[Dart-dev] DART/branches Revision: 13022

[dart at ucar.edu]

raeder at ucar.edu
2019-03-19 09:07:39 -0600 (Tue, 19 Mar 2019)
662
Fixed number of requested nodes to account for not compressing .ha. files.
Removed creation of launch_cf.sh.  The default version works as needed.
Removed exit when a compressed version of the file already exists.
Removed excessive echos.
Defined a 'date' command that prints seconds and fractions
  for diagnosing the performance.
Removed local command MPICMD in favor of calling the default mpiexec_mpt
  with the desired number of tasks.  This prevents running 'null' tasks on the
  unclaimed MPI tasks, which return too quickly.
Better comments.

This has been reviewed and tested in the Reanalysis; 
f.e21.FHIST_BGC.f09_025.CAM6assim.001  (Jan-June 2017).




Modified: DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/compress.csh
===================================================================
--- DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/compress.csh	2019-03-19 15:03:58 UTC (rev 13021)
+++ DART/branches/recam/models/cam-fv/shell_scripts/cesm2_1/compress.csh	2019-03-19 15:07:39 UTC (rev 13022)
@@ -9,46 +9,51 @@
 #PBS  -N compress.csh
 #PBS  -A P86850054
 #PBS  -q premium
-#PBS  -l select=16:ncpus=36:mpiprocs=36
+# For restarts:
+# #PBS  -l select=9:ncpus=36:mpiprocs=36
+# For hist: 6 * 80         = 480
+# For dart: 1 + 2*(2 + 80) = 165  
+#                            645 / 36 = 18
+# For rest: 4 * 80         = 320 / 36 =  9
+#PBS  -l select=18:ncpus=36:mpiprocs=36
 #PBS  -l walltime=00:20:00
-#PBS  -o compress_2010-07-17-21600.out
+#PBS  -o compress.out
 #PBS  -j oe 
 
-# -------------------------
-# Purpose
-
-# (De)Compress files from the forecast or assimilation. 
-
-# -------------------------
-# Method
-
-# This script can compress as well as decompress sets of files.
+# ------------------------------------------------------------------------------
+# Purpose:
+#
+# compresses or uncompresses sets of files from a forecast or assimilation.
+#
+# ------------------------------------------------------------------------------
+#
+# Method:
+#
 # When called from a script (normally assimilate.csh), it compresses the files.
-# When called from the command line, it can uncompress sets of files,
-# if this script has been edited to use the right metadata to
+# When submitted as a batch job, it can also uncompress sets of files -  
+# IF this script has been configured to use the right metadata to
 # construct the expected data directories.
-
-# It operates on all files in parallel using the "command file" mechanism.
-# The file contains a separate task on each line.
-# It has syntax appropriate for the launch script (below), 
-# which may not be the same as this script.  This must include
-# syntax to put stderr and stdout in a single file, e.g. ( &> ) for bash.
-# It is dispatched by the local MPI script to perform N simultaneous operations. 
-
-# Compression method can depend on the file type, and may include lossy compression.
-# It is most often called by assimilate.csh, but can be run as a batch job.
+#
+# The strategy is to create a cmdfile that contains a separate task on each line
+# and dispatch that cmdfile to perform N simultaneous operations. That cmdfile
+# has a syntax ( &> ) to put stderr and stdout in a single file.
+# PBS requires 'setenv MPI_SHEPHERD true' for the cmdfile to work correctly.
+#
+# Compression method can depend on the file type, and in the future may include 
+# lossy compression. This script is most often called by assimilate.csh, but can 
+# be run as a batch job.
+#
 # Assimilate.csh runs this in 2 places:
 # 1) Every cycle: 
 #    +  all the cpl history (forcing) files.
 #    +  DART output
 #       >  stages of state files  
-#             mean, sd  (no inst)
-#       >  obs_seq.final (no inst)   70% of 1 Gb in 35 sec
-#       >  not inflations (no inst)  
-# 1) Before archiving a restart set to archive/rest; all large restart files.
+#             mean, sd  (no instance number)
+#       >  obs_seq.final (no instance number)
+#       >  Note: inflation files are never compressed.
+# 2) Before archiving a restart set to archive/rest; all large restart files.
+# ------------------------------------------------------------------------------
 
-# -------------------------
-
 if ($#argv == 5) then
    # Called from assimilate.csh (or other script).
    set comp_cmd      = 'gzip'
@@ -61,6 +66,7 @@
 
 else if ($#argv == 0) then
    # Edit these and run as a batch job.
+   # 'sets' performs better when ordered by decreasing size (clm2 cpl cam cice hist dart)
    set comp_cmd      = 'gunzip'
    set case_name     = CESM2_1_80_3node
    set ymds          = 2010-07-17-64800
@@ -68,19 +74,33 @@
    set sets          = (hist dart)
    # set sets          = (clm2 cpl cam cice)
    set stages        = (preassim output)
-   set data_dir      = /gpfs/fs1/scratch/raeder/${case_name}/run
-   # set data_dir      = /gpfs/fs1/scratch/raeder/${case_name}/archive/rest/2010-07-15-00000
+   # set data_dir      = /glade/scratch/${USER}/${case_name}/archive/rest/${ymds}
+   set data_dir      = /glade/scratch/${USER}/${case_name}/run