs_sequence_out_name = 'obs_seq.final'
+# &filter_nml: init_time_days = -1,
+# &filter_nml: init_time_seconds = -1,
+# &filter_nml: first_obs_days = -1,
+# &filter_nml: first_obs_seconds = -1,
+# &filter_nml: last_obs_days = -1,
+# &filter_nml: last_obs_seconds = -1,
+# &ensemble_manager_nml: single_restart_file_in = .false.
+#
+#-------------------------------------------------------------------------
+
+# cam always needs a cam_initial.nc and a cam_history.nc to start.
+
+set MODEL_RESTART_FILENAME = `head -1 ../rpointer.atm_0001`
+set MODEL_INITIAL_FILENAME = `echo ${MODEL_RESTART_FILENAME} | sed "s#\.r\.#\.i\.#"`
+set MODEL_HISTORY_FILENAME = `echo ${MODEL_RESTART_FILENAME} | sed "s#\.r\.#\.h0\.#"`
+
+${LINK} ../$MODEL_INITIAL_FILENAME caminput.nc
+#${LINK} ../$MODEL_RESTART_FILENAME cam_restart.nc
+#${LINK} ../$MODEL_HISTORY_FILENAME cam_history.nc
+
+# Determine proper observation sequence file.
+
+set OBSFNAME = `printf syn_obs_seq${MODEL_YEAR}${MODEL_MONTH}${MODEL_DAY}%02d ${MODEL_HOUR}`
+set OBS_FILE = ${OBSDIR}/${OBSFNAME}
+
+${LINK} ${OBS_FILE} obs_seq.out
+
+# FIXME: removed shell vars that are undefined for PBS
+
+
+# FIXME: mpirun, mpirun.lsf, or aprun are popular choices here
+# to start filter:
+
+setenv NTASKS ${TOTALPES}
+echo starting filter executable now with ${NTASKS} MPI tasks
+aprun -n $NTASKS ./filter || exit 7
+
+
+${MOVE} Prior_Diag.nc ../Prior_Diag.${MODEL_DATE_EXT}.nc
+${MOVE} Posterior_Diag.nc ../Posterior_Diag.${MODEL_DATE_EXT}.nc
+${MOVE} obs_seq.final ../obs_seq.${MODEL_DATE_EXT}.final
+${MOVE} dart_log.out ../dart_log.${MODEL_DATE_EXT}.out
+
+# Accomodate any possible inflation files
+# 1) rename file to reflect current date
+# 2) move to CENTRALDIR so the DART INFLATION BLOCK works next time and
+# that they can get archived.
+
+foreach FILE ( ${PRIOR_INF_OFNAME} ${POSTE_INF_OFNAME} ${PRIOR_INF_DIAG} ${POSTE_INF_DIAG} )
+ if ( -e ${FILE} ) then
+ ${MOVE} ${FILE} ../${FILE}.${MODEL_DATE_EXT}
+ else
+ echo "No ${FILE} for ${MODEL_DATE_EXT}"
+ endif
+end
+
+# FIXME: removed shell vars that are undefined for PBS
+
+#-------------------------------------------------------------------------
+# Block 3: Update the cam restart files ... simultaneously ...
+#
+# DART namelist settings required:
+# &filter_nml: restart_out_file_name = 'filter_ic_new'
+# &ensemble_manager_nml: single_restart_file_in = '.false.'
+# &dart_to_cam_nml: dart_to_cam_input_file = 'temp_ic',
+# &dart_to_cam_nml: advance_time_present = .false.
+# &atm_in_xxxx:ncdata = 'cam_initial_x.nc'
+#-------------------------------------------------------------------------
+
+set member = 1
+while ( ${member} <= ${ensemble_size} )
+
+ # Each member will do its job in its own directory.
+ # Cannot do these simultaneously -
+
+ set MYTEMPDIR = member_${member}
+ mkdir -p $MYTEMPDIR
+ cd $MYTEMPDIR
+
+ set DART_RESTART_FILE = `printf filter_ic_new.%04d ${member}`
+ ${LINK} ../$DART_RESTART_FILE temp_ic
+
+ set ATM_POINTER_FILENAME = `printf rpointer.atm_%04d ${member}`
+ set LND_POINTER_FILENAME = `printf rpointer.lnd_%04d ${member}`
+ set ICE_POINTER_FILENAME = `printf rpointer.ice_%04d ${member}`
+
+ set ATM_RESTART_FILENAME = `head -1 ../../${ATM_POINTER_FILENAME}`
+ set LND_RESTART_FILENAME = `echo ${ATM_RESTART_FILENAME} | sed "s#\.cam_#\.clm2_#"`
+ set ICE_RESTART_FILENAME = `echo ${ATM_RESTART_FILENAME} | sed "s#\.cam_#\.cice_#"`
+
+ set ATM_INITIAL_FILENAME = `echo ${ATM_RESTART_FILENAME} | sed "s#\.r\.#\.i\.#"`
+
+# set ATM_HISTORY_FILENAME = `echo ${ATM_RESTART_FILENAME} | sed "s#\.r\.#\.h0\.#"`
+# ${LINK} ../../$ATM_RESTART_FILENAME cam_restart.nc
+# ${LINK} ../../$ATM_HISTORY_FILENAME cam_history.nc
+ ${LINK} ../../$ATM_INITIAL_FILENAME caminput.nc
+
+ echo "starting dart_to_cam for member ${member} at "`date`
+ ../dart_to_cam >! output.${member}.dart_to_cam
+ echo "finished dart_to_cam for member ${member} at "`date`
+
+ # The initial filenames are static and come from the atm_in_xxxx namelist.
+ # We must copy the updated initial files to the static names.
+
+ ${COPY} ../../$ATM_INITIAL_FILENAME ../../cam_initial_${member}.nc
+ ${COPY} ../../$LND_RESTART_FILENAME ../../clm_restart_${member}.nc
+ ${COPY} ../../$ICE_RESTART_FILENAME ../../ice_restart_${member}.nc
+
+ cd ..
+
+ @ member++
+end
+
+wait
+
+#-------------------------------------------------------------------------
+# Now that everything is staged, we have to communicate the current
+# model time to the drv_in&seq_timemgr_inparm namelist
+# which is built from CASEROOT/user_nl_drv by the *.run script
+#-------------------------------------------------------------------------
+
+ex ${CASEROOT}/Buildconf/cpl.buildnml.csh << ex_end
+g; start_ymd;s;=[ ]*.*;= ${MODEL_YEAR}${MODEL_MONTH}${MODEL_DAY};
+g; start_tod;s;=[ ]*.*;= $MODEL_SECONDS;
+wq
+ex_end
+
+#-------------------------------------------------------------------------
+# Cleanup
+#-------------------------------------------------------------------------
+
+exit 0
+
+# <next few lines under version control, do not edit>
+# $URL: https://proxy.subversion.ucar.edu/DAReS/DART/branches/development/models/cam/shell_scripts/assimilate.hopper.csh $
+# $Revision: 5403 $
+# $Date: 2011-11-16 07:20:05 -0800 (Wed, 16 Nov 2011) $
+
Property changes on: DART/branches/development/models/cam/shell_scripts/assimilate.ned.csh
___________________________________________________________________
Added: svn:executable
+ *
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