Merge branch 'feature/stable-nightly' into global-workflow

CMakeLists.txt

@@ -68,15 +68,15 @@ if(BUILD_GDASBUNDLE)
 # Build GSI-B
   option(BUILD_GSIBEC "Build GSI-B" OFF)
   if(BUILD_GSIBEC)
-    ecbuild_bundle( PROJECT gsibec GIT "https://github.com/GEOS-ESM/GSIbec.git" BRANCH develop )
+    ecbuild_bundle( PROJECT gsibec GIT "https://github.com/GEOS-ESM/GSIbec.git" TAG 1.0.7 )
   endif()
 
 # Core JEDI repositories
-  ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  TAG c5d4b39 )
-  ecbuild_bundle( PROJECT vader GIT "https://github.com/jcsda/vader.git" TAG 8d11002 )
-  ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda/saber.git" TAG 2555221 )
-  ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda/ioda.git" TAG 433daa1  )
-  ecbuild_bundle( PROJECT ufo   GIT "https://github.com/jcsda/ufo.git" TAG d308177 )
+  ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  TAG e2b9dc6 )
+  ecbuild_bundle( PROJECT vader GIT "https://github.com/jcsda/vader.git" TAG de52190 )
+  ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda/saber.git" TAG 4c79b8c )
+  ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda/ioda.git" TAG f27bd1c  )
+  ecbuild_bundle( PROJECT ufo   GIT "https://github.com/jcsda/ufo.git" TAG 1a67b67 )
 
 # FMS and FV3 dynamical core
   ecbuild_bundle( PROJECT fms GIT "https://github.com/jcsda/FMS.git" TAG 1f73914 )
@@ -85,22 +85,22 @@ if(BUILD_GDASBUNDLE)
 # fv3-jedi and associated repositories
   ecbuild_bundle( PROJECT femps       GIT "https://github.com/jcsda/femps.git"                TAG cb39681 )
   ecbuild_bundle( PROJECT fv3-jedi-lm GIT "https://github.com/jcsda/fv3-jedi-linearmodel.git" TAG a934a7b )
-  ecbuild_bundle( PROJECT fv3-jedi    GIT "https://github.com/jcsda/fv3-jedi.git"             TAG 53e8a75 )
+  ecbuild_bundle( PROJECT fv3-jedi    GIT "https://github.com/jcsda/fv3-jedi.git"             TAG 07b1a28 )
 
 # SOCA associated repositories
   ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git" TAG 1a02eba )
   ecbuild_bundle( PROJECT mom6 GIT "https://github.com/jcsda-internal/MOM6.git" TAG 51ec489 RECURSIVE )
-  ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" TAG 1c5e0ef )
+  ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" TAG 5d1a7ad )
 
 # Build IODA converters
   option(BUILD_IODA_CONVERTERS "Build IODA Converters" ON)
   if(BUILD_IODA_CONVERTERS)
-    ecbuild_bundle( PROJECT iodaconv GIT "https://github.com/JCSDA-internal/ioda-converters.git" TAG 4c7db32 )
+    ecbuild_bundle( PROJECT iodaconv GIT "https://github.com/JCSDA-internal/ioda-converters.git" TAG c27c1df )
   endif()
 
 # Land associated repositories
   ecbuild_bundle( PROJECT land-imsproc  GIT "https://github.com/NOAA-PSL/land-IMS_proc.git"  TAG 6373819 )
-  ecbuild_bundle( PROJECT land-jediincr GIT "https://github.com/NOAA-PSL/land-apply_jedi_incr.git"  TAG 80b19b8 )
+  ecbuild_bundle( PROJECT land-jediincr GIT "https://github.com/NOAA-PSL/land-apply_jedi_incr.git"  TAG ced6576 )
 
 # ioda, ufo, fv3-jedi, and saber test data
 #---------------------------------

ci/validation/oblist_gfsv16p3.txt

@@ -17,10 +17,10 @@ amsua_n18
 amsua_n19
 atms_n20
 atms_npp
-avhrr_metop-b
-avhrr_metop-c
-avhrr_n18
-avhrr_n19
+avhrr3_metop-b
+avhrr3_metop-c
+avhrr3_n18
+avhrr3_n19
 cris-fsr_n20
 cris-fsr_npp
 gmi_gpm
@@ -41,4 +41,4 @@ ompslp_npp
 ompsnp_n20
 ompsnp_npp
 ompstc8_n20
-ompstc8_npp
+ompstc8_npp

parm/atm/berror/hybvar_bump.yaml

@@ -10,7 +10,7 @@ components:
       active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         io:
-          data directory: !ENV &staticb_dir ${DATA}/berror
+          data directory: &staticb_dir $(DATA)/berror
         drivers:
           multivariate strategy: specific_univariate
           read local nicas: true
@@ -95,17 +95,17 @@ components:
     covariance model: ensemble
     members from template:
       template:
-        datetime: '{{BKG_ISOTIME}}'
+        datetime: '{{ current_cycle | to_isotime }}'
         filetype: fms restart
         state variables: *3dvars
         datapath: ens/mem%mem%/
-        filename_core: '{{BKG_YYYYmmddHHMMSS}}.fv_core.res.nc'
-        filename_trcr: '{{BKG_YYYYmmddHHMMSS}}.fv_tracer.res.nc'
-        filename_sfcd: '{{BKG_YYYYmmddHHMMSS}}.sfc_data.nc'
-        filename_sfcw: '{{BKG_YYYYmmddHHMMSS}}.fv_srf_wnd.res.nc'
-        filename_cplr: '{{BKG_YYYYmmddHHMMSS}}.coupler.res'
+        filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
+        filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
+        filename_sfcd: '{{ current_cycle | to_fv3time }}.sfc_data.nc'
+        filename_sfcw: '{{ current_cycle | to_fv3time }}.fv_srf_wnd.res.nc'
+        filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
       pattern: '%mem%'
-      nmembers: !ENV ${NMEM_ENKF}
+      nmembers: $(NMEM_ENKF)
       zero padding: 3
 #    localization:
 #      localization method: SABER

parm/atm/berror/hybvar_gsibec.yaml

@@ -0,0 +1,67 @@
+covariance model: hybrid
+components:
+- covariance:
+    covariance model: SABER
+    saber central block:
+      saber block name: gsi covariance
+      input variables: &control_vars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+                                      specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+                                      mole_fraction_of_ozone_in_air]
+      output variables: *control_vars
+      gsi akbk: &akbk $(DATA)/fv3jedi/akbk.nc4
+      gsi error covariance file: &gsiberr $(DATA)/berror/gsi-coeffs-gfs-global.nc4
+#     gsi error covariance file: &gsiberr $(DATA)/berror/global_berror.f77
+      gsi berror namelist file: &gsibnml $(DATA)/berror/gfs_gsi_global.nml
+      processor layout x direction: &layout_gsib_x 3
+      processor layout y direction: &layout_gsib_y 2
+      debugging mode: false
+    saber outer blocks:
+    - saber block name: gsi interpolation to model grid
+      input variables: *control_vars
+      output variables: *control_vars
+      gsi akbk: *akbk
+      gsi error covariance file: *gsiberr
+      gsi berror namelist file: *gsibnml
+      processor layout x direction: *layout_gsib_x
+      processor layout y direction: *layout_gsib_y
+      debugging mode: false
+    linear variable change:
+      linear variable change name: Control2Analysis
+      input variables: *control_vars
+      output variables: &3dvars_anal [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+  weight:
+    value: 0.125
+- covariance:
+    covariance model: ensemble
+    members from template:
+      template:
+        datetime: '{{ current_cycle | to_isotime }}'
+        filetype: fms restart
+        state variables: *3dvars_anal
+        datapath: ens/mem%mem%
+        filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
+        filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
+        filename_sfcd: '{{ current_cycle | to_fv3time }}.sfc_data.nc'
+        filename_sfcw: '{{ current_cycle | to_fv3time }}.fv_srf_wnd.res.nc'
+        filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
+      pattern: '%mem%'
+      nmembers: $(NMEM_ENKF)
+      zero padding: 3
+#    localization:
+#      localization method: SABER
+#      saber block:
+#      - saber block name: BUMP_NICAS
+#        input variables: *control_vars
+#        output variables: *control_vars
+#        active variables: *active_vars
+#        bump:
+#          datadir: *staticb_dir
+#          verbosity: main
+#          strategy: specific_univariate
+#          method: loc
+#          load_nicas_local: true
+#          grids:
+#          - prefix: nicas/nicas_3D_gfs
+#            variables: [stream_function,velocity_potential,air_temperature,relative_humidity,cloud_liquid_water,ozone_mass_mixing_ratio]
+  weight:
+    value: 0.875

parm/atm/berror/staticb_bump.yaml

@@ -8,7 +8,7 @@ saber blocks:
   active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
   bump:
     io:
-      data directory: !ENV &staticb_dir ${DATA}/berror
+      data directory: &staticb_dir $(DATA)/berror
     drivers:
       multivariate strategy: specific_univariate
       read local nicas: true

parm/atm/berror/staticb_gsibec.yaml

@@ -6,10 +6,10 @@ saber central block:
                            specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                            mole_fraction_of_ozone_in_air]
   output variables: *control_vars
-  gsi akbk: !ENV &akbk ${DATA}/fv3jedi/akbk.nc4
-  gsi error covariance file: !ENV &gsiberr ${DATA}/berror/gsi-coeffs-gfs-global.nc4
-# gsi error covariance file: !ENV &gsiberr ${DATA}/berror/global_berror.f77
-  gsi berror namelist file: !ENV &gsibnml ${DATA}/berror/gfs_gsi_global.nml
+  gsi akbk: &akbk $(DATA)/fv3jedi/akbk.nc4
+  gsi error covariance file: &gsiberr $(DATA)/berror/gsi-coeffs-gfs-global.nc4
+# gsi error covariance file: &gsiberr $(DATA)/berror/global_berror.f77
+  gsi berror namelist file: &gsibnml $(DATA)/berror/gfs_gsi_global.nml
   processor layout x direction: &layout_gsib_x 3
   processor layout y direction: &layout_gsib_y 2
   debugging mode: false

parm/atm/hofx/hofx4d.yaml

@@ -1,35 +1,35 @@
-window begin: '{{ATM_WINDOW_BEGIN}}'
+window begin: '{{ ATM_WINDOW_BEGIN | to_isotime }}'
 window length: $(ATM_WINDOW_LENGTH)
 forecast length: $(ATM_WINDOW_LENGTH)
 geometry:
   fms initialization:
-    namelist filename: !ENV ${DATA}/fv3jedi/fmsmpp.nml
-    field table filename: !ENV ${DATA}/fv3jedi/field_table
-  akbk: !ENV ${DATA}/fv3jedi/akbk.nc4
+    namelist filename: $(DATA)/fv3jedi/fmsmpp.nml
+    field table filename: $(DATA)/fv3jedi/field_table
+  akbk: $(DATA)/fv3jedi/akbk.nc4
   layout:
-  - !ENV ${layout_x}
-  - !ENV ${layout_y}
+  - $(layout_x)
+  - $(layout_y)
   npx: $(npx_ges)
   npy: $(npy_ges)
   npz: $(npz_ges)
-  field metadata override: !ENV ${DATA}/fv3jedi/gfs-restart.yaml
+  field metadata override: $(DATA)/fv3jedi/gfs-restart.yaml
 initial condition:
-  datapath: !ENV ${DATA}/bkg
+  datapath: $(DATA)/bkg
   filetype: fms restart
-  datetime: '{{ATM_WINDOW_BEGIN}}'
-  filename_core: '{{ATM_BEGIN_YYYYmmddHHMMSS}}.fv_core.res.nc'
-  filename_trcr: '{{ATM_BEGIN_YYYYmmddHHMMSS}}.fv_tracer.res.nc'
-  filename_sfcd: '{{ATM_BEGIN_YYYYmmddHHMMSS}}.sfc_data.nc'
-  filename_sfcw: '{{ATM_BEGIN_YYYYmmddHHMMSS}}.fv_srf_wnd.res.nc'
-  filename_cplr: '{{ATM_BEGIN_YYYYmmddHHMMSS}}.coupler.res'
+  datetime: '{{ ATM_WINDOW_BEGIN | to_isotime }}'
+  filename_core: '{{ ATM_WINDOW_BEGIN | to_fv3time }}.fv_core.res.nc'
+  filename_trcr: '{{ ATM_WINDOW_BEGIN | to_fv3time }}.fv_tracer.res.nc'
+  filename_sfcd: '{{ ATM_WINDOW_BEGIN | to_fv3time }}.sfc_data.nc'
+  filename_sfcw: '{{ ATM_WINDOW_BEGIN | to_fv3time }}.fv_srf_wnd.res.nc'
+  filename_cplr: '{{ ATM_WINDOW_BEGIN | to_fv3time }}.coupler.res'
   state variables: [ua,va,t,delp,sphum,ice_wat,liq_wat,o3mr,phis,
                     slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                     u_srf,v_srf,f10m]
 model:
   name: PSEUDO
-  datapath: !ENV ${DATA}/bkg
+  datapath: $(DATA)/bkg
   filetype: fms restart
-  datetime: '{{ATM_WINDOW_BEGIN}}'
+  datetime: '{{ ATM_WINDOW_BEGIN | to_isotime }}'
   filename is datetime templated: true
   filename_core: '%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc'
   filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'

parm/atm/hofx/hofx_nomodel.yaml

@@ -1,26 +1,26 @@
-window begin: '{{ATM_WINDOW_BEGIN}}'
+window begin: '{{ ATM_WINDOW_BEGIN | to_isotime }}'
 window length: $(ATM_WINDOW_LENGTH)
 geometry:
   fms initialization:
-    namelist filename: !ENV ${DATA}/fv3jedi/fmsmpp.nml
-    field table filename: !ENV ${DATA}/fv3jedi/field_table
-  akbk: !ENV ${DATA}/fv3jedi/akbk.nc4
+    namelist filename: $(DATA)/fv3jedi/fmsmpp.nml
+    field table filename: $(DATA)/fv3jedi/field_table
+  akbk: $(DATA)/fv3jedi/akbk.nc4
   layout:
-  - !ENV ${layout_x}
-  - !ENV ${layout_y}
+  - $(layout_x)
+  - $(layout_y)
   npx: $(npx_ges)
   npy: $(npy_ges)
   npz: $(npz_ges)
-  field metadata override: !ENV ${DATA}/fv3jedi/gfs-restart.yaml
+  field metadata override: $(DATA)/fv3jedi/gfs-restart.yaml
 state:
-  datapath: !ENV ${DATA}/bkg
+  datapath: $(DATA)/bkg
   filetype: fms restart
-  datetime: '{{BKG_ISOTIME}}'
-  filename_core: '{{BKG_YYYYmmddHHMMSS}}.fv_core.res.nc'
-  filename_trcr: '{{BKG_YYYYmmddHHMMSS}}.fv_tracer.res.nc'
-  filename_sfcd: '{{BKG_YYYYmmddHHMMSS}}.sfc_data.nc'
-  filename_sfcw: '{{BKG_YYYYmmddHHMMSS}}.fv_srf_wnd.res.nc'
-  filename_cplr: '{{BKG_YYYYmmddHHMMSS}}.coupler.res'
+  datetime: '{{ current_cycle | to_isotime }}'
+  filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
+  filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
+  filename_sfcd: '{{ current_cycle | to_fv3time }}.sfc_data.nc'
+  filename_sfcw: '{{ current_cycle | to_fv3time }}.fv_srf_wnd.res.nc'
+  filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
   state variables: [ua,va,t,delp,sphum,ice_wat,liq_wat,o3mr,phis,
                     slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                     u_srf,v_srf,f10m]

parm/atm/lgetkf/lgetkf.yaml

@@ -4,32 +4,33 @@ geometry:
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - !ENV ${layout_x}
-  - !ENV ${layout_y}
+  - $(layout_x)
+  - $(layout_y)
   npx: $(npx_ges)
   npy: $(npy_ges)
   npz: $(npz_ges)
   field metadata override: ./fv3jedi/gfs-restart.yaml
-window begin: '$(ATM_WINDOW_BEGIN)'
-window length: PT6H
+window begin: '{{ ATM_WINDOW_BEGIN | to_isotime }}'
+window length: $(ATM_WINDOW_LENGTH)
+increment variables: [ua,va,DZ,delp,t,ps,sphum,ice_wat,liq_wat,o3mr]
 
 background:
-   datetime: '{{BKG_ISOTIME}}'
+   datetime: '{{ current_cycle | to_isotime }}'
    members from template:
      template:
-       datetime: '{{BKG_ISOTIME}}'
+       datetime: '{{ current_cycle | to_isotime }}'
        filetype: fms restart
        state variables: [ua,va,t,DZ,delp,ps,sphum,ice_wat,liq_wat,o3mr,phis,
                         slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                         u_srf,v_srf,f10m]
-       datapath: bkg/mem%mem%/RESTART
-       filename_core: '{{BKG_YYYYmmddHHMMSS}}.fv_core.res.nc'
-       filename_trcr: '{{BKG_YYYYmmddHHMMSS}}.fv_tracer.res.nc'
-       filename_sfcd: '{{BKG_YYYYmmddHHMMSS}}.sfc_data.nc'
-       filename_sfcw: '{{BKG_YYYYmmddHHMMSS}}.fv_srf_wnd.res.nc'
-       filename_cplr: '{{BKG_YYYYmmddHHMMSS}}.coupler.res'
+       datapath: bkg/mem%mem%
+       filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
+       filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
+       filename_sfcd: '{{ current_cycle | to_fv3time }}.sfc_data.nc'
+       filename_sfcw: '{{ current_cycle | to_fv3time }}.fv_srf_wnd.res.nc'
+       filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
      pattern: '%mem%'
-     nmembers: !ENV ${NMEM_ENKF}
+     nmembers: $(NMEM_ENKF)
      zero padding: 3
 
 observations: !INC ${OBS_LIST}
@@ -41,6 +42,7 @@ driver:
   save prior mean: false
   save posterior mean increment: false
   save posterior ensemble increments: true
+  do posterior observer: false
 
 local ensemble DA:
   solver: GETKF

parm/atm/obs/config/aircraft.yaml

@@ -3,15 +3,15 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}aircraft.${CDATE}.nc4
+      obsfile: $(DATA)/obs/$(OPREFIX)aircraft.${{ current_cycle | to_YMDH }}.nc4
     obsgrouping:
       group variables: ["stationIdentification"]
       sort variable: "pressure"
       sort order: "descending"
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/diag_aircraft_${CDATE}.nc4
+      obsfile: $(DATA)/diags/diag_aircraft_${{ current_cycle | to_YMDH }}.nc4
   io pool:
     max pool size: 1
   simulated variables: [windEastward, windNorthward, airTemperature, specificHumidity]