Merge branch 'develop' into feature/msienkie/prepQC_modifications

components.yaml

@@ -28,7 +28,7 @@ NCEP_Shared:
 GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
-  tag: rt1_4_10_stoch_grid_fix
+  tag: rt1_4_10_geosit
   develop: main
 
 MAPL:
@@ -46,13 +46,13 @@ FMS:
 GEOSana_GridComp:
   local: ./src/Components/@GEOSana_GridComp
   remote: ../GEOSana_GridComp.git
-  tag: v1.5.4.1
+  tag: v1.5.4.2
   develop: develop
 
 GEOSgcm_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
-  tag: rt1_12_4_tskinice
+  tag: rt1_12_4_geosit
   sparse: ./config/GEOSgcm_GridComp.sparse
   develop: develop
 
@@ -83,7 +83,7 @@ fvdycore:
 GEOSchem_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp
   remote: ../GEOSchem_GridComp.git
-  tag: rt1.6.2
+  tag: rt1.6.2_geosit
   develop: develop
 
 HEMCO:
@@ -101,7 +101,7 @@ geos-chem:
 GOCART:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@GOCART
   remote: ../GOCART.git
-  tag: rt1.0.1_CEDS
+  tag: rt1.0.1_geosit
   sparse: ./config/GOCART.sparse
   develop: develop
 
@@ -121,7 +121,7 @@ mom6:
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: rt1.5.6_geosit_hist1
+  tag: rt1.5.6_geosit_hist2
   develop: develop
 
 UMD_Etc:

src/Applications/GEOSdas_App/gen_lnbcs.pl

@@ -32,6 +32,7 @@
                "sstdir=s",
                "cubed",
                "merra2",
+	       "r21c",
                "h" );
 
   usage() if $opt_h;
@@ -80,6 +81,8 @@ sub init {
 
 if ( $opt_merra2 ) {
   $pcp_loc = "/discover/nobackup/projects/gmao/share/dao_ops/fvInput/merra_land/precip_CPCUexcludeAfrica-CMAP_corrected_MERRA/GEOSdas-2_1_4";
+} elsif ( $opt_r21c ) { # This will updated
+  $pcp_loc = "/discover/nobackup/projects/gmao/share/dao_ops/fvInput/merra_land/precip_CPCUexcludeAfrica-CMAP_corrected_MERRA/GEOSdas-2_1_4";
 } else {
   $pcp_loc = "/gpfsm/dnb51/projects/p15/iau/merra_land/precip_CPCU-CMAP_corrected_MERRA/GEOSdas-2_1_4";
 }
@@ -425,6 +428,7 @@ sub usage {
      -fvhome  location of FVHOME (default: write script locally)
      -cubed   needed for cubed GCM
      -merra2  specify to set related BCs
+     -r21c    specify to set related BCs
      -h       prints this usage notice
 
 EXAMPLE COMMAND LINE

src/Applications/GEOSdas_App/testsuites/geos_it.input

@@ -45,7 +45,7 @@ The directory /discover/nobackup/projects/gmao/dadev/rtodling/geos_it does not e
 > 
 
 Processing nodes (1:Westmere, 2:SandyBridge, 3:Ivy Bridge, 4:Haswell, 5:Skylake, 6:Cascase)? [4]
-> 5
+> 6
 
 Which case of variational analysis? [1]
 > 
@@ -138,7 +138,7 @@ Which main class of ObsSys (1: NRT; 2: MERRA; 3: MERRA-2; 4: GEOS-IT; 5: R21C)?
 > 4
 
 OBSERVING SYSTEM CLASSES?
-> merra2_cdas0_pre-qc_bufr,merra2_cdas_pre-qc_bufr,merra2_avhrrwnd_pre-qc_bufr,merra2_ascat_pre-qc_bufr,merra2_ers1_pre-qc_bufr,merra2_repro_ers2_pre-qc_bufr,merra2_qscat_jpl_pre-qc_bufr,merra2_wspd_pre-qc_bufr,merra2_nmodis_pre-qc_bufr,merra2_prof_pre-qc_bufr,merra2_cdas0_pre-qc_bufr,merra2_cdas_pre-qc_bufr,merra2_avhrrwnd_pre-qc_bufr,merra2_ascat_pre-qc_bufr,merra2_ers1_pre-qc_bufr,merra2_repro_ers2_pre-qc_bufr,merra2_qscat_jpl_pre-qc_bufr,merra2_wspd_pre-qc_bufr,merra2_nmodis_pre-qc_bufr,merra2_prof_pre-qc_bufr,merra2_ncep_tcvitals,ncep_ssmis_bufr,ncep_1bamua_bufr,ncep_mhs_bufr,ncep_1bhrs4_bufr,ncep_goesfv_bufr,ncep_gpsro_bufr,ncep_mtiasi_bufr,ncep_atms_bufr,ncep_cris_bufr,ncep_crisfsr_bufr,ncep_satwnd_bufr,ncep_sevcsr_bufr,ncep_avcsam_bufr,ncep_avcspm_bufr,disc_airs_bufr,disc_amsua_bufr,ncep_acftpfl_bufr,aura_omieff_nc,npp_ompsnp_nc,npp_ompsnmeff_nc,gmao_gmi_bufr,gmao_amsr2_bufr
+> geosit_cdas_raob_pre-qc_bufr,geosit_cdas_conv_pre-qc_bufr,geosit_prof_pre-qc_bufr,geosit_avhrrwnd_pre-qc_bufr,geosit_nmodis_pre-qc_bufr,geosit_goes_pre-qc_prep_bufr,geosit_metsat_pre-qc_prep_bufr,geosit_jma_pre-qc_prep_bufr,geosit_ascat_pre-qc_bufr,geosit_repro_ers2_pre-qc_bufr,geosit_qscat_jpl_pre-qc_bufr,geosit_wspd_pre-qc_bufr,geosit_satwnd_bufr,geosit_avhrr_satwnd_bufr,geosit_ncep_tcvitals,geosit_tmi_bufr,geosit_gpsro_bufr,geosit_sevcsr_bufr,geosit_1bamua_bufr,geosit_1bamub_bufr,geosit_1bhrs2_bufr,geosit_1bhrs3_bufr,geosit_1bhrs4_bufr,geosit_1bmsu_bufr,geosit_1bmhs_bufr,geosit_1bssu_bufr,geosit_eosairs_bufr,geosit_eosamsua_bufr,geosit_mtiasi_bufr,geosit_atms_bufr,geosit_ssmit11_bufr,geosit_ssmit13_bufr,geosit_ssmit14_bufr,geosit_ssmit15_bufr,geosit_amsre_bufr,geosit_osbuv8_bufr,geosit_npp_ompsnp_nc,geosit_aura_omieff_nc,geosit_npp_ompsnmeff_nc,geosit_avcsam_bufr,geosit_avcspm_bufr,geosit_acftpfl_bufr,geosit_amsr2_bufr,geosit_crisfsr_bufr,geosit_gmi_bufr
 
 CHECKING OBSYSTEM? [2]
 > 1
@@ -195,7 +195,7 @@ Do Aerosol Analysis (y/n)? [y]
 > 
 
 AOD OBSERVING CLASSES [or type 'none']?
-> 
+> mod04_061_his,myd04_061_his
 
 Enable GAAS feedback to model (y/n)? [y]
 > 

src/Applications/GEOSdas_App/write_FVDAS_Run_Config.pl

@@ -14,7 +14,7 @@
 my ($ARCH, $HOST);
 my ($FVHOME, $FVROOT, $RUNDIR);
 my ($AOD_OBSCLASS, $BERROR, $DO_ECS_OUT, $DO_REM_SYNC, $EXPID, $FVARCH,
-    $FVBCS, $GID, $MONTHLY_MEANS, $MKSI_SIDB, $MP_SET_NUMTHREADS, $NCEPINPUT, $NOBACKUP,
+    $FVBCS, $GID, $MONTHLY_MEANS, $MKSI_SIDB, $MKSI_OZDB, $MP_SET_NUMTHREADS, $NCEPINPUT, $NOBACKUP,
     $OBSCLASS, $OBSCLASS_NOAIRS, $OMP_NUM_THREADS, $RUN_QUADS, $PYRADMON,
     $VTRACK, $VTXLEVS, $VTXRELOC);
 my ($BASEDIR, $FCSTID, $FVDMGET, $G5MODULES, $PLOTS_LOC, $GEOSUTIL, $GTAG);
@@ -93,6 +93,7 @@ sub init {
     $GID               = $ENV{"GID"};
     $MONTHLY_MEANS     = $ENV{"MONTHLY_MEANS"};
     $MKSI_SIDB         = $ENV{"MKSI_SIDB"};
+    $MKSI_OZDB         = $ENV{"MKSI_OZDB"};
     $MP_SET_NUMTHREADS = $ENV{"MP_SET_NUMTHREADS"};
     $NCEPINPUT         = $ENV{"NCEPINPUT"};
     $OBSCLASS          = $ENV{"OBSCLASS"};
@@ -323,6 +324,7 @@ sub writefile {
     print RUNCONF "setenv FVDOLMS $FVDOLMS\n" if $FVDOLMS;
     print RUNCONF "setenv CASE $CASE\n" if $CASE;
     print RUNCONF "setenv MKSI_SIDB $MKSI_SIDB\n" if $MKSI_SIDB;
+    print RUNCONF "setenv MKSI_OZDB $MKSI_OZDB\n" if $MKSI_OZDB;
     print RUNCONF "setenv MP_SET_NUMTHREADS $MP_SET_NUMTHREADS\n" if $MP_SET_NUMTHREADS;
     print RUNCONF "setenv OMP_NUM_THREADS $OMP_NUM_THREADS\n" if $OMP_NUM_THREADS;
     print RUNCONF "setenv ARCH_QUEUE \"$ARCH_QUEUE\"\n" if $ARCH_QUEUE;

src/Applications/GEOSdas_App/write_monthly_rc_arc.pl

@@ -32,13 +32,17 @@
 #
 # => %list: keys = analysis products, e.g. "ana.eta", and names of model
 #                  collections found in $histfile, e.g. "inst1_2d_asm_Nx"
-#           value = a single code containing one or more of the following
+#           values = a single code containing one or more of the following
 #                   letters, {C, M, T, P}, with the following meanings:
 #                     C => comment entry in monthly.rc
 #                     M => create monthly products
 #                     T => tar this product
 #                     P => create monthly plots for this product
-#           the code, except for the 'C', is written to the monthly.rc file
+#                the code, except for the 'C', is written to the monthly.rc file
+# => %freq: keys = names of collections found in $histfile
+#           values = hour frequency (e.g. 1, 3, or 6) as specified in $histfile
+# => %mode: keys = names of collections found in $histfile
+#           values = mode ("inst" or "tavg") as specified in $histfile
 #
 # key local variables in main program:
 # => @outRcArr: lines to write to the $outRc file  (monthly.rc)
@@ -56,9 +60,11 @@
 
 # global variables
 #-----------------
-my ($histfile, $siloarc, $ncana, %list);
+my ($histfile, $siloarc, $ncana);
 my ($outRc, $outArc, $outArk);
 my ($rcFLG, $arcFLG, $arkFLG);
+my (%list, %freq, %mode);
+
 my $script = basename $0;
 
 # analysis and aod output names with default hour types
@@ -100,6 +106,7 @@
                     "prog.sfc"     => 1,
                     "ptrj.prs"     => 1,
                     "traj.lcv"     => 1,
+                    "traj_lcv_rst" => 1,
                     "vtx.mix"      => 1,
                     "vtx.prs"      => 1 );
 # main program
@@ -183,15 +190,8 @@ sub init {
 #=======================================================================
 # name - get_list_from_HIST
 # purpose - add collection names from $histfile to list
-#
-# key local variables
-# => %freq: keys = names of collections found in $histfile
-#           values = hour frequency (e.g. 1, 3, or 6) as specified in $histfile
-# => %mode: keys = names of collections found in $histfile
-#           values = mode ("inst" or "tavg") as specified in $histfile
 #=======================================================================
 sub get_list_from_HIST {
-    my (%freq, %mode);
     my ($colFLG, $extFLG);
     my ($colon, $doublecolon);
 
@@ -227,8 +227,8 @@ sub get_list_from_HIST {
 
         # get frequency and mode information
         #-----------------------------------
-        extract_freq($_, \%freq) if /\.frequency\s*$colon/;
-        extract_mode($_, \%mode) if /\.mode\s*$colon/;
+        extract_freq($_) if /\.frequency\s*$colon/;
+        extract_mode($_) if /\.mode\s*$colon/;
     }
     close HIST;
 }
@@ -302,18 +302,12 @@ sub plots_type {
 #
 # input parameter
 # => $line: line from $histfile containing frequency information for a collection
-#
-# input/output parameter
-# => $freqAddr: address of %freq hash containing collection frequency info
 #=======================================================================
 sub extract_freq {
-    my ($line, $freqAddr);
-
+     my ($line);
     $line = shift;
-    $freqAddr = shift;
-
     if ( $line =~  /^\s*(\S*)\.frequency\s*:\s*(\d{6})\s*,/ ) {
-        $$freqAddr{$1} = $2 / 10000;
+        $freq{$1} = $2 / 10000;
     }
 }
 
@@ -323,22 +317,14 @@ sub extract_freq {
 #
 # input parameter
 # => $line: line from $histfile containing mode information for a collection
-#
-# input/output parameter
-# => $modeAddr: address of %mode hash containing collection mode info
 #=======================================================================
 sub extract_mode {
-    my ($line, $modeAddr);
-    my ($name);
-
+     my ($line, $name);
     $line = shift;
-    $modeAddr = shift;
-
-    $name = undef;
-    $name = $1 if $line =~ /^\s*(\S*)\.mode\s*:/;
-    if ($name) { 
-        $$modeAddr{$name} = "inst" if $line =~ /instantaneous/;
-        $$modeAddr{$name} = "tavg" if $line =~ /time-averaged/;
+    if ( $line =~  /^\s*(\S*)\.mode\s*:/ ) {
+        $name = $1;
+        $mode{$name} = "inst" if $line =~ /instantaneous/;
+        $mode{$name} = "tavg" if $line =~ /time-averaged/;
     }
 }
 
@@ -401,6 +387,12 @@ sub get_info_from_SILO {
     }
     close SILO;
 
+    # add additional hourtype requirements
+    #-------------------------------------
+    foreach (qw(traj_lcv_rst)) {
+        $hourtype{$_} = "$mode{$_}$freq{$_}";
+    }
+
     # entries for monthly.rc file
     #----------------------------
     @$outRcArrAddr = ();

src/Applications/NCEP_Etc/NCEP_bias/readme_init_coeffs.txt

@@ -45,6 +45,13 @@ directory with names in the format
      %s.diag_(dtype)_(dplat)_ges.%y4%m2%d2_%h2z.bin
 where the %s is substituted with the expid specified on the command line
 
+Note: Since this program uses the "gsi.rc.tmpl" file to get values for 'dtype',
+'dplat', and 'dsis' for each satellite instrument being fitted, if you are 
+using the 'generic' value for these variables in your "gsi.rc.tmpl" to 
+configure your instrument you will need to supply another file with an 
+'OBS_INPUT::' table like in the "gsi.rc.tmpl" which specifies the actual
+'dtype', 'dplat' and 'dsis' values for your satellite(s).
+
 --------------------- EXAMPLES --------------------------------------------
 
 1) Using archived diag_*_ges.*.bin files as input

src/Applications/NCEP_Etc/NCEP_enkf/scripts/gmao/etc/CMakeLists.txt

@@ -39,3 +39,14 @@ install (
    FILES ${ALLETC}
    DESTINATION etc/atmens
    )
+
+set (R21C_files
+   R21C/atmos_enkf.nml.tmpl  
+   R21C/obs1gsi_mean.rc  
+   R21C/obs1gsi_member.rc
+   )
+
+install (
+   FILES ${R21C_files}
+   DESTINATION etc/atmens/R21C
+   )