[Dart-dev] [6396] DART/trunk/models/CESM/shell_scripts: Modified the usage notes to reflect when to use each script
nancy at ucar.edu
nancy at ucar.edu
Mon Aug 12 11:51:26 MDT 2013
Revision: 6396
Author: thoar
Date: 2013-08-12 11:51:26 -0600 (Mon, 12 Aug 2013)
Log Message:
-----------
Modified the usage notes to reflect when to use each script
and fixed some hanging sentences.
obfuscated the ACCOUNT number.
Modified Paths:
--------------
DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid
DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial
-------------- next part --------------
Modified: DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid
===================================================================
--- DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid 2013-08-12 17:36:20 UTC (rev 6395)
+++ DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid 2013-08-12 17:51:26 UTC (rev 6396)
@@ -11,76 +11,58 @@
# ---------------------
#
# This script is designed to set up, stage, and build a multi-instance run of CESM
-# using a B compset where CAM, POP, and CLM are all active. The initial states for
-# the models come from as single reference case so a CESM hybrid setup is used.
+# using a B compset where CAM, POP, and CLM are all active. The initial states
+# come from a single multi-instance reference case so a CESM hybrid setup is used.
+# While not required for CESM, POP is configured to write out netCDF restart files
+# because they are required by DART (if you are going to assimilate ocean obs).
#
-# POP: uses the result of the 'b40.20th.005_ens${instance}' experiments. The POP
-# restart files were saved as binary files, which is somewhat problematic for
-# data assimilation. Consequently, the entire model state must be advanced for
-# several days before a viable netCDF restart file can be produces. We advance
-# for 72 hours.
+# Because the atmosphere assimilations typically occur every 6 hours, the methodology
+# here reflects that. All of CESM stops every 6 hours (requiring the ocean to couple
+# 4x per day) so that a CAM output file would be available for assimilation.
#
-# RTM: uses the result of the 'b40.20th.005_ens${instance}' experiments. These
-# restart files are actually the CLM restart files from this experiment because
-# the RTM was part of CLM when the experiment was run. The standalone version of
-# RTM can read old CLM restart files.
-#
-# CICE: uses the result of the 'b40.20th.005_ens${instance}' experiments.
-#
-# CLM: uses the result of the 'b40.20th.005_ens${instance}' experiments - sort of.
-# CLM has changed since then and the CLM restart files needed to be converted
-# to the new format. I ran 'interpinic' to (essentially) reformat the files
-# and changed the CASENAME to 'cesm_test' and used the multi-instance naming
-# convention for the new files.
-#
-# CAM: We want to use a newer version of CAM than was used for the b40.20th.005
-# experiments. Consequently, we took a SINGLE instance of CAM and replicated
-# it for all the desired instances. After just a few days, the differences in
-# the ocean and land states will induce enough variability in the CAM states.
-#
-# Much of the complexity comes from ensuring compatibility between the namelists
-# for each instance and staging of the files. The original experiments were run
-# before the multi-instance capacity was developed and the naming convention decided.
-# Consequently, there is a lot of manipulation of the 'instance' portion of the
-# filenames.
-#
# This script results in a viable setup for a CESM multi-instance experiment. You
# are STRONGLY encouraged to run the multi-instance CESM a few times and experiment
# with different settings BEFORE you try to assimilate observations. The amount of
# data volume is quite large and you should become comfortable using CESM's restart
# capability to re-stage files in your RUN directory
#
-# To perform assimilation, it is required only to insert a few dozen lines into the
-# CASEROOT/*.run script. This, and the required setup, is performed in
-# CESM_DART_config - which can be run at a later date. e.g. you can use this
-# script to advance this 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 24 hours,
-# and start assimilating observationg at midnight from 2004-02-01 on ...
+# CASEROOT/CESM_DART_config will augment the CESM case with the required setup
+# and configuration to perform a DART assimilation. CASEROOT/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 assimilating 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 set up the script
+# How to use this script.
# ---------------------
#
-# -- Either edit and run this script in the $DART/models/CESM/shell_scripts
-# directory where it first appears,
+# -- 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 multi-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 'case' directory, where the model will be built,
-# and an execution directory, where each forecast and assimilation will
+# It will create a CESM 'CASE' directory, where the model will be built,
+# and an execution directory, where each forecast (and assimilation) will
# take place. The short term archiver will use a third directory for
# storage of model output until it can be moved to long term storage (HPSS)
+#
# -- Examine the whole script to identify things to change for your experiments.
-# -- Provide any initial files needed by your run:
-# inflation
-# sampling error correction
-# CESM initial ensemble
-# ...
+#
+# -- Provide the CESM initial ensemble needed by your run.
+#
# -- Run this script.
-# -- Edit the DART input.nml that appears in the $CASEROOT directory.
-# -- Submit the job using $CASEROOT/${case}.submit
#
+# -- If you want to run DART, read and understand ${CASEROOT}/CESM_DART_config
+#
+# -- Submit the job using ${CASEROOT}/${CASE}.submit
+#
# ---------------------
# Important features
# ---------------------
@@ -106,7 +88,7 @@
# script names; so consider it's length and information content.
# num_instances: Number of ensemble members
-setenv case cesm_continue
+setenv case cesm_assim
setenv compset B_2000_CAM5
setenv resolution 0.9x1.25_gx1v6
setenv cesmtag cesm1_1_1
@@ -163,11 +145,12 @@
# assim_n Number of time units between assimilations
#
# If the long-term archiver is off, you get a chance to examine the files before
-# you
+# 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 resubmit 12
+setenv resubmit 8
setenv stop_option nhours
setenv stop_n 6
setenv assim_n 6
@@ -180,10 +163,11 @@
# queue can be changed during a series by changing the ${case}.run
# timewall can be changed during a series by changing the ${case}.run
#
-# TJH: 30 instances with 900 pes took about 30 minutes on yellowstone.
+# TJH: Advancing 30 instances for 6 hours with 900 pes
+# took less than 10 minutes on yellowstone.
# ==============================================================================
-setenv ACCOUNT P86850054
+setenv ACCOUNT P8685xxxx
setenv queue economy
setenv timewall 0:20
@@ -220,7 +204,7 @@
# VAR is the shell variable name, DIR is the value
# ==============================================================================
-foreach VAR ( stagedir cesmroot dartroot )
+foreach VAR ( cesmroot dartroot stagedir )
set DIR = `eval echo \${$VAR}`
if ( ! -d $DIR ) then
echo "ERROR: directory '$DIR' not found"
Modified: DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial
===================================================================
--- DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial 2013-08-12 17:36:20 UTC (rev 6395)
+++ DART/trunk/models/CESM/shell_scripts/CESM1_1_1_hybrid_initial 2013-08-12 17:51:26 UTC (rev 6396)
@@ -50,37 +50,43 @@
# data volume is quite large and you should become comfortable using CESM's restart
# capability to re-stage files in your RUN directory
#
-# To perform assimilation, it is required only to insert a few dozen lines into the
-# CASEROOT/*.run script. This, and the required setup, is performed in
-# CESM_DART_config - which can be run at a later date. e.g. you can use this
-# script to advance this 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 24 hours,
-# and start assimilating observationg at midnight from 2004-02-01 on ...
+# CASEROOT/CESM_DART_config will augment the CESM case with the required setup
+# and configuration to perform a DART assimilation. CASEROOT/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 assimilating 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 set up the script
+# How to use this script.
# ---------------------
#
-# -- Either edit and run this script in the $DART/models/CESM/shell_scripts
-# directory where it first appears,
+# -- 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 multi-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 'case' directory, where the model will be built,
-# and an execution directory, where each forecast and assimilation will
+# It will create a CESM 'CASE' directory, where the model will be built,
+# and an execution directory, where each forecast (and assimilation) will
# take place. The short term archiver will use a third directory for
# storage of model output until it can be moved to long term storage (HPSS)
+#
# -- Examine the whole script to identify things to change for your experiments.
-# -- Provide any initial files needed by your run:
-# inflation
-# sampling error correction
-# CESM initial ensemble
-# ...
+#
+# -- Provide the CESM initial ensemble needed by your run.
+#
# -- Run this script.
-# -- Edit the DART input.nml that appears in the $CASEROOT directory.
-# -- Submit the job using $CASEROOT/${case}.submit
#
+# -- If you want to run DART, read and understand ${CASEROOT}/CESM_DART_config
+#
+# -- Submit the job using ${CASEROOT}/${CASE}.submit
+#
# ---------------------
# Important features
# ---------------------
@@ -106,7 +112,7 @@
# script names; so consider it's length and information content.
# num_instances: Number of ensemble members
-setenv case cesm_assim2
+setenv case cesm_multi
setenv compset B_2000_CAM5
setenv resolution 0.9x1.25_gx1v6
setenv cesmtag cesm1_1_1
@@ -164,7 +170,8 @@
# assim_n Number of time units between assimilations
#
# If the long-term archiver is off, you get a chance to examine the files before
-# you
+# 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.
#
# ==============================================================================
@@ -181,10 +188,11 @@
# queue can be changed during a series by changing the ${case}.run
# timewall can be changed during a series by changing the ${case}.run
#
-# TJH: 30 instances with 900 pes took about 30 minutes on yellowstone.
+# TJH: Advancing 30 instances for 72 hours with 900 pes
+# took about 30 minutes on yellowstone.
# ==============================================================================
-setenv ACCOUNT P86850054
+setenv ACCOUNT P8685xxxx
setenv queue economy
setenv timewall 1:00
@@ -221,7 +229,7 @@
# VAR is the shell variable name, DIR is the value
# ==============================================================================
-foreach VAR ( cesmroot dartroot )
+foreach VAR ( cesmroot dartroot RTM_stagedir CLM_stagedir CAM_stagedir POP_stagedir )
set DIR = `eval echo \${$VAR}`
if ( ! -d $DIR ) then
echo "ERROR: directory '$DIR' not found"
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