geos_ocean no more (#550)

* erase geos_ocean configurations

* erase every mention of geos_ocean

* minor fixes

* fix eva yamls

* changes related to documentation

* erase geos_ocean from ever existing

Author: Dooruk

docs/adding_a_suite.md

@@ -37,13 +37,13 @@ final_cycle_point: '2021-07-01T12:00:00Z'
 
 # List of models in this experiment
 model_components:
-- geos_ocean
+- geos_marine
 
 # Configurations for the model components.
 models:
 
-  # Configuration for the geos_ocean model component.
-  geos_ocean:
+  # Configuration for the geos_marine model component.
+  geos_marine:
 
     # Enter the cycle times for this model.
     cycle_times:
@@ -53,7 +53,7 @@ models:
     background_error_model: explicit_diffusion
 ```
 
-The questions near the top of the file are suite questions, and are referred to as "model independent". The section under "models" describes parameters used by the `geos_ocean` model. Some tasks are shared across models, necessitating different values for the same parameter depending on model. Thus, these parameters are referred to as "model dependent".
+The questions near the top of the file are suite questions, and are referred to as "model independent". The section under "models" describes parameters used by the `geos_marine` model. Some tasks are shared across models, necessitating different values for the same parameter depending on model. Thus, these parameters are referred to as "model dependent".
 
 ## Example Experiment Workflow
 
@@ -358,10 +358,11 @@ class SuiteConfig(QuestionContainer, Enum):
             qd.start_cycle_point("2021-07-01T12:00:00Z"),
             qd.final_cycle_point("2021-07-01T12:00:00Z"),
             qd.jedi_build_method("use_existing"),
-            qd.model_components(['geos_ocean']),
+            qd.model_components(['geos_marine']),
         ],
-        geos_ocean=[
+        geos_marine=[
             qd.cycle_times(['T12']),
+            qd.marine_models(['mom6']),
             qd.window_length("P1D"),
             qd.window_offset("PT12H"),
             qd.horizontal_resolution("72x36"),

docs/configs/slurm_configuration.md

@@ -59,7 +59,7 @@ When SLURM directives conflict, the pattern of overrides generally proceeds such
 The full priority list is as follows (directives higher in this list override directives lower):
 
 1. Task- and model-specific directives (`slurm_directives_tasks`) set via `--slurm <somefile.yaml>` (e.g., `RunHofxExecutable.geos_atmosphere` would have `--nodes=4`).
-2. Task-specific (but model-agnostic) directives (`slurm_directives_tasks`) from `--slurm <somefile.yaml>` (e.g., `RunHofxExecutable.geos_ocean` and all other `RunHofxExecutable` tasks would have `--nodes=2`)
+2. Task-specific (but model-agnostic) directives (`slurm_directives_tasks`) from `--slurm <somefile.yaml>` (e.g., `RunHofxExecutable.geos_marine` and all other `RunHofxExecutable` tasks would have `--nodes=2`)
 3. Global directives set from `--slurm <somefile.yaml>` (e.g., all tasks use account `x1234`; all tasks _except_ `RunHofxExecutable` and `BuildJEDI` use `--nodes=1`)
 4. User-level global directives in `$HOME/.swell/swell-slurm.yaml`
 5. Hard-coded platform specific directives (in SWELL source code `.../platforms/{platform_name}/slurm.yaml`)

docs/examples/soca/3dfgat_cycle.md

@@ -69,10 +69,10 @@ existing_geos_gcm_build_path: /discover/nobackup/projects/gmao/SIteam/Models/GEO
 existing_geos_gcm_source_path: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-v11.6.0/
 
 # What is the path to the existing JEDI build directory?
-existing_jedi_build_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_02062025/build-intel-release
+existing_jedi_build_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_04152025/build-intel-release
 
 # What is the path to the existing JEDI source code directory?
-existing_jedi_source_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_02062025
+existing_jedi_source_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_04152025
 
 # GEOS forecast duration
 forecast_duration: PT12H

docs/examples/soca/3dvar.md

@@ -1,5 +1,5 @@
 <div style="border:1px solid red; padding: 5px; background-color: #ffe6e6; color: black; margin-bottom: 10px;">
-    <strong>Warning:</strong> Currently, <strong>3dvar</strong> suite only contains the <strong>geos_ocean</strong> configuration and <strong>3dvar_atmos</strong> only contains the <strong>geos_atmosphere</strong> configuration. This will likely change in a future SWELL version.
+    <strong>Warning:</strong> Currently, <strong>3dvar</strong> suite only contains the <strong>geos_marine</strong> configuration and <strong>3dvar_atmos</strong> only contains the <strong>geos_atmosphere</strong> configuration. This will likely change in a future SWELL version.
 </div>
 
 ## Create a Swell 3DVar experiment:
@@ -53,27 +53,31 @@ runahead_limit: P4
 
 # List of models in this experiment
 model_components:
-- geos_ocean
+- geos_marine
 
 # Do you want to use an existing JEDI build or create a new build?
 jedi_build_method: use_existing
 
 # What is the path to the existing JEDI build directory?
-existing_jedi_build_directory: /discover/nobackup/gmao_ci/swell/tier2/stable/build_jedi/jedi_bundle/build/
+existing_jedi_build_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_04152025/build-intel-release
 
 # What is the path to the existing JEDI source code directory?
-existing_jedi_source_directory: /discover/nobackup/gmao_ci/swell/tier2/stable/build_jedi/jedi_bundle/source/
+existing_jedi_source_directory: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_04152025
 
 # Configurations for the model components.
 models:
 
-  # Configuration for the geos_ocean model component.
-  geos_ocean:
+  # Configuration for the geos_marine model component.
+  geos_marine:
 
     # Enter the cycle times for this model.
     cycle_times:
     - T12
 
+    # Select the active SOCA models for this model.
+    marine_models:
+    - mom6
+
     # Enter the cycle times for this model.
     window_type: 3D
 
@@ -176,14 +180,19 @@ platform: nccs_discover_sles15
 suite_to_run: 3dvar
 ```
 
-Most of these configurations are self explanatory, we will mention only two here for now.
+Most of these configurations are self explanatory, we will mention only a few here for now.
 
 `clean_patterns`: This key controls which files will be erased after the experiment run is complete.
 Currently, `IODA` output files are erased after the diagnostic plots (using EVA) are created.
 
 `generate_yaml_and_exit`: When this key is `True`, the code will progress right before the execution
 and generate a JEDI Config YAML. This could be useful while debugging problems.
 
+
+`marine_models`: JEDI/SOCA interface is designed to handle multiple marine model outputs. Currently in SWELL,
+`mom6` and `cice6` model interfaces are supported. `mom6` should always be active for `SOCA` however `cice6` is
+optional. If `cice6` model is not active one should take out sea-ice related observations and variables from the `experiment.yaml` and from the `analysis_variables`.
+
 If you would like to change any of these parameters, it is suggested to copy `experiment.yaml`
 to `override.yaml` and make desired configuration changes. Afterwards, create the experiment again:
 
@@ -232,14 +241,14 @@ If all goes well, the run will complete successfully.
 
 ## After the run is complete:
 
-In this default example, there is a single model type (`geos_ocean`) that contains a single cycle (`20210701T120000Z`).
+In this default example, there is a single model type (`geos_marine`) that contains a single cycle (`20210701T120000Z`).
 
-Let's take a look at the `geos_ocean` folder after the run is complete.
+Let's take a look at the `geos_marine` folder after the run is complete.
 
 ```bash
 run
 └── 20210701T120000Z
-    └── geos_ocean
+    └── geos_marine
         ├── background_error_model/
         ├── INPUT/
         ├── eva/

src/swell/configuration/jedi/interfaces/geos_marine/task_questions.yaml

@@ -1,6 +1,7 @@
 analysis_forecast_window_offset:
   default_value: -PT6H
   options:
+  - -PT12H
   - -PT6H
 
 analysis_variables:
@@ -30,6 +31,8 @@ background_frequency:
 
 background_time_offset:
   default_value: PT9H
+  options:
+  - PT9H
 
 clean_patterns:
   default_value:
@@ -38,6 +41,8 @@ clean_patterns:
   - '*MOM*'
   - logfile.*.out
   options:
+  - logfile.*.out
+  - background_error_model/*.nc
   - '*.nc4'
   - '*.txt'
   - '*MOM*'
@@ -49,6 +54,7 @@ gradient_norm_reduction:
 horizontal_resolution:
   default_value: 1440x1080
   options:
+  - 72x36
   - 360x320
   - 1440x1080
 
@@ -115,12 +121,16 @@ observations:
   - sst_viirs_n20_l3u
   - temp_profile_xbt
 
+path_to_ensemble:
+  default_value: test
+
 total_processors:
   default_value: 24
 
 vertical_resolution:
   default_value: '75'
   options:
+  - '50'
   - '75'
 
 window_length: