Feature/jstassi/#73 integrate radmon into adas 2

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -140,6 +140,7 @@
   if ( !($?LOCAL_ACQUIRE) )       setenv LOCAL_ACQUIRE 0
   if ( !($?MAP05RST) )            setenv MAP05RST      0
   if ( !($?MKRESRST ) )           setenv MKRESRST      0
+  if ( !($?MONTHLY_RADMON) )      setenv MONTHLY_RADMON 0
   if ( !($?MPIRUN_IDF) )          setenv MPIRUN_IDF    0
   if ( !($?MPIRUN_UPRST) )        setenv MPIRUN_UPRST  /dev/null
   if ( !($?NEWRADBC) )            setenv NEWRADBC      0

src/Applications/GEOSdas_App/fvsetup

@@ -514,6 +514,7 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
   if ($DAO == 0) { while3 ( \&get_mhost ) }
   while3 ( \&get_output );
   while3 ( \&get_history );
+  while3 ( \&get_pyradmon );
   while3 ( \&get_rstype );
   while3 ( \&get_GID );
 
@@ -4556,6 +4557,29 @@ sub get_GID {
     return 0;
 }
 
+#=======================================================================
+sub get_pyradmon {
+
+    #=========================================================#
+    # FOR NOW, TAKE DEFAULT RATHER THAN QUERYING FOR LOCATION #
+    #=========================================================#
+    $pyradmon = "/discover/nobackup/jstassi/GEOSadas/pyradmon";
+    return;
+    #=========================================================#
+
+    print "\n------------------------\n"
+        .   "Pyradmon Source Location\n"
+        .   "------------------------\n";
+
+    $pyradmon_dflt = "/discover/nobackup/jstassi/GEOSadas/pyradmon";
+    $pyradmon = query("\n  Pyradmon code location?", $pyradmon_dflt);
+    if (-d $pyradmon) {
+        $ENV{"PYRADMON"} = $pyradmon;
+        return;
+    }
+    return 1;
+}
+
 #=======================================================================
 sub get_dimsg5gcm {
 
@@ -5184,9 +5208,11 @@ sub secs2hhmmss {
 sub mkdir_fvhome {  # create directories on FVHOME
 
   print "\nSetting up FVHOME directory for $expid experiment ...\n";
-  foreach $dir (qw(ana diag daotovs etc obs prog rs run recycle fcst asens anasa)) {
-      mkpath("$fvhome/$dir")
-          or die ">>> ERROR <<< creating directory $fvhome/$dir;";
+  foreach $dir (qw(ana diag daotovs etc obs prog radmon)) {
+      mkpath("$fvhome/$dir") or die ">>> ERROR <<< creating directory $fvhome/$dir;";
+  }
+  foreach $dir (qw(rs run recycle fcst asens anasa)) {
+      mkpath("$fvhome/$dir") or die ">>> ERROR <<< creating directory $fvhome/$dir;";
   }
   foreach $subdir (qw( gaas gocart )) {
       mkpath("$fvhome/run/$subdir")
@@ -7313,9 +7339,10 @@ if ((\$arch_type == "ADAS") && (\$\?yyyymm) && (\$\?dd)) then
 
       # defaults
       #---------
-      if (! \$\?MONTHLY_MEANS ) set MONTHLY_MEANS = 1
-      if (! \$\?MONTHLY_TAR )   set MONTHLY_TAR   = 1
-      if (! \$\?MONTHLY_PLOTS ) set MONTHLY_PLOTS = 0
+      if (! \$\?MONTHLY_MEANS )  set MONTHLY_MEANS  = 1
+      if (! \$\?MONTHLY_TAR )    set MONTHLY_TAR    = 1
+      if (! \$\?MONTHLY_PLOTS )  set MONTHLY_PLOTS  = 0
+      if (! \$\?MONTHLY_RADMON ) set MONTHLY_RADMON = 0
 
       # create job script for monthly post processing
       #----------------------------------------------
@@ -7335,14 +7362,12 @@ if ((\$arch_type == "ADAS") && (\$\?yyyymm) && (\$\?dd)) then
           # execute job script for monthly means processing
           #------------------------------------------------
           set flags = ""
-          if (\$MONTHLY_MEANS) set flags = "\$flags -means"
-          if (\$MONTHLY_TAR)   set flags = "\$flags -tar"
-          if (\$MONTHLY_PLOTS) set flags = "\$flags -plots"
-
-          if (\$MONTHLY_MEANS || \$MONTHLY_TAR || \$MONTHLY_PLOTS) then
-              \$monthlyPost \$flags
-          endif
+          if (\$MONTHLY_MEANS)  set flags = "\$flags -means"
+          if (\$MONTHLY_TAR)    set flags = "\$flags -tar"
+          if (\$MONTHLY_PLOTS)  set flags = "\$flags -plots"
+          if (\$MONTHLY_RADMON) set flags = "\$flags -radmon \$MONTHLY_RADMON"
 
+          if (\$flags != "") \$monthlyPost \$flags
       endif  
    endif
 endif
@@ -7631,6 +7656,7 @@ print  SCRIPT <<"EOF";
   setenv MONTHLY_MEANS $monthly_means   # 1 = submit monthly means at end of month;     0 = don't
   setenv MONTHLY_TAR $monthly_tar   # 1 = submit monthly tar job at end of month;   0 = don't
   setenv MONTHLY_PLOTS $monthly_plots   # 1 = submit monthly plots job at end of month; 0 = don't
+  setenv MONTHLY_RADMON 0 # 1 = submit monthly radmon job; 2 = 2 jobs/month; 3 = 3 jobs/month; 0 = don't
   setenv NCSUFFIX $ncsuffix
   setenv STAGE4FSENS /dev/null
   setenv GAAS_ANA $gaas_ana # 1 = aerosol analysis, 0 = disables it
@@ -8412,6 +8438,10 @@ EOF
          set vars = "\$vars,MONTHLY_PLOTS=\$MONTHLY_PLOTS"
       endif
 
+      if (\$\?MONTHLY_RADMON) then
+         set vars = "\$vars,MONTHLY_RADMON=\$MONTHLY_RADMON"
+      endif
+
 #     submit archive job
 #     ------------------
       if ( \$BATCH_SUBCMD == "sbatch" ) then
@@ -9965,6 +9995,12 @@ sub copy_resources {
   $fname = "fvsavecf"; # config saving script
   $rc = system("/bin/cp $fvbin/$fname $fvhome/run/$fname");
   die "Cannot write file $fvhome/run/$fname: $!" if ( $rc );
+
+  # Copy radmon.defaults.rc file to FVHOME/radmon
+  #----------------------------------------------
+  if (-e "$pyradmon/scripts/radmon.defaults.rc") {
+      cp("$pyradmon/scripts/radmon.defaults.rc", "$fvhome/radmon");
+  }
 }
 
 #=======================================================================

src/Applications/GEOSdas_App/gen_silo_arc.pl

@@ -86,7 +86,7 @@ sub init {
     # check for needed executables and rc
     #------------------------------------
     $edhist_pl = "$fvroot/bin/edhist.pl";
-    $echorc_x = "$fvroot/bin/echorc.x";
+    $echorc_x = "$fvroot/bin/echorc.pl";
     $gsidiags_rc = "$fvroot/etc/gsidiags.rc";
 
     die "Error. Cannot find $edhist_pl;"   unless -x $edhist_pl;

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

@@ -6,6 +6,7 @@
 #           > compute monthly means
 #           > tar and clean monthly means inputs
 #           > create monthly plots
+#           > run monthly radmon plots
 # Notes:
 # 1. To use this script,
 #    - copy to experiment run directory
@@ -53,12 +54,12 @@ use WriteLog qw(chdir_ mkpath_ unlink_ system_);
 
 # global variables
 #-----------------
-my ($meansFLG, $plotsFLG, $tarFLG, $finish, $nopush, %doMeans);
-my ($EXPID, $FVHOME, $PBS_BIN, $account, $listdir, $mnthlyRC);
+my ($meansFLG, $plotsFLG, $radmonFLG, $tarFLG, $finish, $nopush, %doMeans);
+my ($EXPID, $FVHOME, $PBS_BIN, $PYRADMON, $account, $listdir, $mnthlyRC);
 my ($numnodes_mm, $numnodes_mp, $plotHISTrc, $qcmd, $rundir);
 my ($script, $siteID, $workdir, $yyyymm, %newrc, %JOBID);
 my ($walltime_cl, $walltime_mm, $walltime_mp, $walltime_pf);
-my ($partition, $qos);
+my ($partition, $qos, $runlocal);
 
 #$partition = "preops";
 #$qos = "dastest";
@@ -88,6 +89,7 @@ my %valid = ( "fetch" => 1,
         archive_monthly_keep_files();
     }
     monthly_plots() if $plotsFLG;
+    radmon() if $radmonFLG;
 }
 
 #=======================================================================
@@ -111,10 +113,14 @@ sub init {
     #-----------------------
     GetOptions( "means"        => \$meansFLG,
                 "tar"          => \$tarFLG,
+
                 "plots"        => \$plotsFLG,
                 "finish_plots" => \$finish,
                 "nopush"       => \$nopush,
 
+                "radmon:i"    => \$radmonFLG,
+                "runlocal"    => \$runlocal,
+
                 "partition=s" => \$partition,
                 "qos=s"       => \$qos,
 
@@ -125,6 +131,10 @@ sub init {
                 "h|help"   => \$help );
     usage() if $help;
 
+    if (defined($radmonFLG)) {
+        $radmonFLG = 1 if $radmonFLG < 1 or $radmonFLG > 3;
+    }
+
     # flags indicating whether to create new resource files
     #------------------------------------------------------
     if ($#newrc == 0 and $newrc[0] eq "") { $newrc[0] = "1,2" }
@@ -134,7 +144,8 @@ sub init {
         next unless m/^1$/ or m/^2$/;
         $newrc{$_} = 1;
     }
-    usage() unless $meansFLG or $tarFLG or $plotsFLG or $finish or %newrc;
+    usage() unless $meansFLG or $tarFLG or $plotsFLG or $finish
+        or $radmonFLG or %newrc;
 
     # process options
     #----------------
@@ -153,10 +164,11 @@ sub init {
     $opts{"debug"} = $debug if $debug;
     perl_config(%opts);
 
-    $EXPID   = $ENV{"EXPID"};
-    $FVHOME  = $ENV{"FVHOME"};
-    $PBS_BIN = $ENV{"PBS_BIN"};
-    $GID     = $ENV{"GID"};
+    $EXPID    = $ENV{"EXPID"};
+    $FVHOME   = $ENV{"FVHOME"};
+    $PBS_BIN  = $ENV{"PBS_BIN"};
+    $PYRADMON = $ENV{"PYRADMON"};
+    $GID      = $ENV{"GID"};
 
     $ENV{"PATH"} = "$rundir:$fvroot/bin:$ENV{PATH}";
 
@@ -870,6 +882,43 @@ sub finish_monthly_plots {
     }
 }
 
+#=======================================================================
+# name - radmon
+# purpose - run pyradmon code
+#=======================================================================
+sub radmon {
+    my ($qFLG, $flags, $pyflags, $radmonRC);
+
+    $qFLG = "";
+    $qFLG = "-qjobs" unless $runlocal;
+    $flags = "-expid $EXPID -fvhome $FVHOME -np $qFLG";
+
+    $radmonRC = "$FVHOME/radmon/radmon.defaults.rc";
+    $radmonRC = "" unless -e $radmonRC;
+
+    if ($radmonFLG == 1) {
+        $pyflags = $flags ." -startdate ${yyyymm}01";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+    }
+    elsif ($radmonFLG == 2) {
+        $pyflags = $flags ." -startdate ${yyyymm}01 -enddate ${yyyymm}15";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+
+        $pyflags = $flags ." -startdate ${yyyymm}16";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+    }
+    elsif ($radmonFLG == 3) {
+        $pyflags = $flags ." -startdate ${yyyymm}01 -enddate ${yyyymm}10";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+
+        $pyflags = $flags ." -startdate ${yyyymm}11 -enddate ${yyyymm}20";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+
+        $pyflags = $flags ." -startdate ${yyyymm}21";
+        system("$PYRADMON/scripts/pyradmon_driver.pl $radmonRC $pyflags");
+    }
+}
+
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #                         UTILITY subroutines
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1043,11 +1092,21 @@ usage: $script [process options] [plot option] [other options]
 process options (see Notes below)
   -means                calculate monthly means
   -tar                  tar input files
+
   -plots                produce monthly plots from monthly means
   -finish_plots         finish monthly plots job which stopped before completion
-
-plot option (only valid when used with -plots or -finish_plots)
-  -nopush               do not transfer gif files to Web server after plotting
+  -nopush               do not transfer gif files to Web server after plotting;
+                        only valid when used with -plots or -finish_plots flag
+
+  -radmon [val]         produce radmon plots (see -qjobs option)
+                        if val == 1 ... produce plots for entire month
+                        if val == 2 ... split month into 2 sets
+                        if val == 3 ... split month into 3 sets
+                        if no val is given, then set val to 1
+  -runlocal             run radmon jobs locally if archive is visible; otherwise,
+                        jobs will automatically be sent to slurm queue; they will
+                        be sent there regardless if archive is not visible;
+                        only valid when used with -radmon flag
 
 slurm directive options
   -partition partition  send monthly means jobs to specified partition

src/Applications/GEOSdas_App/monthly_setup.pl

@@ -180,6 +180,10 @@ sub write_plotfiles {
     $values{"\@GEOSBIN"} = "$FVROOT/bin";
     $values{"\@GEOSSRC"} = $ENV{"GEOSUTIL"};
 
+    $values{"\@BATCH_TIME"} = "SBATCH --time=";
+    $values{"\@BATCH_JOBNAME"} = "SBATCH --jobname=";
+    $values{"\@BATCH_OUTPUTNAMEOUTPUT"} = "SBATCH --output=OUTPUT";
+
     replaceLabels($infile, $outfil, \%values,\@setenvs);
 
     # write gcm_moveplot.j; copy gcm_quickplot.csh

src/Applications/GEOSdas_App/testsuites/C48f.input

@@ -221,6 +221,9 @@ Output Restart TYPE (bin or nc4) [nc4]
 Select group: [g0613]
 > 
 
+Continue without missing resource files? [y]
+> 
+
 Edit COLLECTIONS list in run/HISTORY.rc.tmpl (y/n)? [n]
 > y
 

src/Applications/GEOSdas_App/write_FVDAS_Run_Config.pl

@@ -15,8 +15,8 @@
 my ($FVHOME, $FVROOT, $RUNDIR);
 my ($AOD_OBSCLASS, $BERROR, $DO_ECS_OUT, $DO_REM_SYNC, $EXPID, $FVARCH,
     $FVBCS, $GID, $MONTHLY_MEANS, $MP_SET_NUMTHREADS, $NCEPINPUT, $NOBACKUP,
-    $OBSCLASS, $OBSCLASS_NOAIRS, $OMP_NUM_THREADS, $RUN_QUADS, $VTRACK,
-    $VTXLEVS, $VTXRELOC);
+    $OBSCLASS, $OBSCLASS_NOAIRS, $OMP_NUM_THREADS, $RUN_QUADS, $PYRADMON,
+    $VTRACK, $VTXLEVS, $VTXRELOC);
 my ($BASEDIR, $FCSTID, $FVDMGET, $G5MODULES, $PLOTS_LOC, $GEOSUTIL, $GTAG);
 my ($qalter, $PBS_BIN, $DISCOVERSHARE);
 my ($FVSHARE, $SHARE, $REM_GRADS_CONFIG, $G5MGRAM, $LATS4DLOC, $FVBIN,
@@ -97,6 +97,7 @@ sub init {
     $OBSCLASS          = $ENV{"OBSCLASS"};
     $OBSCLASS_NOAIRS   = $ENV{"OBSCLASS_NOAIRS"};
     $OMP_NUM_THREADS   = $ENV{"OMP_NUM_THREADS"};
+    $PYRADMON          = $ENV{"PYRADMON"};
     $RUN_QUADS         = $ENV{"RUN_QUADS"};
     $VTRACK            = $ENV{"VTRACK"};
     $VTXLEVS           = $ENV{"VTXLEVS"};
@@ -278,6 +279,7 @@ sub writefile {
     print RUNCONF "setenv FVARCH $FVARCH\n" if $FVARCH;
     print RUNCONF "setenv FVSPOOL $FVSPOOL\n" if $FVSPOOL;
     print RUNCONF "setenv BASEDIR $BASEDIR\n" if $BASEDIR;
+    print RUNCONF "setenv PYRADMON $PYRADMON\n" if $PYRADMON;
     print RUNCONF "#------------------------------\n";
     print RUNCONF "setenv G5MODULES \"$G5MODULES\"\n" if $G5MODULES;
     print RUNCONF "source \$FVROOT/bin/g5_modules\n";