update GSI for GEOS-IT config; minor script adjustments merging 5.27.…

components.yaml

@@ -46,7 +46,7 @@ FMS:
 GEOSana_GridComp:
   local: ./src/Components/@GEOSana_GridComp
   remote: ../GEOSana_GridComp.git
-  tag: v1.5.2
+  tag: v1.5.3
   develop: develop
 
 GEOSgcm_GridComp:

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -177,6 +177,12 @@
 
 #_RT  if ( !($?STAGE4FCST) )    setenv STAGE4FCST  0   # need to resolve redundancies
 
+# Sanity setting
+# --------------
+  if ( $SKIPANA ) then
+       setenv ASYNBKG   360
+  endif
+
   if ( $?RUN_OPT_BEGIN ) then
         set run_opt_begin = ( $RUN_OPT_BEGIN ) 
   else 
@@ -445,7 +451,7 @@ exit 1
 # Cannot do GAASFDBK unless GAAS_ANA is on 
 # ----------------------------------------
   if ( ! $FORECAST ) then
-     if ( $GAAS_ANA && ( ! $GAASFDBK ) ) then
+     if ( $GAASFDBK && ( ! $GAAS_ANA ) ) then
        echo $myname": GAAS inconsistency, GAASFDBK=$GAASFDBK, GAAS_ANA=$GAAS_ANA"
        exit 1
      endif
@@ -495,6 +501,7 @@ exit 1
 # -----------------------------------------------------
   if ( !($?obsclass) && !($?req_obsclass) ) then
         setenv SKIPANA 1   # no ANALYSIS
+        setenv ASYNBKG 360
   endif
 
 # For readability, introduce DOING_ANA
@@ -4187,7 +4194,12 @@ endif
      setenv NCPUS_AOD 1
   endif
 
-  @ xtra = $NCPUS - $NCPUS_GSI
+  if ( $?SLURM_CPUS_ON_NODE && $?SLURM_JOB_NUM_NODES ) then
+     @ total_cpus_slurm = $SLURM_CPUS_ON_NODE * $SLURM_JOB_NUM_NODES
+     @ xtra = $total_cpus_slurm - $NCPUS_GSI
+  else
+     @ xtra = $NCPUS - $NCPUS_GSI
+  endif
 
   if ($xtra < $NCPUS_AOD) then
      setenv aod_parallel_flag 0
@@ -5742,6 +5754,11 @@ endif
   if ( $FORECAST ) then
        /bin/rm d_rst
        mkdrstdate.x $fcst_end    # create d_rst with current date and time
+  else if ( $SKIPANA ) then
+        set GcmEndDate = $GcmEndEpoch[1]
+        set GcmEndTime = $GcmEndEpoch[2]
+       /bin/rm d_rst
+       mkdrstdate.x $GcmEndDate $GcmEndTime
   endif
 
   set buf  = `rst_date d_rst`

src/Applications/GEOSdas_App/fvsetup

@@ -595,6 +595,7 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
     . " -expid $expid"
     . " -fvhome $fvhome"
     . " -fvroot $fvroot"
+    . " -nodeflg $nodeflg"
     . " -res $res";
   $cmd .= " -gid $gid" if $gid;
   print "$cmd\n";

src/Applications/GEOSdas_App/gen_silo_arc.pl

@@ -341,6 +341,7 @@ sub append_other_info {
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.ana.obs.%y4%m2%d2.ods
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.ana.obs.%y4%m2%d2_%h2z.ods
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.prepbufr.%y4%m2%d2.t%h2z.blk
+\${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.acft_profl.%y4%m2%d2.t%h2z.bfr
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.gmao_global_satinfo.%y4%m2%d2_%h2z.txt
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.gmao_global_ozinfo.%y4%m2%d2_%h2z.txt
 \${PESTOROOT}%s/obs/Y%y4/M%m2/D%d2/H%h2/%s.sac.nl.%y4%m2%d2_%h2z.txt

src/Applications/GEOSdas_App/monthly.yyyymm.pl.tmpl

@@ -49,6 +49,7 @@ BEGIN {
 }
 use lib "$fvroot/bin";
 use GMAO_utils qw(get_siteID);
+use Manipulate_time qw(get_htype token_resolve);
 use Perl_Config qw(perl_config);
 use WriteLog qw(chdir_ mkpath_ unlink_ system_);
 
@@ -239,6 +240,7 @@ sub init {
         $walltime_pf = "2:00:00";
         $numnodes_mm = 6;
     }
+    $walltime_mm = "1:00:00" if $qos eq "debug";
     $walltime_mp = "1:00:00";
     $numnodes_mp = 1;
 
@@ -287,7 +289,7 @@ sub fetch_calc_tar_and_clean {
     my (%opts, $MMWORK, $filestring, $lastFLG);
     my (@fetchArr, $processflags);
     my ($max, $label, $num, $job_tarfile, @list);
-    my ($fileToken, @parts, %ftype, %htype, $ftype, $htype);
+    my ($fileToken, $fileTemplate, @parts, %ftype, %htype, $ftype, $htype);
     my (%doFetch, %doTar);
 
     # check for existence of work directory
@@ -325,10 +327,7 @@ sub fetch_calc_tar_and_clean {
 
         # get $htype from $ftype, unless alternate htype value given
         #-----------------------------------------------------------
-        unless ($htype) {
-            if ($ftype =~  /\./) { $htype = $ftype }
-            else                 { $htype = (split(/_/, $ftype))[0] }
-        }
+        $htype = get_htype($ftype) unless $htype;
 
         $ftype{$filestring} = $ftype;
         $htype{$filestring} = $htype;
@@ -351,11 +350,14 @@ sub fetch_calc_tar_and_clean {
     #-------------------------------------
     $lastFLG = 0;
     foreach $filestring (@fetchArr) {
+        $fileToken = basename($filestring);
+        $fileTemplate = token_resolve($fileToken, $yyyymm);
 
         %opts = ();
         $opts{"filestring"} = $filestring;
         $opts{"ftype"} = $ftype{$filestring};
         $opts{"htype"} = $htype{$filestring};
+        $opts{"fileTemplate"} = $fileTemplate;
 
         $opts{"do_dmput"} = 1;
         $opts{"do_dmput"} = 0 if $doTar{$filestring}; 
@@ -456,6 +458,7 @@ sub fetch_inputs {
     $value{"__RUNDIR__"}     = $rundir;
     $value{"__WORKDIR__"}    = $workdir;
     $value{"__DO_DMPUT__"}   = $do_dmput;
+    $value{"__DO_SKIP_CHK__"}   = 0;
     $value{"__DO_TAR__"}     = $do_tar;
 
     replaceLabels($tmpl, $prefetch_j, %value);
@@ -546,6 +549,7 @@ sub calc_monthly_means {
     $value{"__RUNDIR__"}     = $rundir;
     $value{"__WORKDIR__"}    = $workdir;
     $value{"__DO_DMPUT__"}   = $do_dmput;
+    $value{"__DO_SKIP_CHK__"}   = 1;
 
     replaceLabels($tmpl, $means_j, %value);
 
@@ -574,7 +578,7 @@ sub calc_monthly_means {
 # => $lastFLG: flag indicating whether this is last data collection
 #=======================================================================
 sub tar_and_clean_inputs {
-    my (%opts, $filestring, $ftype, $do_tar, $lastFLG);
+    my (%opts, $filestring, $fileTemplate, $ftype, $do_tar, $lastFLG);
     my ($tmpl, $tarandclean_j, $jobname, $outfile);
     my ($job_name, $time, $output, $parFLG, $vFLG);
     my ($constraint);
@@ -583,10 +587,11 @@ sub tar_and_clean_inputs {
     # input arguments
     #----------------
     %opts = @_;
-    $filestring = $opts{"filestring"};
-    $ftype      = $opts{"ftype"};
-    $do_tar     = $opts{"do_tar"};
-    $lastFLG    = $opts{"lastFLG"};
+    $filestring   = $opts{"filestring"};
+    $fileTemplate = $opts{"fileTemplate"};
+    $ftype        = $opts{"ftype"};
+    $do_tar       = $opts{"do_tar"};
+    $lastFLG      = $opts{"lastFLG"};
 
     # create tarandclean job script
     #-------------------------------
@@ -621,12 +626,13 @@ sub tar_and_clean_inputs {
     $value{"__PARTITION__"}  = $parFLG;
     $value{"__CONSTRAINT__"} = $constraint;
 
-    $value{"__FILESTRING__"} = $filestring;
-    $value{"__YYYYMM__"}     = $yyyymm;
-    $value{"__RUNDIR__"}     = $rundir;
-    $value{"__WORKDIR__"}    = $workdir;
-    $value{"__DO_TAR__"}     = $do_tar;
-    $value{"__LASTFLG__"}    = $lastFLG;
+    $value{"__FILESTRING__"}    = $filestring;
+    $value{"__FILETEMPLATE__"}  = $fileTemplate;
+    $value{"__YYYYMM__"}        = $yyyymm;
+    $value{"__RUNDIR__"}        = $rundir;
+    $value{"__WORKDIR__"}       = $workdir;
+    $value{"__DO_TAR__"}        = $do_tar;
+    $value{"__LASTFLG__"}       = $lastFLG;
 
     replaceLabels($tmpl, $tarandclean_j, %value);
 
@@ -659,7 +665,7 @@ sub archive_monthly_keep_files {
 
     # command flags
     #--------------
-    $outfile = "$listdir/$EXPID.KEEParc.$yyyymm.log.$$.txt.FAILED";
+    $outfile = "$listdir/$EXPID.KEEParc.$yyyymm.log.$$.txt";
     $vars = "arch_type=MKEEP,"
         .   "arch_date=$yyyymm,"
         .   "outfile=$outfile";
@@ -721,7 +727,7 @@ sub archive_monthly_files {
 
     # command flags
     #--------------
-    $outfile = "$listdir/$EXPID.MPParc.$yyyymm.log.$$.txt.FAILED";
+    $outfile = "$listdir/$EXPID.MPParc.$yyyymm.log.$$.txt";
     $vars = "arch_type=MNTHLY,"
         .   "arch_date=$yyyymm,"
         .   "outfile=$outfile,"

src/Applications/GEOSdas_App/monthly_setup.pl

@@ -54,6 +54,7 @@
 #-----------------
 my ($EXPID, $FVETC, $GID, $numnodes, $scriptname, $siteID, $walltime);
 my ($rundir, $run_mp_dir, $FVHOME, $FVROOT);
+my ($thisnode);
 
 # main program
 #-------------
@@ -69,17 +70,18 @@
 # purpose - get runtime options; check environment variables
 #=======================================================================
 sub init {
-    my ($res, $hres, $help, %opts);
+    my ($res, $hres, $help, $nodeflg, %opts);
 
     $scriptname = basename($0);
     $siteID = get_siteID();
 
-    GetOptions( "expid=s"  => \$EXPID,
-                "fvhome=s" => \$FVHOME,
-                "fvroot=s" => \$FVROOT,
-                "gid=s"    => \$GID,
-                "res=s"    => \$res,
-                "h"        => \$help );
+    GetOptions( "expid=s"   => \$EXPID,
+                "fvhome=s"  => \$FVHOME,
+                "fvroot=s"  => \$FVROOT,
+                "gid=s"     => \$GID,
+                "nodeflg=s" => \$nodeflg,
+                "res=s"     => \$res,
+                "h"         => \$help );
     usage() if $help;
 
     $EXPID  = $ENV{"EXPID"} unless $EXPID;
@@ -115,6 +117,10 @@ sub init {
     if    ($siteID eq "nccs") { $walltime =  "8:00:00" }
     elsif ($siteID eq "nas")  { $walltime = "12:00:00" }
 
+    $thisnode = "hasw";
+    if ($nodeflg) {
+      $thisnode = $nodeflg;
+    }
     if ($res) {
         $hres = substr($res, 0, 1) if $res;
 
@@ -174,7 +180,7 @@ sub write_plotfiles {
     %values = ();
     $values{"\@PLOT_T"} = "12:00:00";
     $values{"\@PLOT_P"} = "SBATCH --nodes=4";
-    $values{"\@PLOT_Q"} = "SBATCH --constraint=hasw";
+    $values{"\@PLOT_Q"} = "SBATCH --constraint=$thisnode";
     $values{"\@BATCH_GROUP"} = "SBATCH --account=$GID";
     $values{"\@SITE"} = uc($siteID);
     $values{"\@GEOSBIN"} = "$FVROOT/bin";
@@ -286,6 +292,7 @@ sub usage {
   -fvhome fvhomedir   FVHOME directory location; defaults to \$ENV{"FVHOME"}
   -fvroot fvrootdir   FVROOT directory location; defaults to \$ENV{"FVROOT"}
   -gid groupid        Group ID; defaults to getsponsor.pl default
+  -nodeflg            Node flag: hasw, sky, cas (default: hasw)
   -res                Horizontal resolution of atmosphere grid
 EOF
 exit;