FMS 2023.04 change and using relative paths in config (#395)

* fms version update * switch to relative path for configurations * switch to relative path for rcov * flow.cylc changes, abandan static stage for now * sles15 modules
GEOS-ESM · Jul 31, 2024 · e951bac · e951bac
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diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background.yaml
@@ -1,9 +1,9 @@
 datetime: '{{local_background_time_iso}}'
 filetype: cube sphere history
 provider: geos
-datapath: ''
-filenames: ['{{cycle_dir}}/bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
-            '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
+datapath: '{{cycle_dir}}'
+filenames: ['bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
+            'fv3-jedi/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
 state variables: [ua,va,t,delp,ps,q,qi,ql,qr,qs,o3ppmv,phis,
                   qls,qcn,cfcn,frocean,frland,varflt,ustar,bstar,
                   zpbl,cm,ct,cq,kcbl,tsm,khl,khu,frlake,frseaice,vtype,

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml
@@ -2,9 +2,9 @@ covariance model: SABER
 saber central block:
   saber block name: gsi hybrid covariance
   read:
-    gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
-    gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
-    gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
+    gsi akbk: './fv3-jedi/fv3files/akbk{{vertical_resolution}}.nc4'
+    gsi error covariance file: './fv3-jedi/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
+    gsi berror namelist file: './fv3-jedi/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
     processor layout x direction: {{gsibec_npx_proc}}
     processor layout y direction: {{gsibec_npy_proc}}
     debugging mode: false
@@ -15,9 +15,9 @@ saber outer blocks:
                                       mole_fraction_of_ozone_in_air,
                                       fraction_of_ocean,fraction_of_lake,fraction_of_ice,
                                       sfc_geopotential_height_times_grav]
-  gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
-  gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
-  gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
+  gsi akbk: './fv3-jedi/fv3files/akbk{{vertical_resolution}}.nc4'
+  gsi error covariance file: './fv3-jedi/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
+  gsi berror namelist file: './fv3-jedi/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml'
   processor layout x direction: {{gsibec_npx_proc}}
   processor layout y direction: {{gsibec_npy_proc}}
   debugging mode: false

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry.yaml
@@ -1,9 +1,9 @@
 fms initialization:
-  namelist filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/fmsmpp.nml'
-  field table filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/field_table_gmao'
-akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
+  namelist filename: './fv3-jedi/fv3files/fmsmpp.nml'
+  field table filename: './fv3-jedi/fv3files/field_table_gmao'
+akbk: './fv3-jedi/fv3files/akbk{{vertical_resolution}}.nc4'
 layout: [{{npx_proc}},{{npy_proc}}]
 npx: {{horizontal_resolution}}
 npy: {{horizontal_resolution}}
 npz: {{vertical_resolution}}
-field metadata override: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/geos.yaml'
+field metadata override: './fv3-jedi/fieldmetadata/geos.yaml'
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry_inner.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry_inner.yaml
@@ -1,9 +1,9 @@
 fms initialization:
-  namelist filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/fmsmpp.nml'
-  field table filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/field_table_gmao'
-akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
+  namelist filename: './fv3-jedi/fv3files/fmsmpp.nml'
+  field table filename: './fv3-jedi/fv3files/field_table_gmao'
+akbk: './fv3-jedi/fv3files/akbk{{vertical_resolution}}.nc4'
 layout: [{{npx_proc}},{{npy_proc}}]
 npx: {{horizontal_resolution}}
 npy: {{horizontal_resolution}}
 npz: {{vertical_resolution}}
-field metadata override: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/geos.yaml'
+field metadata override: './fv3-jedi/fieldmetadata/geos.yaml'
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/pseudo-model.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/pseudo-model.yaml
@@ -2,6 +2,6 @@ name: PSEUDO
 tstep: {{background_frequency}}
 filetype: cube sphere history
 provider: geos
-datapath: ''
-filenames: ['{{cycle_dir}}/bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
-            '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
+datapath: '{{cycle_dir}}'
+filenames: ['bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
+            'fv3-jedi/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage_cycle.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage_cycle.yaml
@@ -0,0 +1,8 @@
+- link_files:
+    directories:
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{cycle_dir}}/fv3-jedi/bkg/']
+      - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fieldmetadata/*', '{{cycle_dir}}/fv3-jedi/fieldmetadata/']
+      - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fv3files/*', '{{cycle_dir}}/fv3-jedi/fv3files/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4', '{{cycle_dir}}/fv3-jedi/gsibec/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/{{gsibec_configuration}}_c{{horizontal_resolution}}.nml', '{{cycle_dir}}/fv3-jedi/gsibec/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/rcov/1.0.0/*', '{{cycle_dir}}/fv3-jedi/rcov/']
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/airs_aqua.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/airs_aqua.yaml
@@ -56,7 +56,7 @@ obs bias:
 
 obs error:
   covariance model: cross variable covariances
-  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/airs_aqua_119_jedi_rcov.nc4'
+  input file: 'fv3-jedi/rcov/airs_aqua_119_jedi_rcov.nc4'
 
 obs prior filters:
 - filter: Perform Action

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_n20.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_n20.yaml
@@ -55,7 +55,7 @@ obs bias:
 
 obs error:
   covariance model: cross variable covariances
-  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/cris-fsr_108_jedi_rcov.nc4'
+  input file: 'fv3-jedi/rcov/cris-fsr_108_jedi_rcov.nc4'
 
 obs prior filters:
 - filter: Perform Action

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_npp.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/cris-fsr_npp.yaml
@@ -55,7 +55,7 @@ obs bias:
 
 obs error:
   covariance model: cross variable covariances
-  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/cris-fsr_108_jedi_rcov.nc4'
+  input file: 'fv3-jedi/rcov/cris-fsr_108_jedi_rcov.nc4'
 
 obs prior filters:
 - filter: Perform Action

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-b.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-b.yaml
@@ -55,7 +55,7 @@ obs bias:
 
 obs error:
   covariance model: cross variable covariances
-  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/iasi_metop_141_jedi_rcov.nc4'
+  input file: 'fv3-jedi/rcov/iasi_metop_141_jedi_rcov.nc4'
 
 obs prior filters:
 - filter: Perform Action

diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-c.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/observations/iasi_metop-c.yaml
@@ -55,7 +55,7 @@ obs bias:
 
 obs error:
   covariance model: cross variable covariances
-  input file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/rcov/iasi_metop_141_jedi_rcov.nc4'
+  input file: 'fv3-jedi/rcov/iasi_metop_141_jedi_rcov.nc4'
 
 obs prior filters:
 - filter: Perform Action

diff --git a/src/swell/deployment/platforms/nccs_discover/modules b/src/swell/deployment/platforms/nccs_discover/modules
@@ -18,7 +18,8 @@ module load stack-python/3.10.13
 module load jedi-fv3-env
 module load soca-env
 module load gmao-swell-env/1.0.0
-module unload gsibec crtm
+module unload gsibec crtm fms
+module load fms/2023.04
 
 # JEDI Python Path
 # ----------------

diff --git a/src/swell/deployment/platforms/nccs_discover/task_questions.yaml b/src/swell/deployment/platforms/nccs_discover/task_questions.yaml
@@ -8,10 +8,10 @@ existing_geos_gcm_source_path:
   default_value: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-v11.6.0/
 
 existing_jedi_build_directory:
-  default_value: /discover/nobackup/gmao_ci/swell/tier2/stable/build_jedi/jedi_bundle/build/
+  default_value: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES12/build-intel-release
 
 existing_jedi_source_directory:
-  default_value: /discover/nobackup/gmao_ci/swell/tier2/stable/build_jedi/jedi_bundle/source/
+  default_value: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES12
 
 geos_experiment_directory:
   default_value: 5deg_v11

diff --git a/src/swell/deployment/platforms/nccs_discover_sles15/modules b/src/swell/deployment/platforms/nccs_discover_sles15/modules
@@ -19,7 +19,8 @@ module load py-pip/23.1.2
 module load jedi-fv3-env
 module load soca-env
 module load gmao-swell-env/1.0.0
-module unload gsibec crtm
+module unload gsibec crtm fms
+module load fms/2023.04
 
 # JEDI Python Path
 # ----------------

diff --git a/src/swell/suites/3dfgat_atmos/flow.cylc b/src/swell/suites/3dfgat_atmos/flow.cylc
@@ -36,9 +36,6 @@
             BuildJediByLinking:fail? => BuildJedi
 
             {% for model_component in model_components %}
-            # Stage JEDI static files
-            CloneJedi => StageJedi-{{model_component}}
-
             # Clone geos ana for generating observing system records
             CloneGeosMksi-{{model_component}}
             {% endfor %}
@@ -73,7 +70,7 @@
 
             # Run Jedi variational executable
             BuildJediByLinking[^]? | BuildJedi[^]  => RunJediVariationalExecutable-{{model_component}}
-            StageJedi-{{model_component}}[^] => RunJediVariationalExecutable-{{model_component}}
+            CloneJedi[^] => StageJediCycle-{{model_component}}
             StageJediCycle-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
             GetBackgroundGeosExperiment-{{model_component}}? | GetBackground-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
             GetObservations-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
@@ -138,9 +135,6 @@
     [[GenerateObservingSystemRecords-{{model_component}}]]
         script = "swell task GenerateObservingSystemRecords $config -d $datetime -m {{model_component}}"
 
-    [[StageJedi-{{model_component}}]]
-        script = "swell task StageJedi $config -m {{model_component}}"
-
     [[StageJediCycle-{{model_component}}]]
         script = "swell task StageJedi $config -d $datetime -m {{model_component}}"
 

diff --git a/src/swell/suites/3dvar_atmos/flow.cylc b/src/swell/suites/3dvar_atmos/flow.cylc
@@ -36,9 +36,6 @@
             BuildJediByLinking:fail? => BuildJedi
 
             {% for model_component in model_components %}
-            # Stage JEDI static files
-            CloneJedi => StageJedi-{{model_component}}
-
             # Clone geos ana for generating observing system records
             CloneGeosMksi-{{model_component}}
             {% endfor %}
@@ -73,7 +70,7 @@
 
             # Run Jedi variational executable
             BuildJediByLinking[^]? | BuildJedi[^]  => RunJediVariationalExecutable-{{model_component}}
-            StageJedi-{{model_component}}[^] => RunJediVariationalExecutable-{{model_component}}
+            CloneJedi[^] => StageJediCycle-{{model_component}}
             StageJediCycle-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
             GetBackgroundGeosExperiment-{{model_component}}? | GetBackground-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
             GetObservations-{{model_component}} => RunJediVariationalExecutable-{{model_component}}
@@ -138,9 +135,6 @@
     [[GenerateObservingSystemRecords-{{model_component}}]]
         script = "swell task GenerateObservingSystemRecords $config -d $datetime -m {{model_component}}"
 
-    [[StageJedi-{{model_component}}]]
-        script = "swell task StageJedi $config -m {{model_component}}"
-
     [[StageJediCycle-{{model_component}}]]
         script = "swell task StageJedi $config -d $datetime -m {{model_component}}"
 

diff --git a/src/swell/suites/hofx/flow.cylc b/src/swell/suites/hofx/flow.cylc
@@ -36,9 +36,6 @@
             BuildJediByLinking:fail? => BuildJedi
 
             {% for model_component in model_components %}
-            # Stage JEDI static files
-            CloneJedi => StageJedi-{{model_component}}
-
             # Clone geos ana for generating observing system records
             CloneGeosMksi-{{model_component}}
             {% endfor %}
@@ -65,7 +62,7 @@
 
             # Run Jedi hofx executable
             BuildJediByLinking[^]? | BuildJedi[^]  => RunJediHofxExecutable-{{model_component}}
-            StageJedi-{{model_component}}[^] => RunJediHofxExecutable-{{model_component}}
+            CloneJedi[^] => StageJediCycle-{{model_component}}
             StageJediCycle-{{model_component}} => RunJediHofxExecutable-{{model_component}}
             GetBackground-{{model_component}} => RunJediHofxExecutable-{{model_component}}
             GetObservations-{{model_component}} => RunJediHofxExecutable-{{model_component}}
@@ -124,9 +121,6 @@
     [[GenerateObservingSystemRecords-{{model_component}}]]
         script = "swell task GenerateObservingSystemRecords $config -d $datetime -m {{model_component}}"
 
-    [[StageJedi-{{model_component}}]]
-        script = "swell task StageJedi $config -m {{model_component}}"
-
     [[StageJediCycle-{{model_component}}]]
         script = "swell task StageJedi $config -d $datetime -m {{model_component}}"