Syn jedi 08142026

components.yaml

@@ -35,7 +35,7 @@ NCEP_Shared:
 GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
-  tag: v5.42.4
+  tag: g5.42.4.2
   sparse: ./config/GMAO_Shared.sparse
   develop: main
 
@@ -55,7 +55,7 @@ AeroML:
 GEOS_Util:
   local: ./src/Shared/@GMAO_Shared/@GEOS_Util
   remote: ../GEOS_Util.git
-  tag: v2.1.13
+  tag: g3.0.2
   develop: main
 
 GMAO_perllib:
@@ -69,13 +69,13 @@ GMAO_perllib:
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.57.1
+  tag: v2.57.2
   develop: develop
 
 GEOSldas_GridComp:
   local: ./src/Components/@GEOSldas_GridComp
   remote: ../GEOSldas_GridComp.git
-  tag: v3.1.0
+  tag: g3.1.1
 
 FMS:
   local: ./src/Shared/@FMS
@@ -86,19 +86,19 @@ FMS:
 GEOSana_GridComp:
   local: ./src/Components/@GEOSana_GridComp
   remote: ../GEOSana_GridComp.git
-  tag: v5.45.2
+  tag: v5.45.5
   develop: develop
 
 mksi:
    local: ./src/Components/@GEOSana_GridComp/GEOSaana_GridComp/GSI_GridComp/@mksi
    remote: ../GEOS_mksi.git
-   tag: v5.44.0
+   tag: v5.44.2
    develop: develop
 
 GEOSgcm_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
-  tag: v2.7.6.1
+  tag: g2.7.6.2
   sparse: ./config/GEOSgcm_GridComp.sparse
   develop: develop
 
@@ -153,7 +153,7 @@ geos-chem:
 GOCART:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@GOCART
   remote: ../GOCART.git
-  tag: g2.3.2
+  tag: g2.3.3
   develop: develop
 
 QuickChem:
@@ -287,7 +287,7 @@ umwm:
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: g2.3.8.12
+  tag: g2.3.8.13
   develop: develop
 
 Ocean-LETKF:

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -3252,9 +3252,13 @@ endif
 
 #             then run analysis
 #             -----------------
-              $dryrun analyzer $nymdb $nhmsb -expid $EXPID -t $SPECRES -levs $gsinlev -x $gsinlon -y $gsinlat -jiter $Viter_ $lnobs -log ana.log
-              if ( ${status} ) then
-                  Call AbnormalExit_( 3 )
+              if ( -e $FVHOME/geos_run_analyzer ) then
+                 $BATCH_SUBCMD $BLOCKFLAG $FVHOME/geos_run_analyzer.j
+              else
+                 $dryrun analyzer $nymdb $nhmsb -expid $EXPID -t $SPECRES -levs $gsinlev -x $gsinlon -y $gsinlat -jiter $Viter_ $lnobs -log ana.log
+                 if ( ${status} ) then
+                     Call AbnormalExit_( 3 )
+                 endif
               endif
 
               set ana_check = ( `grep ">>> WARNING <<< does not exist" ana.log | cut -d '<' -f4` )
@@ -3329,7 +3333,7 @@ endif
   endif
 
 
-  jedi_driver.csh $gcm_nymd0 $gcm_nhms0 $ana_datetime[1] $ana_datetime[2] |& tee -a $FVWORK/$EXPID.jedi_drv.log.${gcm_nymd0}_${this_hh0}z.txt
+  jedi_driver.csh $gcm_nymd0 $gcm_nhms0 $ana_datetime[1] $ana_datetime[2] 0 |& tee -a $FVWORK/$EXPID.jedi_drv.log.${gcm_nymd0}_${this_hh0}z.txt
   if ( $status ) then
      echo "JEDI analysis failed, aborting ..."
      Call AbnormalExit_( 1 )
@@ -4282,7 +4286,11 @@ endif
             if ( $use_shmem ) RmShmKeys_sshmpi.csh
             /bin/rm -f ./EGRESS
                                    zeit_ci.x gcm
-            $dryrun $run_opt_begin |& tee -a fvpsas.log
+            if ( -e $FVHOME/geos_run_gcm.j ) then
+               $BATCH_SUBCMD $BLOCKFLAG geos_run_gcm.j
+            else
+               $dryrun $run_opt_begin |& tee -a fvpsas.log
+            endif
             echo "GCM status = $status"
                                    zeit_co.x gcm
             if ( $use_shmem ) RmShmKeys_sshmpi.csh
@@ -4871,7 +4879,11 @@ endif
          setenv  REPACK_PBS 0
    endif
                           zeit_ci.x gcm
-   $dryrun $run_opt_begin |& tee fvpsas.log
+   if ( -e $FVHOME/geos_run_gcm.j ) then
+      $BATCH_SUBCMD $BLOCKFLAG geos_run_gcm.j
+   else
+      $dryrun $run_opt_begin |& tee fvpsas.log
+   endif
                           zeit_co.x gcm
 
 #  Check whether we ran without errors

src/Applications/GEOSdas_App/fvsetup

@@ -572,6 +572,11 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
 # ------------------------------------
   create_fscript();
 
+# Create offline GCM and Analysis run jobs
+# ----------------------------------------
+  create_geos_run_gcm("run");
+  create_geos_run_ana("run");
+
 # Create job scripts to run stand-alone analysis
 # ----------------------------------------------
    set_inputparams();
@@ -3187,7 +3192,7 @@ sub get_nodeflg {
   if    ($ans == 1) { $nodeflg = "hasw"; $ncpus_per_node = 24 }
   elsif ($ans == 2) { $nodeflg = "sky";  $ncpus_per_node = 36 }
   elsif ($ans == 3) { $nodeflg = "cas";  $ncpus_per_node = 45 }
-  elsif ($ans == 4) { $nodeflg = "mil";  $ncpus_per_node = 54 }
+  elsif ($ans == 4) { $nodeflg = "mil";  $ncpus_per_node = 64 }
 
   # currently not applicable at nccs
   #---------------------------------
@@ -9226,6 +9231,72 @@ sub write_FVDAS_Run_Config {
     system("$fvbin/write_FVDAS_Run_Config.pl -remNODE $remNODE -remID $remID");
 }
 
+#=======================================================================
+sub create_geos_run_gcm {
+
+  return 0 unless ( $fulldas );
+
+  my($mydir) = @_;
+
+  my($frun, $ft, $acq);
+
+  $acq = "$fvhome/$mydir/_geos_run_gcm.j";
+ open(SCRIPT,">$acq") or
+ die ">>> ERROR <<< cannot write $acq";
+ print  SCRIPT <<"EOF";
+#!/bin/csh -fx
+# ------------------------------
+#$group_list
+#_SBATCH --qos=dastest
+#_SBATCH --partition=preops
+#SBATCH --job-name=gcm_${expid}
+#SBATCH --output=gcm_${expid}.log.o%j.txt
+#SBATCH --ntasks=$xncpus
+#SBATCH --ntasks-per-node=$ncpus_per_node
+#SBATCH --constraint=$nodeflg
+#SBATCH --time=2:00:00
+
+source \$FVROOT/modules
+
+cd \$FVWORK
+
+\$RUN_OPT_BEGIN |& tee -a fvpsas.log
+
+EOF
+}
+#=======================================================================
+sub create_geos_run_ana {
+
+  return 0 unless ( $fulldas );
+
+  my($mydir) = @_;
+
+  my($frun, $ft, $acq);
+
+  $acq = "$fvhome/$mydir/_geos_run_analyzer.j";
+ open(SCRIPT,">$acq") or
+ die ">>> ERROR <<< cannot write $acq";
+ print  SCRIPT <<"EOF";
+#!/bin/csh -fx
+# ------------------------------
+#$group_list
+#_SBATCH --qos=dastest
+#_SBATCH --partition=preops
+#SBATCH --job-name=ana_${expid}
+#SBATCH --output=ana_${expid}.log.o%j.txt
+#SBATCH --nodes=10
+#SBATCH --constraint=$nodeflg
+#SBATCH --time=2:00:00
+
+source \$FVROOT/modules
+
+cd \$FVWORK
+
+analyzer \$nymdb \$nhmsb -expid \$EXPID -t \$SPECRES -levs \$gsinlev -x \$gsinlon -y \$gsinlat \
+         -jiter \$Viter_ \$lnobs -log ana.log
+
+EOF
+}
 #=======================================================================
 sub create_ana_aod_script_tmpl {
     my ($infl, $outf);

src/Applications/GEOSdas_App/gen_silo_arc.pl

@@ -706,6 +706,7 @@ sub append_other_info {
 #                 ---------------------------
 #
 \${PESTOROOT}%s/prog/Y%y4/M%m2/D%d2/H%h2/%s.prog.inst3d_met_p.%y4%m2%d2_%h2z+%y4%m2%d2_%h2%n2z.nc4
+\${PESTOROOT}%s/prog/Y%y4/M%m2/D%d2/H%h2/%s.prog.ceta.%y4%m2%d2_%h2z+%y4%m2%d2_%h2%n2z.nc4
 \${PESTOROOT}%s/prog/Y%y4/M%m2/D%d2/H%h2/%s.prog.eta.%y4%m2%d2_%h2z+%y4%m2%d2_%h2%n2z.nc4
 \${PESTOROOT}%s/prog/Y%y4/M%m2/D%d2/H%h2/%s.prog.prs.%y4%m2%d2_%h2z+%y4%m2%d2_%h2%n2z.nc4
 \${PESTOROOT}%s/prog/Y%y4/M%m2/D%d2/H%h2/%s.prog.sfc.%y4%m2%d2_%h2z+%y4%m2%d2_%h2%n2z.nc4

src/Applications/GEOSdas_App/jedi/etc/CMakeLists.txt

@@ -5,6 +5,7 @@ set (ALLETC
    diag2ioda.yaml
    geos_3dvar.yaml
    geos_3dfgat.yaml
+   geos_hofx.yaml
    geos_hyb3dcenvar.yaml
    geos_hyb4dcenvar.yaml
    geos_hyb4dcenvar_seq.yaml
@@ -15,8 +16,10 @@ set (ALLETC
    jedi_acquire_ioda.j
    jedi_acquire_vbc.j
    jedi_diffstates.j
+   jedi_anasa.j
    jedi_run_var.j
    mkiau.rc.tenv
+   mkiau_cubed.rc.tenv
    obsop_name_map.yaml
    ut_jedi.j
    )

src/Applications/GEOSdas_App/jedi/etc/JEDIadanaConfig.csh

@@ -44,7 +44,7 @@ setenv JEDI_FV3VAR_MPIRUN "mpirun -perhost @JEDI_VAR_PERHOST -np $JEDI_NCPUS"
 setenv JEDI_MKIAU_MPIRUN "mpirun "
 
 setenv JEDI_STATIC_FILES @JEDI_STATIC_FILES
-setenv JEDI_CRTM_COEFFS  $FVHOME/fvInput/gsi/etc/JEDI-CRTM-2.4.1j1-GMAO/Little_Endian/
+setenv JEDI_CRTM_COEFFS  $FVHOME/fvInput/gsi/etc/JEDI-CRTM-2.4.1j1-GMAO-1/Little_Endian/
 setenv JEDI_INPUT @JEDI_INPUT
 
 # post

src/Applications/GEOSdas_App/jedi/etc/JEDIanaConfig.csh

@@ -9,6 +9,7 @@ setenv JEDI_HYBRID @JEDI_HYBRID           # control opts for hyb JEDI
 setenv JEDI_MKIAU  1           # calculates IAU output
 setenv JEDI_POST   0           # process results (move files, etc)
 setenv JEDI_IAU_OVERWRITE  @JEDI_IAU_OVERWRITE   # overwrite GSI-IAU with JEDI-IAU (when cycling)
+setenv JEDI_MKIAU_CUBED 0      # 0=use lat-lon ana/bkg; 1=use cubed ana/bkg (no remap)
 setenv JEDI_RUN_ADANA_TEST 0   # run adjoint JEDI-Var
 setenv JEDI_VAROFFSET 10800    # background time offset
 setenv JEDI_FEEDBACK_VARBC @JEDI_FEEDBACK_VARBC   # controls whether or not to feedback biases
@@ -41,11 +42,12 @@ setenv JEDI_CNVENS_MPIRUN "mpirun -np 12"
 setenv JEDI_CNVINC_MPIRUN "mpirun -np 12"
 setenv JEDI_GETINC_MPIRUN "mpirun -np $JEDI_DIF_NCPUS"
 setenv JEDI_FV3VAR_MPIRUN "mpirun -perhost @JEDI_VAR_PERHOST -np $JEDI_NCPUS"
+setenv JEDI_FV3HOX_MPIRUN "mpirun -perhost 16 -np 96"
 
 setenv JEDI_MKIAU_MPIRUN "mpirun "
 
 setenv JEDI_STATIC_FILES @JEDI_STATIC_FILES
-setenv JEDI_CRTM_COEFFS  $FVHOME/fvInput/gsi/etc/JEDI-CRTM-2.4.1j1-GMAO/Little_Endian/
+setenv JEDI_CRTM_COEFFS  $FVHOME/fvInput/gsi/etc/JEDI-CRTM-2.4.1j1-GMAO-1/Little_Endian/
 setenv JEDI_INPUT @JEDI_INPUT
 
 # post

src/Applications/GEOSdas_App/jedi/etc/geos_3dfgat.yaml

@@ -11,7 +11,7 @@ cost function:
   - rain_water
   - snow_water
   - mole_fraction_of_ozone_in_air
-  - geopotential_height_times_gravity_at_surface
+  - geopotential_at_surface
   - fraction_of_ocean
   - fraction_of_lake
   - fraction_of_ice
@@ -38,7 +38,7 @@ cost function:
     - rain_water
     - snow_water
     - mole_fraction_of_ozone_in_air
-    - geopotential_height_times_gravity_at_surface
+    - geopotential_at_surface
     - initial_mass_fraction_of_large_scale_cloud_condensate
     - initial_mass_fraction_of_convective_cloud_condensate
     - convective_cloud_area_fraction
@@ -78,7 +78,7 @@ cost function:
       rain_water: qr
       snow_water: qs
       mole_fraction_of_ozone_in_air: o3ppmv
-      geopotential_height_times_gravity_at_surface: phis
+      geopotential_at_surface: phis
       initial_mass_fraction_of_large_scale_cloud_condensate: qls
       initial_mass_fraction_of_convective_cloud_condensate: qcn
       convective_cloud_area_fraction: cfcn
@@ -106,7 +106,7 @@ cost function:
 #     mole_fraction_of_carbon_dioxide_in_air: co2
   background error:
     covariance model: SABER
-#   covariance type: gsi static covariance
+    covariance type: gsi static covariance
 #   adjoint test: true
     saber central block:
       saber block name: gsi hybrid covariance
@@ -205,7 +205,7 @@ variational:
         rain_water: qr
         snow_water: qs
         mole_fraction_of_ozone_in_air: o3ppmv
-        geopotential_height_times_gravity_at_surface: phis
+        geopotential_at_surface: phis
         fraction_of_ocean: frocean
         fraction_of_lake: frlake
         fraction_of_ice: frseaice

src/Applications/GEOSdas_App/jedi/etc/geos_3dvar.yaml

@@ -28,7 +28,7 @@ cost function:
   - rain_water
   - snow_water
   - mole_fraction_of_ozone_in_air
-  - geopotential_height_times_gravity_at_surface
+  - geopotential_at_surface
   - fraction_of_ocean
   - fraction_of_lake
   - fraction_of_ice
@@ -55,7 +55,7 @@ cost function:
     - rain_water
     - snow_water
     - mole_fraction_of_ozone_in_air
-    - geopotential_height_times_gravity_at_surface
+    - geopotential_at_surface
     - initial_mass_fraction_of_large_scale_cloud_condensate
     - initial_mass_fraction_of_convective_cloud_condensate
     - convective_cloud_area_fraction
@@ -94,7 +94,7 @@ cost function:
       rain_water: qr
       snow_water: qs
       mole_fraction_of_ozone_in_air: o3ppmv
-      geopotential_height_times_gravity_at_surface: phis
+      geopotential_at_surface: phis
       initial_mass_fraction_of_large_scale_cloud_condensate: qls
       initial_mass_fraction_of_convective_cloud_condensate: qcn
       convective_cloud_area_fraction: cfcn
@@ -121,7 +121,7 @@ cost function:
       sea_surface_temperature: ts_found
   background error:
     covariance model: SABER
-#   covariance type: gsi static covariance
+    covariance type: gsi static covariance
     saber central block:
       saber block name: gsi hybrid covariance
       read: