Merge branch 'develop' into feature/mathomp4/mapldevelop

Author: mathomp4

components.yaml

@@ -75,7 +75,7 @@ MAPL:
 GEOSldas_GridComp:
   local: ./src/Components/@GEOSldas_GridComp
   remote: ../GEOSldas_GridComp.git
-  tag: v1.0.2
+  tag: v2.0.0
 
 FMS:
   local: ./src/Shared/@FMS
@@ -251,7 +251,7 @@ umwm:
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: g2.3.8.1
+  tag: g2.3.8.2
   develop: develop
 
 Ocean-LETKF:

src/Applications/GEOSdas_App/AGCMrc.pm

@@ -17,6 +17,7 @@ package AGCMrc;
 # 03May2010  Todling   Add reference to CARMA rst
 # 19Aug2010  Todling   turb_internal_rst is needed for reproduc/ble fcst
 # 09Oct2013  Todling   Add logics to handle precip-forcing option
+# 07Jan2024  Stassi    No longer need '#' in front of key in %uncomment hash
 #
 #########################################################################
 use strict;
@@ -35,6 +36,7 @@ my ($gocart_tracers, $carma_tracers, $iau, $pcp_forced, $lsmodel_flag);
 my ($fvhome, $fvroot);
 my ($coupled);
 my ($envvars_set, $flags_set, %subst);
+my ($ldas_flag);
 
 #----------------------------------
 # GCM Restart files
@@ -123,7 +125,6 @@ my %list = (rs5_core     => \@rs5_core,
                     stratchem_internal_rst 
                     stratchem_import_rst );
 
-
 #=======================================================================
 # name - set_AGCM_envvars
 # purpose - set global variables: $fvhome and $fvroot
@@ -144,7 +145,6 @@ sub set_AGCM_envvars {
       @rs5_notused = (@rs5_notused, @rs5_coupled);
       @rs5_files = (@rs5_core, @rs5_boot, @rs5_others);
     }
-
 }
 
 #=======================================================================
@@ -160,6 +160,7 @@ sub set_AGCM_flags {
     $lsmodel_flag   = hashextract("lsmodel_flag",  %flags);
     $iau            = hashextract("iau",           %flags);
     $pcp_forced     = hashextract("pcp_forced",    %flags);
+    $ldas_flag      = hashextract("ldas_flag",     %flags);
     $flags_set = 1;
 }
 
@@ -290,6 +291,10 @@ sub ed_g5agcm_rc {
     if ( $gocart_tracers ) { $comment{"GOCART.data_INTERNAL"} = 1 }
     else                   { $comment{"GOCART_INTERNAL"} = 1 }
 
+    # uncomment ldas increment flag
+    #------------------------------
+    if ($ldas_flag == 1) { $uncomment{"LDAS_INCR"} = 1 }
+
     # comment unused catch or catchCN restart
     #----------------------------------------
     if ($lsmodel_flag == 1) { 
@@ -310,8 +315,8 @@ sub ed_g5agcm_rc {
     # uncomment precipation force except when specified
     # -------------------------------------------------
     if ( $pcp_forced ) {
-        $uncomment{"#PRECIP_FILE"}  = 1;
-        $uncomment{"#USE_PP_TAPER"} = 1;
+        $uncomment{"PRECIP_FILE"}  = 1;
+        $uncomment{"USE_PP_TAPER"} = 1;
     }
 
     # edit and output AGCM.rc.tmpl
@@ -350,6 +355,7 @@ sub outputAGCM {
     my ($outfile, $ox_friendlies);
     my ($rcd, $label, $key, $rst);
     my (@DEFAULT_TYPE_FOUND);
+    my ($space, $pound);
 
     $tmpl  = shift @_;
     $outfl = shift @_;
@@ -409,8 +415,11 @@ sub outputAGCM {
         # uncomment specified lines if key is in first non-blank position
         #----------------------------------------------------------------
         foreach $key ( keys %uncomment ) {
-            if ($rcd =~ /^(\s*)$key/) {
-                if ( $uncomment{"$key"} ) {$rcd = substr $rcd, 1;};
+            $key =~ s/^\#//;  # no longer need '#' in front of key
+            if ($rcd =~ /^(\s*)(\#*)\s*$key/) {
+                $space = $1;
+                $pound = $2;
+                $rcd =~ s/^$space$pound/$space/;
             }
         }
         print(LUN2 "$rcd\n");

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -6089,6 +6089,10 @@ endif
          /bin/mv $momoutdir/MOM.res_${fn}.nc $FVHOME/recycle/hold/$EXPID.mom${fn}_rst.${momtag}.nc4 
        end
     endif
+    set lstbkglfo = `ls $FVWORK/$EXPID.bkg.lfo*.$NCSUFFIX`
+    if ( ${%lstbkglfo}  ) then
+       tar cvf $FVWORK/$EXPID.bkglforst.${rtag}.tar $EXPID.bkg.lfo*.$NCSUFFIX
+    endif 
     cd $FVHOME/recycle/hold
     tar cvf $FVWORK/$EXPID.rst.${rtag}.tar $EXPID.* 
     /bin/mv $FVWORK/$EXPID.xinc*$NCSUFFIX .
@@ -6124,9 +6128,8 @@ endif
 #------------------------------------ 
 
   if ( $LDAS_ANA ) then
-    mkdir -p               $FVHOME/recycle/holdpredout 
-    /bin/mv -f $FVWORK/*lfo_Nx+-* $FVHOME/recycle/holdpredout/. 
-    /bin/cp $FVHOME/recycle/holdpredout/*lfo_Nx+-*  $LDHOME/input/met_forcing/. 
+    /bin/rm -f $FVHOME/recycle/holdpredout/*lfo*
+    /bin/cp  $FVWORK/*bkg.lfo*.nc4  $FVHOME/recycle/holdpredout/. 
   endif 
 
   exit 0                      

src/Applications/GEOSdas_App/fvsetup

@@ -589,22 +589,22 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
   $rc = system("$fvbin/fix_gocart_rc.csh $vres $fvhome/run/gocart");
   die "Failed to fix GOCART levels-referencing $!" if ( $rc );
 
-# LDAS Setup is done separately, follow instructions in GEOSldas/README.md
-# Provide ldas config input files: YOUR_det_exeinp.txt, YOUR_det_batinp.txt 
-# ln -s YOUR_det_exeinp.txt  $fvbin/det_exeinp.txt 
-# ln -s YOUR_det_batinp.txt  $fvbin/det_batinp.txt  
-# For Hyb-4dEnVar, do same for ens_exeinp.txt and ens_batinp.txt
+# Call LDAS setup script.
+#  Provide LDAS config input files in $ldassetup/: det_exeinp.txt, det_batinp.txt. 
+#  For Hyb-4dEnVar, do same for ens_exeinp.txt, ens_batinp.txt. 
+#  See GEOSldas/README.md for generating sample config input files.
 # ------------------------------------------------------------------------
     print "\n checkprintout  ldas_ana == 1 ($ldas_ana)\n";
     if ($ldas_ana == 1 ) {
-       $rc = system("$fvbin/ldas_setup setup $fvhome/lana $fvbin/det_exeinp.txt $fvbin/det_batinp.txt");
-       die "Failed to setup ldas for det, check ldas config input files $!" if ( $rc );
-      
-       if ($hyb_ens == 4 ) {
-          $rc = system("$fvbin/ldas_setup setup $fvhome/lana $fvbin/ens_exeinp.txt $fvbin/ens_batinp.txt");
-          die "Failed to setup ldas for ens, check ldas config input files $!" if ( $rc );
+        $cmd = "$fvbin/ldas_setup setup $fvhome/lana --account $gid --nymdb $nymdb --nhmsb $nhmsb $ldassetup/det_exeinp.txt $ldassetup/det_batinp.txt";
+        print "$cmd\n";
+        $rc = system $cmd;
+        die "Failed to setup LDAS for det, check LDAS config input files $!" if ( $rc );
+        chomp($aens_replay);
+        if (($hyb_ens == 4) && ($aens_replay eq "no")) { 
+           $rc = system("$fvbin/ldas_setup setup $fvhome/lana --account $gid --nymdb $nymdb --nhmsb $nhmsb $ldassetup/ens_exeinp.txt $ldassetup/ens_batinp.txt");
+           die "Failed to setup LDAS for ens, check LDAS config input files $!" if ( $rc );
        }
-
      }
 
 # Monthly Setup
@@ -3177,7 +3177,7 @@ sub get_nodeflg {
   $proc = "";
   # reset default if applicable
 
-  $ans = query(" Processing nodes (1:Haswell, 2:Skylake, 3:Cascase, 4:Milan)?", "2");
+  $ans = query(" Processing nodes (1:Haswell, 2:Skylake, 3:Cascade, 4:Milan)?", "4");
 
   if    ($ans == 1) { $nodeflg = "hasw"; $ncpus_per_node = 24 }
   elsif ($ans == 2) { $nodeflg = "sky";  $ncpus_per_node = 36 }
@@ -3518,42 +3518,54 @@ sub set_newradbc {
 }
 #=======================================================================
 sub set_ldasANA {
+    my ($dflt, $ans1, $ans2);
+    my (@bkglfo_files);
 
     # initialize Land DAS processing flag
     #------------------------------------ 
-    my($dflt, $ans1, $ans2, $ans3, $ans4);
     $ldas_ana = 0;
-    $ldasfdbk = 0;
     $ldas_flag = 0;
-    $dflt = "n";
-    $ldashome = "${fvhome}/lana/${expid}_LDAS" ;
-    $ldashome4ens = "${fvhome}/lana/${expid}_LDAS4ens" ;
+    $ldasfdbk = 0;
+
+    $ldashome = "${fvhome}/lana/${expid}_LDAS";
+    $ldashome4ens = dirname($ldashome) ."/${expid}_LDAS4ens";
 
     print "\n-------------\n";
     print   "LDAS Analysis\n";
     print   "-------------\n\n";
 
+    $dflt = "n";
     $ans1 = query("  Land DAS Analysis (y/n)?", $dflt) ;
-    $ldas_ana = 1 if yes($ans1);
+    if (yes($ans1)) {
+        $ldas_ana = 1;
+        $ldas_flag = 1;
 
-   if ($ldas_ana == 1) {
-      $ans2 = query("  Enable LDAS feedback to model y/n ? ", $dflt);
-      $ldasfdbk = 1 if yes($ans2);
+        $prompt = "  Location of LDAS initial forcing ";
+        $dflt = $fvics;
+        $dflt = dirname($fvics) unless -d $fvics;
 
-      if ($ldasfdbk == 1 ) {
-          $ldas_flag = 1;
-      }
+        $ldashold = query($prompt, $dflt);
+            die ">>> Error <<< Cannot find directory, $ldashold;"
+                unless -d $ldashold;
 
-      $ans3 = query(" LDAS HOME?  [DEFAULT: $ldashome]");
-      $ldashome = $ans3  unless blank($ans3); 
+        @bkglfo_files = (<$ldashold/*bkg*lfo*${nymdb}_${hhb}*>);
+            die ">>> Error <<< Cannot find bkglfo files in $ldashold;"
+                unless scalar(@bkglfo_files);
+        
+        $dflt = "n";
+        $ans2 = query("  Enable LDAS feedback to model y/n?", $dflt);
+        if (yes($ans2)) {
+            $ldasfdbk = 1;
+        }
+        $dflt = "/discover/nobackup/$user/ldasSaveInput";
+        $ldassetup = query("  LDAS setup input path?", $dflt);
       
-      if ($hyb_ens == 4 ) {
-         $ans4 = query(" LDAS HOME for atmens? [DEFAULT: $ldashome4ens]");
-         $ldashome4ens = $ans4  unless blank($ans4); 
-      }
-
-   } 
-return 0;
+        if ($hyb_ens == 4 ) {
+            $dflt = "/discover/nobackup/$user/ldasSaveInput";
+            $ldassetup4ens = query("  LDAS setup input path for ens?", $dflt);
+        }
+    }
+    return 0;
 }
 
 #=======================================================================
@@ -3794,6 +3806,7 @@ EOF
   } 
   $flags = "-nlevs $aens_lev $setacftbc $rcorrarg $setradbc $aens_lsmodel -expdir $fvhome/.. $sppt_flag $bcopt";
   $flags .= " -fvhome $fvhome" if $checkFLG;
+  $flags .= " -ldasflg $ldas_flag";
   $params = " $aens_ana $expid $aens_im $aens_jm $aens_ocn $landbcs"; 
 
   $cmd = "$fvbin/setup_atmens.pl -nodename $nodeflg $flags $params";
@@ -5473,6 +5486,10 @@ sub mkdir_fvhome {  # create directories on FVHOME
       mkpath("$fvhome/run/$subdir")
           or die ">> Error << creating subdir, $fvhome/run/$subdir;";
   }
+  if ($ldas_flag) {
+      mkpath("$fvhome/recycle/holdpredout")
+          or die ">> Error << creating subdir, $fvhome/recycle/holdpredout;";
+  }
   unlink("$fvhome/fvInput") if ( -e "$fvhome/fvInput" ) ; 
   symlink("$fvbcs","$fvhome/fvInput"); 
 
@@ -10275,6 +10292,8 @@ sub init_agcm_pert_rc {
 sub copy_resources {
   my ($chemrc, $ensFLG);
   my ($flags, $label, $string, $vars, $cmd);
+  my ($fname, $fname_old, $expid_old, $target);
+  my ($bkglfo_tarfile, @bkglfo_files, $target, $expid_old, $fname, $fname_old);
 
   cp("$fvroot/etc/VERSION","$fvhome/run/VERSION")
           || die "Cannot write file $fvhome/run/VERSION: $!";
@@ -10331,6 +10350,40 @@ sub copy_resources {
           system("$fvbin/vED -vv SHARE=$SHARE $ensFLG $source -o $target");
       }
       system("touch $fvhome/run/gaas/GAAS.BOOTSTRAP_");
+
+      if ($ldas_flag) {
+          die ">>> Error <<< Cannot find directory, $ldashold;"
+              unless -d $ldashold;
+
+          $target = "$fvhome/recycle/holdpredout";
+          die ">>> Error <<< Cannot find directory, $target;"
+              unless -d $target;
+
+          # extract lfo files from tarfile
+          #-------------------------------
+          $bkglfo_tarfile = (<$ldashold/*.bkglforst.${nymdb}_${hhb}z.tar>)[0];
+          if ($bkglfo_tarfile) {
+              $expid_old = find_expid($bkglfo_tarfile, 1);
+              chdir($target);
+              system("tar xf $bkglfo_tarfile");
+              system("rename $expid_old $expid *");
+          }
+
+          # or copy them from directory
+          #----------------------------
+          else {
+              $expid_old = find_expid($ldashold);
+              @bkglfo_files = (<$ldashold/$expid_old.bkg.lfo*.nc4>);
+              die ">>> Error <<< No $expid_old lfo files found in $ldashold;"
+                  unless scalar(@bkglfo_files);
+              
+              foreach $fname_old ( @bkglfo_files ) {
+                  ($fname = basename($fname_old)) =~ s/$expid_old/$expid/;
+                  cp($fname_old, "$target/$fname");
+                  print "cp $fname_old $target/$fname\n";
+              }
+          }
+      }
   }
 
   # Model perturbation-related settings
@@ -10756,7 +10809,48 @@ sub copy_resources {
     }
   }
 }
- 
+
+#=======================================================================
+# name - find_expid
+# purpose - find expid from single filename or from multiple files in a
+#           directory.
+#
+# input parameters
+# - $name: name of file or directory
+# - $flag: (optional) 1=filename, 2=directory [default = 2]
+#
+# notes -
+#   1. If $name is a file, then this routine extracts expid from front
+#      portion of the filename.
+#   2. If $name is a directory, then this routine extracts expid from
+#      each file in the directory and returns the most prevalent value
+#      as the expid.
+#=======================================================================
+sub find_expid {
+    my ($name, $expid_found, $flag, $fname, $most, $front, %count);
+    $name = shift @_;
+    $flag = shift @_;
+
+    if ($flag == 1) {
+        die ">>> ERROR <<< $name is not a file;" unless -f $name;
+        $expid_found = (split(/\./, basename($name)))[0];
+    } else {
+        die ">>> ERROR <<< $name is not a directory;" unless -d $name;
+        for $fname ( <$name/*> ) {
+            $front = (split(/\./, basename($fname)))[0];
+            $count{$front}++;
+        }
+        $most = -1;
+        foreach $front (keys(%count)) {
+            if ($count{$front} > $most) {
+                $expid_found = $front;
+                $most = $count{$front};
+            }
+        }
+    }
+    return $expid_found;
+}    
+
 #=======================================================================
 sub edit_collections {
 

src/Applications/GEOSdas_App/gen_silo_arc.pl

@@ -221,6 +221,8 @@ sub restart_info {
     printarc("$lineTAR\n");
     $lineTAR = '${PESTOROOT}%s/rs/Y%y4/M%m2/%s.bkgcrst.%y4%m2%d2_%h2z.tar';
     printarc("$lineTAR\n");
+    $lineTAR = '${PESTOROOT}%s/rs/Y%y4/M%m2/%s.bkglforst.%y4%m2%d2_%h2z.tar';
+    printarc("$lineTAR\n");
     $lineTAR = '${PESTOROOT}%s/jedi/rs/Y%y4/M%m2/%s.jedi_agcmrst.%y4%m2%d2_%h2z.tar';
     printarc("$lineTAR\n");
 

src/Applications/GEOSdas_App/testsuites/x3dvar_ladas.input

@@ -44,7 +44,7 @@ FVHOME? [/discover/nobackup/qzhang/x3dvar_ladas]
 The directory /discover/nobackup/qzhang/x3dvar does not exist. Create it now? [y]
 > 
 
-Processing nodes (1:Haswell, 2:Skylake, 3:Cascade, 4:Milan)? [2]
+Processing nodes (3:Cascade, 4:Milan)? [3]
 > 4
 
 Which case of variational analysis? [1]