Merge pull request #396 from NCAR/clm_shell_scripts

Fixing dtlimit and single instance bug for clm shell scripts
NCAR · Sep 16, 2022 · a456bf2 · a456bf2
2 parents cb9cb51 + 938c865
commit a456bf2
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -22,6 +22,14 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**September 16 2022 :: Bug-fix for CLM shell scripts. Tag: v10.3.2**
+
+- Fixes dtlimit bug in cesm2.2 CLM shell scripts.  Loads all CAM
+  reanalysis files within datm data stream file regardless if it
+  is single year or multi-year run.
+- Fixes single instance bug in cems2.2 CLM shell scripts. Allows
+  for freerun scripts to generate single instance simulations.
+
 **September 14 2022 :: Bug-fix for POP shell scripts. Tag: v10.3.1**
 
 - Fixes bug in POP CESM2.1 shell scripts in which inflation files were not

diff --git a/conf.py b/conf.py
@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.3.1'
+release = '10.3.2'
 master_doc = 'README'
 
 # -- General configuration ---------------------------------------------------

diff --git a/models/clm/shell_scripts/cesm2_2/CLM5_hybrid_freerun b/models/clm/shell_scripts/cesm2_2/CLM5_hybrid_freerun
@@ -89,6 +89,15 @@ ${REMOVE} ${rundir}
 
 echo " Starting create_newcase ..."
 
+if (${num_instances} == 1) then
+${cesmroot}/cime/scripts/create_newcase  --res  ${resolution} \
+                                         --mach ${machine} \
+                                         --compset ${compset} \
+                                         --case ${caseroot} \
+                                         --project ${project} \
+                                         --run-unsupported || exit 2
+else
+
 ${cesmroot}/cime/scripts/create_newcase  --res  ${resolution} \
                                          --mach ${machine} \
                                          --compset ${compset} \
@@ -98,6 +107,9 @@ ${cesmroot}/cime/scripts/create_newcase  --res  ${resolution} \
                                          --ninst ${num_instances} \
                                          --multi-driver || exit 2
 
+endif
+
+
 # ==============================================================================
 # Preserve a copy of this script and the parameter file as it was run.
 # Copy the DART setup script (CESM_DART_config) to CASEROOT.
@@ -241,46 +253,42 @@ endif
 ./xmlchange INFO_DBUG=0
 
 # ==============================================================================
-# If the experiment only spans one year, copy a stream template for a single year
-# otherwise, use 'all' the years.
-
-if (${stream_year_first} == ${stream_year_last}) then
-   set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_single_year
-   set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_single_year
-   set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_single_year
-   set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year
-else
+# Use the stream template that has all CAM reanalysis years available.
+
    set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_complete
    set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_complete
    set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_complete
    set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete
-endif
 
 # ==============================================================================
 # Modify namelist templates for each instance.
 
 @ inst = 1
 while ( $inst <= $num_instances )
-
-   set inst_string = `printf %04d $inst`
-
+
+   if (${num_instances} == 1) then
+      set inst_string = '' 
+   else
+      set inst_string = `printf _%04d $inst`
+      set inst_string2 = `printf %04d $inst`
+   endif
    # ===========================================================================
-   set fname = "user_nl_datm_${inst_string}"
+   set fname = "user_nl_datm${inst_string}"
    # ===========================================================================
    # DATM namelist
 
-   set FILE1 = datm.streams.txt.CPLHISTForcing.Solar_${inst_string}
-   set FILE2 = datm.streams.txt.CPLHISTForcing.State1hr_${inst_string}
-   set FILE3 = datm.streams.txt.CPLHISTForcing.State3hr_${inst_string}
-   set FILE4 = datm.streams.txt.CPLHISTForcing.nonSolarFlux_${inst_string}
+   set FILE1 = datm.streams.txt.CPLHISTForcing.Solar${inst_string}
+   set FILE2 = datm.streams.txt.CPLHISTForcing.State1hr${inst_string}
+   set FILE3 = datm.streams.txt.CPLHISTForcing.State3hr${inst_string}
+   set FILE4 = datm.streams.txt.CPLHISTForcing.nonSolarFlux${inst_string}
    set DOMAINFILE = '/glade/p/cesmdata/cseg/inputdata/share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc'
 
    echo "domainfile = '${DOMAINFILE}'" >> ${fname}
    echo "streams = '$FILE1 $stream_year_align $stream_year_first $stream_year_last',"  >> ${fname}
    echo "          '$FILE2 $stream_year_align $stream_year_first $stream_year_last',"  >> ${fname}
    echo "          '$FILE3 $stream_year_align $stream_year_first $stream_year_last',"  >> ${fname}
    echo "          '$FILE4 $stream_year_align $stream_year_first $stream_year_last',"  >> ${fname}
-   echo "          'datm.streams.txt.presaero.clim_2000_${inst_string} 2000 2000 2000'" >> ${fname}
+   echo "          'datm.streams.txt.presaero.clim_2000${inst_string} 2000 2000 2000'" >> ${fname}
    echo "vectors  = 'u:v' "     >> ${fname}
    echo "mapmask  = 'nomask', " >> ${fname}
    echo "           'nomask', " >> ${fname}
@@ -290,9 +298,6 @@ while ( $inst <= $num_instances )
    echo "           'linear', " >> ${fname}
    echo "           'linear', " >> ${fname}
    echo "           'nearest' " >> ${fname}
-   if ($startdate == 2011-01-01) then
-      echo "dtlimit = 1.0e30"   >> ${fname}
-   endif
 
    # Create stream files for each ensemble member
    set SOURCEDIR = ${dartroot}/models/clm/shell_scripts/cesm2_2
@@ -301,15 +306,24 @@ while ( $inst <= $num_instances )
    ${COPY} ${SOURCEDIR}/${STREAMFILE_STATE3HR}      user_${FILE3} || exit 5
    ${COPY} ${SOURCEDIR}/${STREAMFILE_NONSOLARFLUX}  user_${FILE4} || exit 5
 
-   foreach FNAME ( user_datm.streams.txt*${inst_string} )
-      echo "modifying $FNAME"
-      sed s/NINST/${inst_string}/g $FNAME >! temp
-      sed s/RUNYEAR/${stream_year_first}/g temp >! $FNAME
-   end
+
+   if (${num_instances} == 1) then
+     foreach FNAME ( user_datm.streams.txt* )
+        echo "modifying $FNAME"
+        sed s/NINST/0001/g $FNAME >! temp
+        sed s/RUNYEAR/${stream_year_first}/g temp >! $FNAME
+     end
+   else
+     foreach FNAME ( user_datm.streams.txt*${inst_string} )
+        echo "modifying $FNAME"
+        sed s/NINST/${inst_string2}/g $FNAME >! temp
+        sed s/RUNYEAR/${stream_year_first}/g temp >! $FNAME
+     end
+   endif
    ${REMOVE} temp
 
    # ===========================================================================
-   set fname = "user_nl_clm_${inst_string}"
+   set fname = "user_nl_clm${inst_string}"
    # ===========================================================================
 
    # This is the opportunity to output additional items at your own discretion.
@@ -333,14 +347,14 @@ while ( $inst <= $num_instances )
 
 
    # ===========================================================================
-   set fname = "user_nl_mosart_${inst_string}"
+   set fname = "user_nl_mosart${inst_string}"
    # ===========================================================================
 
    # We are explicitly constructing the 'finidat_rtm' to match what is getting
    # staged by the 'stage_cesm_files' script
    # If this file is not available or you do not want stage this file set finidat_rtm = ' '.
 
-   echo "finidat_rtm = '"${refcase}.mosart_${inst_string}.r.${reftimestamp}.nc"'" >> ${fname}
+   echo "finidat_rtm = '"${refcase}.mosart${inst_string}.r.${reftimestamp}.nc"'" >> ${fname}
 
 @ inst ++
 end
@@ -438,8 +452,12 @@ if ( \${CONTINUE_RUN} == TRUE ) then
       @ inst=1
       while (\$inst <= $num_instances)
 
-         set inst_string = \`printf _%04d \$inst\`
-
+         if ( \${num_instances} == 1) then
+	   set inst_string = ''
+	 else
+           set inst_string = \`printf _%04d \$inst\`
+         endif
+	 
          echo "\${CASE}.cpl\${inst_string}.r.\${restart_time}.nc"    >! rpointer.drv\${inst_string}
          echo "\${CASE}.clm2\${inst_string}.r.\${restart_time}.nc"   >! rpointer.lnd\${inst_string}
          echo "\${CASE}.datm\${inst_string}.r.\${restart_time}.nc"   >! rpointer.atm\${inst_string}
@@ -468,21 +486,30 @@ else     # CONTINUE_RUN == FALSE
 
    @ inst=1
    while (\$inst <= $num_instances)
+     
+      if ( \${num_instances} == 1) then
+         set inst_string = \`printf _%04d \$inst\`   
+         set inst_string2 = ''
+      else
+         set inst_string = \`printf _%04d \$inst\`
+         set inst_string2 = \`printf _%04d \$inst\`
+      endif
 
-      set inst_string = \`printf _%04d \$inst\`
 
       echo "Staging initial files for instance \$inst of $num_instances"
 
       if ( -e    ${stagedir}/${refcase}.clm2\${inst_string}.r.${init_time}.nc ) then
-         ${LINK} ${stagedir}/${refcase}.clm2\${inst_string}.r.${init_time}.nc .
+         ${LINK} ${stagedir}/${refcase}.clm2\${inst_string}.r.${init_time}.nc \
+                             ${refcase}.clm2\${inst_string2}.r.${init_time}.nc
       else
          echo "ERROR: ${stagedir}/${refcase}.clm2\${inst_string}.r.${init_time}.nc does not exist."
          echo "       Check your 'reftimestamp' setting, or maybe your 'stagedir' or 'refcase' or ..."
          exit 8
       endif
 
       if ( -e    ${stagedir}/${refcase}.mosart\${inst_string}.r.${init_time}.nc ) then
-         ${LINK} ${stagedir}/${refcase}.mosart\${inst_string}.r.${init_time}.nc .
+         ${LINK} ${stagedir}/${refcase}.mosart\${inst_string}.r.${init_time}.nc \
+                             ${refcase}.mosart\${inst_string2}.r.${init_time}.nc
       else
          echo "WARNING: ${stagedir}/${refcase}.mosart\${inst_string}.r.${init_time}.nc does not exist."
          echo "       Check your 'reftimestamp' setting, or maybe your 'stagedir' or 'refcase' or ..."

diff --git a/models/clm/shell_scripts/cesm2_2/CLM5_setup_assimilation b/models/clm/shell_scripts/cesm2_2/CLM5_setup_assimilation
@@ -230,20 +230,12 @@ endif
 ./xmlchange INFO_DBUG=0
 
 # ==============================================================================
-# If the experiment only spans one year, copy a stream template for a single year
-# otherwise, use 'all' the years.
-
-if (${stream_year_first} == ${stream_year_last}) then
-   set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_single_year
-   set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_single_year
-   set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_single_year
-   set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year
-else
+# Use the stream template that has all CAM reanalysis years available.
+
    set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_complete
    set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_complete
    set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_complete
    set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete
-endif
 
 # ==============================================================================
 # Modify namelist templates for each instance.
@@ -284,9 +276,6 @@ while ( $inst <= $num_instances )
    echo "           'linear', " >> ${fname}
    echo "           'linear', " >> ${fname}
    echo "           'nearest' " >> ${fname}
-   if ($startdate == 2011-01-01) then
-      echo "dtlimit = 1.0e30"   >> ${fname}
-   endif
 
    # Create stream files for each ensemble member
    set SOURCEDIR = ${dartroot}/models/clm/shell_scripts/cesm2_2

diff --git a/models/clm/shell_scripts/cesm2_2/CLM5_setup_pmo b/models/clm/shell_scripts/cesm2_2/CLM5_setup_pmo
@@ -224,20 +224,12 @@ endif
 ./xmlchange INFO_DBUG=0
 
 # ==============================================================================
-# If the experiment only spans one year, copy a stream template for a single year
-# otherwise, use 'all' the years.
-
-if (${stream_year_first} == ${stream_year_last}) then
-   set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_single_year
-   set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_single_year
-   set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_single_year
-   set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year
-else
+# Use the stream template that has all CAM reanalysis years available.
+
    set STREAMFILE_SOLAR        = datm.streams.txt.CPLHISTForcing.Solar_complete
    set STREAMFILE_STATE1HR     = datm.streams.txt.CPLHISTForcing.State1hr_complete
    set STREAMFILE_STATE3HR     = datm.streams.txt.CPLHISTForcing.State3hr_complete
    set STREAMFILE_NONSOLARFLUX = datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete
-endif
 
 # ==============================================================================
 # Modify namelist templates for each instance.
@@ -285,9 +277,6 @@ while ( $inst <= $num_instances )
    echo "           'linear', " >> ${fname}
    echo "           'linear', " >> ${fname}
    echo "           'nearest' " >> ${fname}
-   if ($startdate == 2011-01-01) then
-      echo "dtlimit = 1.0e30"   >> ${fname}
-   endif
 
    # Create stream files for each ensemble member
    set SOURCEDIR = ${dartroot}/models/clm/shell_scripts/cesm2_2