Feature/r2d2v2

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

@@ -48,7 +48,7 @@ geovals_experiment:
   default_value: x0048-geovals
 
 geovals_provider:
-  default_value: ncdiag
+  default_value: x0048-geovals
 
 gradient_norm_reduction:
   default_value: 10e-5
@@ -85,7 +85,7 @@ obs_experiment:
   default_value: x0048
 
 obs_provider:
-  default_value: ncdiag
+  default_value: x0048
 
 observations:
   default_value:

src/swell/configuration/jedi/interfaces/geos_ocean/model/r2d2.yaml

@@ -5,6 +5,7 @@ fetch:
   fc:
     - file_type: MOM.res
       filename: '{{cycle_dir}}/MOM6.res.{{local_background_time}}.nc'
+      domain: global
 store:
   fc:
     - file_type: MOM.res

src/swell/deployment/bin/swell_create_experiment.py

@@ -20,7 +20,6 @@
 from swell.deployment.prep_suite import prepare_cylc_suite_jinja2
 from swell.swell_path import get_swell_path
 from swell.utilities.dictionary import dict_get
-from swell.utilities.jinja2 import template_string_jinja2
 from swell.utilities.logger import Logger
 from swell.utilities.welcome_message import write_welcome_message
 
@@ -70,25 +69,6 @@ def main(config_file):
     if os.path.exists(os.path.join(swell_suite_path, 'eva')):
         copy_eva_files(logger, swell_suite_path, exp_suite_path)
 
-    # Create R2D2 database file
-    # -------------------------
-    r2d2_local_path = dict_get(logger, experiment_dict, 'r2d2_local_path', None)
-    if r2d2_local_path is not None:
-        r2d2_conf_path = os.path.join(exp_suite_path, 'r2d2_config.yaml')
-
-        # Write R2D2_CONFIG to modules
-        with open(os.path.join(exp_suite_path, 'modules'), 'a') as module_file:
-            module_file.write(f'export R2D2_CONFIG={r2d2_conf_path}')
-
-        # Open the r2d2 file to dictionary
-        with open(r2d2_conf_path, 'r') as r2d2_file_open:
-            r2d2_file_str = r2d2_file_open.read()
-        r2d2_file_str = template_string_jinja2(logger, r2d2_file_str, experiment_dict)
-        r2d2_file_str = os.path.expandvars(r2d2_file_str)
-
-        with open(r2d2_conf_path, 'w') as r2d2_file_open:
-            r2d2_file_open.write(r2d2_file_str)
-
     # Set the swell paths in the modules file and create csh versions
     # ---------------------------------------------------------------
     template_modules_file(logger, experiment_dict, exp_suite_path)

src/swell/deployment/platforms/generic/suite_questions.yaml

@@ -3,6 +3,3 @@ experiment_id:
 
 experiment_root:
   default_value: /home/${USER}/SwellExperiments
-
-r2d2_local_path:
-  default_value: /home/${USER}/R2D2DataStore/Local

src/swell/deployment/platforms/generic/task_questions.yaml

@@ -21,6 +21,24 @@ geos_restarts_directory:
   default_value:
   - /home/geos/restarts
 
+r2d2_fetch_datastores:
+  default_value:
+  - swell-r2d2-${USER}
+  - swell-r2d2-archive
+  - swell-r2d2
+  options:
+  - swell-r2d2-${USER}
+  - swell-r2d2-archive
+  - swell-r2d2
+
+r2d2_store_datastores:
+  default_value:
+  - swell-r2d2-${USER}
+  - swell-r2d2
+  options:
+  - swell-r2d2-${USER}
+  - swell-r2d2
+
 swell_static_files:
   default_value: This would need to be provided by user
 

src/swell/deployment/platforms/nccs_discover/suite_questions.yaml

@@ -1,5 +1,2 @@
 experiment_root:
   default_value: /discover/nobackup/${USER}/SwellExperiments
-
-r2d2_local_path:
-  default_value: /discover/nobackup/${USER}/R2D2DataStore/Local

src/swell/deployment/platforms/nccs_discover/task_questions.yaml

@@ -19,6 +19,24 @@ geos_experiment_directory:
 geos_restarts_directory:
   default_value: restarts_20210620_000000
 
+r2d2_fetch_datastores:
+  default_value:
+  - swell-r2d2-discover-${USER}
+  - swell-r2d2-discover-archive
+  - swell-r2d2-discover
+  options:
+  - swell-r2d2-discover-${USER}
+  - swell-r2d2-discover-archive
+  - swell-r2d2-discover
+
+r2d2_store_datastores:
+  default_value:
+  - swell-r2d2-discover-${USER}
+  - swell-r2d2-discover
+  options:
+  - swell-r2d2-discover-${USER}
+  - swell-r2d2-discover
+
 swell_static_files:
   default_value: /discover/nobackup/drholdaw/SwellStaticFiles
 

src/swell/deployment/prep_exp_dirs.py

@@ -46,13 +46,12 @@ def copy_platform_files(logger, exp_suite_path, platform=None):
         swell_lib_path = get_swell_path()
         platform_path = os.path.join(swell_lib_path, 'deployment', 'platforms', platform)
 
-        for s in ['modules', 'r2d2_config.yaml']:
-            src_file = os.path.split(s)[1]
-            src_path_file = os.path.join(platform_path, os.path.split(s)[0], src_file)
-            dst_path_file = os.path.join(exp_suite_path, '{}'.format(src_file))
-            if os.path.exists(src_path_file):
-                logger.trace('Copying {} to {}'.format(src_path_file, dst_path_file))
-                shutil.copy(src_path_file, dst_path_file)
+        src_path_file = os.path.join(platform_path, 'modules')
+        dst_path_file = os.path.join(exp_suite_path, 'modules')
+
+        if os.path.exists(src_path_file):
+            logger.trace('Copying {} to {}'.format(src_path_file, dst_path_file))
+            shutil.copy(src_path_file, dst_path_file)
 
 
 # --------------------------------------------------------------------------------------------------

src/swell/suites/3dvar/suite_questions.yaml

@@ -16,12 +16,6 @@ runahead_limit:
   prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
   type: string
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/suites/3dvar_cycle/suite_questions.yaml

@@ -10,12 +10,6 @@ final_cycle_point:
   prompt: What is the time of the final cycle (middle of the window)?
   type: iso-datetime
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/suites/convert_ncdiags/suite_questions.yaml

@@ -16,12 +16,6 @@ runahead_limit:
   prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
   type: string
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/suites/forecast_geos/suite_questions.yaml

@@ -10,12 +10,6 @@ final_cycle_point:
   prompt: What is the time of the final cycle (middle of the window)?
   type: iso-datetime
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value:

src/swell/suites/geosadas/suite_questions.yaml

@@ -10,12 +10,6 @@ final_cycle_point:
   prompt: What is the time of the final cycle (middle of the window)?
   type: iso-datetime
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/suites/hofx/suite_questions.yaml

@@ -16,12 +16,6 @@ runahead_limit:
   prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
   type: string
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/suites/ufo_testing/suite_questions.yaml

@@ -16,12 +16,6 @@ runahead_limit:
   prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
   type: string
 
-r2d2_local_path:
-  ask_question: False
-  default_value: defer_to_platform
-  prompt: Enter the path where R2D2 will store experiment output
-  type: string
-
 cycle_times:
   ask_question: True
   default_value: defer_to_model

src/swell/tasks/get_background.py

@@ -7,13 +7,11 @@
 
 # --------------------------------------------------------------------------------------------------
 
-
 from swell.tasks.base.task_base import taskBase
+from swell.utilities.store_fetch import fetch
 
 import isodate
 import os
-from r2d2 import fetch
-
 
 # --------------------------------------------------------------------------------------------------
 
@@ -50,6 +48,12 @@ def execute(self):
         window_offset = self.config.window_offset()
         window_type = self.config.window_type()
 
+        r2d2_fetch_datastores = self.config.r2d2_fetch_datastores(['swell-r2d2-archive'])
+        r2d2_fetch_datastores = [r.replace("${USER}", os.getenv('USER'))
+                                 for r in r2d2_fetch_datastores]
+
+        self.logger.info("Fetching from R2D2 data_stores: " + ', '.join(r2d2_fetch_datastores))
+
         # Get window parameters
         local_background_time = self.da_window_params.local_background_time(window_offset,
                                                                             window_type)
@@ -118,6 +122,9 @@ def execute(self):
         # Get r2d2 dictionary
         r2d2_dict = self.jedi_rendering.render_interface_model('r2d2')
 
+        # To force localhost r2d2
+        # os.environ['R2D2_HOST'] = 'localhost'
+
         # Loop over fc
         # ------------
         for fc in r2d2_dict['fetch']['fc']:
@@ -126,6 +133,7 @@ def execute(self):
             # --------------------
             file_type = fc['file_type']
             target_file_template = fc['filename']
+            domain = fc.get('domain', '')
 
             # Loop over background steps
             # --------------------
@@ -139,18 +147,22 @@ def execute(self):
                 # ---------------------------------------------------
                 target_file = background_time.strftime(target_file_template)
 
-                fetch(
-                    date=forecast_start_time,
-                    target_file=target_file,
-                    model=r2d2_model_dict[model_component],
-                    file_type=file_type,
-                    fc_date_rendering='analysis',
-                    step=bkg_step,
-                    resolution=horizontal_resolution,
-                    type='fc',
-                    experiment=background_experiment)
+                target_dir = os.path.dirname(target_file)
+                os.makedirs(target_dir, exist_ok=True)
+
+                fetched_from = fetch(r2d2_fetch_datastores,
+                                     item='forecast',
+                                     target_file=target_file,
+                                     model=r2d2_model_dict[model_component],
+                                     experiment=background_experiment,
+                                     file_extension="nc",
+                                     resolution=horizontal_resolution,
+                                     domain=domain,
+                                     file_type=file_type,
+                                     step=bkg_step,
+                                     date=forecast_start_time)
+
+                self.logger.info("Fetched R2D2 data from " + fetched_from + " to " + target_file)
 
                 # Change permission
                 os.chmod(target_file, 0o644)
-
-# --------------------------------------------------------------------------------------------------