Faster/Better ens. B processing/recentering

CMakeLists.txt

@@ -74,7 +74,7 @@ if(BUILD_GDASBUNDLE)
   ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git" BRANCH develop )
 
 # Core JEDI repositories
-  ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  BRANCH develop )
+  ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  BRANCH develop)
   ecbuild_bundle( PROJECT vader GIT "https://github.com/jcsda/vader.git" BRANCH develop )
   ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda/saber.git" BRANCH develop )
   ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda/ioda.git" BRANCH develop  )

parm/soca/berror/soca_apply_steric.yaml → parm/soca/berror/old/soca_apply_steric.yaml

@@ -31,14 +31,15 @@ linear variable change:
   - linear variable change name: BkgErrFILT
     ocean_depth_min: 500  # zero where ocean is shallower than 500m
     rescale_bkgerr: 1.0   # rescale perturbation
-    efold_z: 1500.0       # Apply exponential decay
+    efold_z: 2500.0       # Apply exponential decay
   - linear variable change name: BalanceSOCA
-  trajectory:
-    state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld]
-    date: '{{ATM_WINDOW_BEGIN}}'
-    basename: ./INPUT/
-    ocn_filename: MOM.res.nc
-    read_from_file: 1
+
+trajectory:
+  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld]
+  date: '{{ATM_WINDOW_BEGIN}}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  read_from_file: 1
 
 output increment:
   datadir: ./static_ens/

parm/soca/berror/soca_clim_ens_moments.yaml → parm/soca/berror/old/soca_clim_ens_moments.yaml

@@ -11,7 +11,6 @@ ensemble:
       basename: ./static_ens/
       ocn_filename: ocn.%mem%.nc
       ice_filename: ice.%mem%.nc
-      remap_filename: ./INPUT/MOM.res.nc
       state variables: [tocn, socn, ssh, uocn, vocn, hocn, cicen, hicen, hsnon]
     pattern: '%mem%'
     nmembers: ${CLIM_ENS_SIZE}

parm/soca/berror/soca_clim_ens_perts.yaml → parm/soca/berror/old/soca_clim_ens_perts.yaml

@@ -23,7 +23,6 @@ ensemble:
       basename: ./static_ens/
       ocn_filename: ocn.%mem%.nc
       ice_filename: ice.%mem%.nc
-      remap_filename: ./INPUT/MOM.res.nc
       state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh, hocn, mld, layer_depth]
     pattern: '%mem%'
     nmembers: ${CLIM_ENS_SIZE}

parm/soca/berror/saber_blocks.yaml

@@ -28,9 +28,8 @@ components:
       - linear variable change name: BkgErrSOCA
         read_from_file: 3
         basename: ./static_ens/
-        ocn_filename: 'ocn.orig_ens_stddev.incr.{{ATM_WINDOW_BEGIN}}.nc'
-        ice_filename: 'ice.orig_ens_stddev.incr.{{ATM_WINDOW_BEGIN}}.nc'
-        #remap_filename: ./INPUT/MOM.res.nc
+        ocn_filename: 'ocn.bkgerr_stddev.incr.{{ATM_WINDOW_BEGIN}}.nc'
+        ice_filename: 'ice.bkgerr_stddev.incr.{{ATM_WINDOW_BEGIN}}.nc'
         date: '{{ATM_WINDOW_MIDDLE}}'
         t_min: 0.1
         t_max: 10.0
@@ -45,8 +44,7 @@ components:
         standard deviation: true
 
       - linear variable change name: BalanceSOCA
-        ksshts:
-          nlayers: 10
+
   weight:
     value: 1.0
 - covariance:
@@ -56,8 +54,8 @@ components:
         read_from_file: 1
         date: '{{ATM_WINDOW_MIDDLE}}'
         basename: ./static_ens/
-        ocn_filename: 'ocn.pert.steric.%mem%.{{ATM_WINDOW_BEGIN}}.nc'
-        ice_filename: 'ice.pert.ens.%mem%.{{ATM_WINDOW_BEGIN}}.PT0S.nc'
+        ocn_filename: 'ocn.pert.steric.%mem%.nc'
+        ice_filename: 'ice.%mem%.nc'
         state variables: [tocn, socn, ssh, uocn, vocn, cicen, hicen, hsnon]
       pattern: '%mem%'
       nmembers: ${CLIM_ENS_SIZE}

parm/soca/berror/soca_ensb.yaml

@@ -0,0 +1,92 @@
+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{ATM_WINDOW_BEGIN}}'
+
+layers variable: [hocn]
+
+increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
+
+set increment variables to zero: [ssh]
+
+vertical geometry:
+  date: '{{ATM_WINDOW_BEGIN}}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  read_from_file: 3
+
+soca increments:
+  number of increments: ${CLIM_ENS_SIZE}
+  pattern: '%mem%'
+  template:
+    date: '{{ATM_WINDOW_BEGIN}}'
+    basename: ./static_ens/
+    ocn_filename: 'ocn.%mem%.nc'
+    ice_filename: 'ice.%mem%.nc'
+    read_from_file: 3
+
+steric height:
+  linear variable changes:
+  - linear variable change name: BalanceSOCA  # Only the steric balance is applied
+
+ssh output:
+  unbalanced:
+    datadir: ./static_ens
+    date: '{{ATM_WINDOW_BEGIN}}'
+    exp: ssh_unbal_stddev
+    type: incr
+
+  steric:
+    datadir: ./static_ens
+    date: '{{ATM_WINDOW_BEGIN}}'
+    exp: ssh_steric_stddev
+    type: incr
+
+  total:
+    datadir: ./static_ens
+    date: '{{ATM_WINDOW_BEGIN}}'
+    exp: ssh_total_stddev
+    type: incr
+
+  explained variance:
+    datadir: ./static_ens
+    date: '{{ATM_WINDOW_BEGIN}}'
+    exp: steric_explained_variance
+    type: incr
+
+  recentering error:
+    datadir: ./static_ens
+    date: '{{ATM_WINDOW_BEGIN}}'
+    exp: ssh_recentering_error
+    type: incr
+
+background error output:
+  datadir: ./static_ens
+  date: '{{ATM_WINDOW_BEGIN}}'
+  exp: bkgerr_stddev
+  type: incr
+
+linear variable change:
+  linear variable changes:
+#  - linear variable change name: BkgErrFILT
+#    ocean_depth_min: 500  # zero where ocean is shallower than 500m
+#    rescale_bkgerr: 1.0   # rescale perturbation
+#    efold_z: 1500.0       # Apply exponential decay
+  - linear variable change name: BalanceSOCA
+
+trajectory:
+  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
+  date: '{{ATM_WINDOW_BEGIN}}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  read_from_file: 1
+
+output increment:
+  datadir: ./static_ens
+  date: '{{ATM_WINDOW_BEGIN}}'
+  exp: trash
+  type: incr
+  output file: 'ocn.pert.steric.%mem%.nc'
+  pattern: '%mem%'

parm/soca/variational/3dvarfgat.yaml

@@ -33,7 +33,7 @@ variational:
       mom6_input_nml: mom_input.nml
       fields metadata: ./fields_metadata.yaml
     ninner: !ENV ${SOCA_NINNER}
-    gradient norm reduction: 1e-10
+    gradient norm reduction: 1e-7
     diagnostics:
       departures: ombg
 

scripts/exgdas_global_marine_analysis_bmat.sh

@@ -123,40 +123,14 @@ fi
 # 3 - Copy h from deterministic to unbalanced perturbations
 # 4 - Compute moments of converted ensemble perturbations
 
-# Compute ensemble moments
+# Process static ensemble
 clean_yaml soca_clim_ens_moments.yaml
-$APRUN_OCNANAL $JEDI_BIN/soca_ensmeanandvariance.x soca_clim_ens_moments.yaml
+$APRUN_OCNANAL $JEDI_BIN/gdas_ens_handler.x soca_ensb.yaml
 export err=$?; err_chk
 if [ $err -gt 0  ]; then
     exit $err
 fi
 
-# Zero out std. dev of ssh to use the balance as a strong constraint
-# TODO: Apply the inverse of the balance
-clean_yaml soca_clim_ens_moments.yaml
-$APRUN_OCNANAL $JEDI_BIN/gdas_incr_handler.x soca_postproc_stddev.yaml
-export err=$?; err_chk
-if [ $err -gt 0  ]; then
-    exit $err
-fi
-
-# Compute ensemble perturbations, vertically remap to cycle's vertical geometry
-clean_yaml soca_clim_ens_perts.yaml
-$APRUN_OCNANAL $JEDI_BIN/soca_ensrecenter.x soca_clim_ens_perts.yaml
-export err=$?; err_chk
-if [ $err -gt 0  ]; then
-    exit $err
-fi
-
-# Vertical filtering of the 3D perturbations and recompute the steric height perturbation
-clean_yaml soca_apply_steric.yaml
-$APRUN_OCNANAL $JEDI_BIN/gdas_incr_handler.x soca_apply_steric.yaml
-export err=$?; err_chk
-if [ $err -gt 0  ]; then
-    exit $err
-fi
-
-
 ################################################################################
 # Correlation and Localization operators
 shopt -s nullglob
@@ -224,14 +198,6 @@ if [ $err -gt 0  ]; then
     exit $err
 fi
 
-################################################################################
-# Create ensemble of perturbations for the cycle
-
-# Use ensemble recenter with "zerocenter"
-
-# Apply inverse balance to perturbations, use deterministic background as trajectory
-
-
 ################################################################################
 set +x
 if [ $VERBOSE = "YES" ]; then

scripts/exgdas_global_marine_analysis_post.py

@@ -59,28 +59,33 @@ def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
 post_file_list.append([os.path.join(anl_dir, 'inc.nc'),
                        os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocninc.nc')])
 
-# Copy of the diagonal of the background error for the cycle
-post_file_list.append([os.path.join(anl_dir, 'static_ens', f'ocn.orig_ens_stddev.incr.{bdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.bkgerr_stddev.nc')])
-post_file_list.append([os.path.join(anl_dir, 'static_ens', f'ice.orig_ens_stddev.incr.{bdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ice.bkgerr_stddev.nc')])
-
-# Copy the ice and ocean increments
-post_file_list.append([os.path.join(anl_dir, 'Data', f'ocn.3dvarfgat_pseudo.incr.{mdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.incr.nc')])
-post_file_list.append([os.path.join(anl_dir, 'Data', f'ice.3dvarfgat_pseudo.incr.{mdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ice.incr.nc')])
+domains = ['ocn', 'ice']
+for domain in domains:
+    # Copy of the diagonal of the background error for the cycle
+    post_file_list.append([os.path.join(anl_dir, 'static_ens', f'{domain}.bkgerr_stddev.incr.{bdate}.nc'),
+                           os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.bkgerr_stddev.nc')])
+
+    # Copy the recentering error
+    post_file_list.append([os.path.join(anl_dir, 'static_ens', f'{domain}.ssh_recentering_error.incr.{bdate}.nc'),
+                           os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.recentering_error.nc')])
+
+    # Copy the ice and ocean increments
+    post_file_list.append([os.path.join(anl_dir, 'Data', f'{domain}.3dvarfgat_pseudo.incr.{mdate}.nc'),
+                           os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.incr.nc')])
+
+    # Copy the analysis at the start of the window
+    post_file_list.append([os.path.join(anl_dir, 'Data', f'{domain}.3dvarfgat_pseudo.an.{mdate}.nc'),
+                           os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}ana.nc')])
+
+# Copy of the ssh diagnostics
+for string in ['ssh_steric_stddev', 'ssh_unbal_stddev', 'ssh_total_stddev', 'steric_explained_variance']:
+    post_file_list.append([os.path.join(anl_dir, 'static_ens', f'ocn.{string}.incr.{bdate}.nc'),
+                           os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.{string}.nc')])
 
 # Copy DA grid (computed for the start of the window)
 post_file_list.append([os.path.join(anl_dir, 'soca_gridspec.nc'),
                        os.path.join(com_ocean_analysis, f'{RUN}.t{bcyc}z.ocngrid.nc')])
 
-# Copy the analysis at the start of the window
-post_file_list.append([os.path.join(anl_dir, 'Data', f'ocn.3dvarfgat_pseudo.an.{mdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocnana.nc')])
-post_file_list.append([os.path.join(anl_dir, 'Data', f'ice.3dvarfgat_pseudo.an.{mdate}.nc'),
-                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.iceana.nc')])
-
 # Copy the CICE analysis restart
 cdateice = pdy + '.' + cyc + '0000'
 post_file_list.append([os.path.join(anl_dir, 'Data', f'{cdateice}.cice_model.res.nc'),
@@ -97,10 +102,6 @@ def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
 fh_list = list_all_files(os.path.join(anl_dir, 'diags'),
                          os.path.join(com_ocean_analysis, 'diags'))
 
-# localization and correlation operators
-fh_list = list_all_files(os.path.join(anl_dir, 'bump'),
-                         os.path.join(com_ocean_analysis, 'bump'), fh_list=fh_list)
-
 # yaml configurations
 fh_list = list_all_files(os.path.join(anl_dir),
                          os.path.join(com_ocean_analysis, 'yaml'), wc='*.yaml', fh_list=fh_list)

scripts/exgdas_global_marine_analysis_prep.py

@@ -339,56 +339,17 @@ def find_clim_ens(input_date):
 gridgen_yaml_dst = os.path.abspath(os.path.join(stage_cfg['stage_dir'], 'gridgen.yaml'))
 FileHandler({'copy': [[gridgen_yaml_src, gridgen_yaml_dst]]}).sync()
 
-
 ################################################################################
-# generate YAML file for parametric diag of B
-
-logging.info(f"---------------- generate parametric_stddev_b.yaml")
-berr_yaml = os.path.join(anl_dir, 'parametric_stddev_b.yaml')
-berr_yaml_template = os.path.join(gdas_home,
-                                  'parm',
-                                  'soca',
-                                  'berror',
-                                  'parametric_stddev_b.yaml')
-config = YAMLFile(path=berr_yaml_template)
-config = Template.substitute_structure(config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
-config = Template.substitute_structure(config, TemplateConstants.DOLLAR_PARENTHESES, envconfig.get)
-config.save(berr_yaml)
-
-################################################################################
-# generate YAMLS file for diag of clim. ens. B
+# generate the YAML file for the post processing of the clim. ens. B
 berror_yaml_dir = os.path.join(gdas_home, 'parm', 'soca', 'berror')
 
-logging.info(f"---------------- generate soca_clim_ens_moments.yaml")
-berr_yaml = os.path.join(anl_dir, 'soca_clim_ens_moments.yaml')
-berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_clim_ens_moments.yaml')
+logging.info(f"---------------- generate soca_ensb.yaml")
+berr_yaml = os.path.join(anl_dir, 'soca_ensb.yaml')
+berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_ensb.yaml')
 config = YAMLFile(path=berr_yaml_template)
 config = Template.substitute_structure(config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
 config.save(berr_yaml)
 
-logging.info(f"---------------- generate soca_postproc_stddev.yaml")
-berr_yaml = os.path.join(anl_dir, 'soca_postproc_stddev.yaml')
-berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_postproc_stddev.yaml')
-config = YAMLFile(path=berr_yaml_template)
-config = Template.substitute_structure(config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
-config.save(berr_yaml)
-
-logging.info(f"---------------- generate soca_clim_ens_perts.yaml")
-berr_yaml = os.path.join(anl_dir, 'soca_clim_ens_perts.yaml')
-berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_clim_ens_perts.yaml')
-config = YAMLFile(path=berr_yaml_template)
-config = Template.substitute_structure(config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
-config = Template.substitute_structure(config, TemplateConstants.DOLLAR_PARENTHESES, envconfig.get)
-config.save(berr_yaml)
-
-logging.info(f"---------------- generate soca_apply_steric.yaml")
-berr_yaml = os.path.join(anl_dir, 'soca_apply_steric.yaml')
-berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_apply_steric.yaml')
-config = YAMLFile(path=berr_yaml_template)
-config = Template.substitute_structure(config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
-config = Template.substitute_structure(config, TemplateConstants.DOLLAR_PARENTHESES, envconfig.get)
-config.save(berr_yaml)
-
 logging.info(f"---------------- generate soca_ensweights.yaml")
 berr_yaml = os.path.join(anl_dir, 'soca_ensweights.yaml')
 berr_yaml_template = os.path.join(berror_yaml_dir, 'soca_ensweights.yaml')