[Dart-dev] DART/branches Revision: 13024

[dart at ucar.edu]

raeder at ucar.edu
2019-03-19 14:34:38 -0600 (Tue, 19 Mar 2019)
1104
This is an anonymized, slightly pared down version of setup_advanced_test,
which was used in the Reanalysis (f.e21.FHIST_BGC.f09_025.CAM6assim.001)
(Jan-June 2017).
Replaced user-defined rundir and exedir by cime_output, which will define them.
Improved comment about ...TASKS_PER_NODE
Local system commands no longer have arguments (-f and -v).
   Those arguments are given, as needed, when the commands are used.
   Removed the variables that controlled verbose output (REMOVEV, COPYV).
Rearranged small sections to improve grouping of similar tasks
Generalized the mechanism for managing the component characteristics;
  COMP_$comp, CAM_CONFIG_OPTS.
Simplified task layout by specifying number of whole nodes, instead of tasks.
Removed references to Reanalyis project and writing couple history files.
Use a 'here' file to write out CESM instructions at the end, instead of echoes
Removed spurious, end of line spaces.

Many of these changes were prompted by a review, but some have been
implemented since.  This exact version was minimally tested by case Test_merged2,
a 3 member, SEC assimilation.




Modified: DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/setup_advanced
===================================================================
--- DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/setup_advanced	2019-03-19 19:54:42 UTC (rev 13023)
+++ DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/setup_advanced	2019-03-19 20:34:38 UTC (rev 13024)
@@ -9,7 +9,7 @@
 # This script can be run interactively, but on some systems (e.g. cheyenne)
 # it takes longer than is allowed for an interactive job.
 # In that case, it can be run as a batch job using the directives below,
-# or using a command like qcmd.
+# or using "qcmd -q share -l select=1 -- <thisfilename>".
 # The job name should be the name of this script(file), 
 # or this file may not be archived in $caseroot causing DART_config to fail.
 #--------------------------------------------
@@ -28,23 +28,31 @@
 #PBS  -N setup_advanced
 #PBS  -A P86850054
 #PBS  -q share
+#
+# Resources to specify:
+#    select=#nodes
+#    ncpus=#CPUs/node
+#    mpiprocs=#MPI_tasks/node
 #PBS  -l select=1:ncpus=4:mpiprocs=4
 #PBS  -l walltime=01:00:00
 #PBS  -m ae
+#PBS  -M you at email.org
+# Send standard output and error to this file.
+# It's helpful to use the $casename here.
+#PBS  -o Test_0.bld1
 #PBS  -j oe 
-#PBS  -o Debug_80_layout_36x1.bld1
 #
-#--------------------------------------------
+# ---------------------
 # Purpose
-#--------------------------------------------
+# ---------------------
 #
-# This script is designed to set up, stage, and build a multi-instance, 
-# multi-driver, CESM using an F compset, where CAM-FV, CLM and CICE are active. 
-# In contrast to setup_hybrid, it also sets up the environment for doing 
+# This script is designed to set up, stage, and build a multi-instance,
+# multi-driver, CESM using an F compset, where CAM-FV, CLM and CICE are active.
+# In contrast to setup_hybrid, it also sets up the environment for doing
 # a CAM assimilation by setting up and running DART_config.
-# It is intended to be used after you have tested the basic set up 
+# It is intended to be used after you have tested the basic set up
 # of CESM and DART for your case, using setup_hybrid and DART_config.
-# It also provides more mechanisms for optimizing the assimilation 
+# It also provides more mechanisms for optimizing the assimilation
 # for scientific studies.
 #
 # Because the atmosphere assimilations typically occur every 6 hours,
@@ -53,7 +61,7 @@
 #
 # ${caseroot}/DART_config is automatically run by this script and will
 # augment the CESM case with the required setup and configuration to use DART
-# to perform an assimilation. 
+# to perform an assimilation.
 #
 # ---------------------
 # How to use this script.
@@ -71,10 +79,10 @@
 #    It archives itself to the $caseroot directory during its execution.
 #
 # -- Locate or create the initial ensemble files that CESM will need.
-#    The initial ensemble can come from a single- or multi-instance reference case. 
+#    The initial ensemble can come from a single- or multi-instance reference case.
 #
 # -- DOCN: The compsets required by this script use a single data ocean.
-#    This script can use a daily, 1/4 degree resolution, ocean data set, 
+#    This script can use a daily, 1/4 degree resolution, ocean data set,
 #    in place of the monthly, 1 or 2 degree set.
 #
 # -- Run this script. When it is executed, it will create:
@@ -84,16 +92,16 @@
 #    4) CESM's short term archiver (st_archive) will use a fourth directory for
 #    storage of model output until it can be moved to long term storage (HPSS)
 #
-#    This script also executes ${caseroot}/DART_config which augments the case 
+#    This script also executes ${caseroot}/DART_config which augments the case
 #    with all the pieces necessary to run DART in the first job.
 #    Read the instructions in that file too.
 #
 # -- Confirm the variable values in $caseroot/env_{build,run,batch,...}.xml.
-# 
+#
 # -- (if running DART) Edit the DART input.nml that appears in the ${caseroot}
 #    directory to replace default values with your preferred values.
 #
-# -- Submit the job using ${caseroot}/case.submit
+# -- Submit the job using ${caseroot}/case.submit -M begin,end
 #
 # ---------------------
 # Important features
@@ -105,7 +113,7 @@
 #
 # https://ncar.github.io/CAM/doc/build/html/users_guide/index.html
 # --> https://ncar.github.io/CAM/doc/build/html/users_guide/building-and-running-cam.html
-#    --> http://esmci.github.io/cime/users_guide/building-a-case.html 
+#    --> http://esmci.github.io/cime/users_guide/building-a-case.html