Checkpoint lfric_coupled

applications/jules/build/compile_options.mk

@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)

applications/lfric_atm/Makefile

@@ -75,7 +75,7 @@ build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = YES
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -exec egrep -l "^\s*program" {} \;)))
 build: export PROJECT      = lfric_atm
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export WORKING_DIR := $(WORKING_DIR)
 
 build: export LDFLAGS_GROUPS = OPENMP

applications/lfric_atm/build/compile_options.mk

@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)

applications/lfric_atm/metadata/lfric_dictionary.xml

@@ -279,6 +279,10 @@
   <field id="tile_fraction" name="tile_fraction" long_name="surface_tile_fraction" unit="1" domain_ref="face" axis_ref="surface_tiles" />
   <field id="tile_temperature" name="tile_temperature" long_name="surface_tile_temperature" unit="K" domain_ref="face" axis_ref="surface_tiles" />
   <field id="tile_lw_grey_albedo" name="tile_lw_grey_albedo" long_name="surface_tile_lw_grey_albedo" unit="1" domain_ref="face" axis_ref="surface_tiles" />
+  <field id="tile_moisture_flux" name="tile_moisture_flux" long_name="tile_moisture_flux" unit="kg m-2 s-1"  domain_ref="face" axis_ref="surface_tiles"/>  
+  <field id="snowice_melt" name="snowice_melt" long_name="snowice_melt" unit="kg m-2 s-1"  domain_ref="face" axis_ref="surface_tiles"/>
+  <field id="surf_ht_flux" name="surf_ht_flux" long_name="surf_ht_flux" unit="W m-2"  domain_ref="face" axis_ref="surface_tiles"/>
+  <field id="snowice_sublimation" name="snowice_sublimation" long_name="snowice_sublimation" unit="kg m-2 s-1"  domain_ref="face" axis_ref="surface_tiles"/>
   <field id="screen_temperature" name="screen_temperature" long_name="screen_temperature_on_tiles" unit="K" domain_ref="face" axis_ref="surface_tiles" />
   <field id="time_since_transition" name="time_since_transition" long_name="time_since_decoupled_screen_transition" unit="s" domain_ref="face" />
   <field id="canopy_water" name="canopy_water" long_name="canopy_water_content_on_tiles" unit="kg m-2" domain_ref="face" axis_ref="surface_tiles" />
@@ -288,6 +292,7 @@
   <field id="albedo_obs_scaling" name="albedo_obs_scaling" long_name="albedo_obs_scaling" unit="1" domain_ref="face" axis_ref="land_tile_rad_band" />
   <field id="sea_ice_thickness" name="sea_ice_thickness" long_name="sea_ice_thickness" unit="m" domain_ref="face" axis_ref="sea_ice_categories" />
   <field id="sea_ice_temperature" name="sea_ice_temperature" long_name="sea_ice_bulk_temperature" unit="K" domain_ref="face" axis_ref="sea_ice_categories" />
+  <field id="sea_ice_pensolar" name="sea_ice_pensolar" long_name="sea_ice_pensolar" unit="W m-2"  domain_ref="face" axis_ref="sea_ice_categories"/>        
   <field id="sea_surf_temp_pert" name="sea_surf_temp_pert" long_name="sea_surface_temperature_perturbation" unit="K" domain_ref="face" />
   <field id="internal_flux" name="internal_flux" long_name="internal_flux" unit="W m-2" domain_ref="face" />
   <!-- orography fields -->
@@ -393,5 +398,31 @@
   <field id="frozen_soil_moisture" name="frozen_soil_moisture" long_name="mass_fraction_of_frozen_water_in_saturated_soil_moisture" unit="1" domain_ref="face" axis_ref="soil_levels" />
   <!-- energy correction -->
   <field id="temperature_correction_rate" name="temperature_correction_rate" long_name="temperature_rate_for_energy_correction" unit="K s-1" axis_ref="scalar_axis" />
+     <field id="lf_icefrc" name="lf_icefrc" long_name="lf_icefrc" unit="1" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_icetck" name="lf_icetck" long_name="lf_icetck" unit="m" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_icelayert" name="lf_icelayert" long_name="lf_icelayert" unit="m" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_ocn_sst" name="lf_ocn_sst" long_name="lf_ocn_sst" unit="K" domain_ref="face" />
+     <field id="lf_taux" name="lf_taux" long_name="lf_taux" unit="m" domain_ref="face" />
+     <field id="lf_tauy" name="lf_tauy" long_name="lf_tauy" unit="m" domain_ref="face" />
+     <field id="lf_solar" name="lf_solar" long_name="lf_solar" unit="m" domain_ref="face" />
+     <field id="lf_heatflux" name="lf_heatflux" long_name="lf_heatflux" unit="m" domain_ref="face" />
+     <field id="lf_train" name="lf_train" long_name="lf_train" unit="m" domain_ref="face" />
+     <field id="lf_tsnow" name="lf_tsnow" long_name="lf_tsnow" unit="" domain_ref="face" />
+     <field id="lf_w10" name="lf_w10" long_name="lf_w10" unit="" domain_ref="face" />
+     <field id="lf_rsurf" name="lf_rsurf" long_name="lf_rsurf" unit="kg m-2 s-1" domain_ref="face" />
+     <field id="lf_rsub" name="lf_rsub" long_name="lf_rsub" unit="kg m-2 s-1" domain_ref="face" />
+     <field id="lf_evap" name="lf_evap" long_name="lf_evap" unit="kg m-2 s-1" domain_ref="face" />
+     <field id="lf_topmelt" name="lf_topmelt" long_name="lf_topmelt" unit="W m-2" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_iceheatflux" name="lf_iceheatflux" long_name="lf_iceheatflux" unit="W m-2" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_sublimation" name="lf_sublimation" long_name="lf_sublimation" unit="kg m-2 s-1" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_iceskint" name="lf_iceskint" long_name="lf_iceskint" unit="K" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_pensolar" name="lf_pensolar" long_name="lf_pensolar" unit="W m-2" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_conductivity" name="lf_conductivity" long_name="lf_conductivity" unit="W m-2 K-1" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_snow_depth" name="lf_snow_depth" long_name="snow depth on sea ice" unit="m" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_pond_frac" name="lf_pond_frac" long_name="lf_pond_frac" unit="1" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_pond_depth" name="lf_pond_depth" long_name="lf_pond_depth" unit="m" domain_ref="face" axis_ref="sea_ice_categories" />
+     <field id="lf_sunocean" name="lf_sunocean" long_name="lf_sunocean" unit="ms-1" domain_ref="face" />
+     <field id="lf_svnocean" name="lf_svnocean" long_name="lf_svnocean" unit="ms-1" domain_ref="face" />
+
 </field_group>
 </field_definition>

applications/lfric_coupled/Makefile

@@ -102,7 +102,7 @@ document-api: api-documentation
 build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = TRUE
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -print)))
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export PROJECT      = $(PROJECT_NAME)
 build: export WORKING_DIR := $(WORKING_DIR)/$(PROJECT_NAME)
 

applications/lfric_coupled/build/compile_options.mk

@@ -9,7 +9,8 @@ $(info UM physics specific compile options for $(FORTRAN_COMPILER) compiler)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
+casim/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
+ukca/%.o science/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 jules/%.o jules/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 socrates/%.o socrates/%.mod: private FFLAGS_EXTRA += $(FFLAGS_UM_PHYSICS)
 legacy/%.o legacy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)

applications/ngarch/Makefile

@@ -100,7 +100,7 @@ document-api: api-documentation
 build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
 build: export CXX_LINK     = TRUE
 build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -print)))
-build: export SCRATCH_DIR := $(WORKING_DIR)/../physics_scratch
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export PROJECT      = $(PROJECT_NAME)
 build: export WORKING_DIR := $(WORKING_DIR)
 

applications/ngarch/build/compile_options.mk

@@ -13,7 +13,8 @@ $(info UM physics specific compile options)
 
 include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
 
-science/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+casim/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o science/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 jules/%.o jules/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 socrates/%.o socrates/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
 legacy/%.o legacy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)

build/extract/extract_physics.mk

@@ -20,7 +20,4 @@
 
 extract:
 	# Retrieve and preprocess the UKCA and CASIM code
-	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(SCRATCH_DIR) -e $(APPS_ROOT_DIR)/build/extract/extract.yaml
-	$Qrsync -acvz $(SCRATCH_DIR)/ukca $(WORKING_DIR)/science/
-	$Qrsync -acvz $(SCRATCH_DIR)/casim $(WORKING_DIR)/science/
-
+	python $(APPS_ROOT_DIR)/build/extract/extract_science.py -d $(APPS_ROOT_DIR)/dependencies.yaml -w $(WORKING_DIR) -e $(APPS_ROOT_DIR)/build/extract/extract.yaml

build/extract/extract_science.py

@@ -1,35 +1,12 @@
 import argparse
-import subprocess
 import os
-import tempfile
 import yaml
-from shutil import rmtree
 from pathlib import Path
-from typing import Dict, List
+from get_git_sources import clone_and_merge, run_command
+import logging
 
 
-def run_command(command):
-    """
-    Run a subprocess command and check output
-    Inputs:
-        - command, str with command to run
-    """
-    command = command.split()
-    result = subprocess.run(
-        command,
-        capture_output=True,
-        text=True,
-        timeout=120,
-        shell=False,
-        check=False,
-    )
-    if result.returncode:
-        raise RuntimeError(
-            f"The command '{command}' failed with error:\n\n{result.stderr}"
-        )
-
-
-def load_yaml(fpath: Path) -> Dict:
+def load_yaml(fpath: Path) -> dict:
     """
     Read in the dependencies.yaml file
     """
@@ -40,56 +17,45 @@ def load_yaml(fpath: Path) -> Dict:
     return sources
 
 
-def clone_dependency(values: Dict, temp_dep: Path) -> None:
-    """
-    Clone the physics dependencies into a temporary directory
-    """
-
-    source = values["source"]
-    ref = values["ref"]
-
-    commands = (
-        f"git -C {temp_dep} init",
-        f"git -C {temp_dep} remote add origin {source}",
-        f"git -C {temp_dep} fetch origin {ref}",
-        f"git -C {temp_dep} checkout FETCH_HEAD"
-    )
-    for command in commands:
-        run_command(command)
-
-
-def extract_files(dependency: str, values: Dict, files: List[str], working: Path):
+def extract_files(dependencies: dict, extract_lists: dict, working: Path) -> None:
     """
     Clone the dependency to a temporary location
     Then copy the desired files to the working directory
     Then delete the temporary directory
     """
 
-    tempdir = Path(tempfile.mkdtemp())
-    if (
-        "PHYSICS_ROOT" not in os.environ
-        or not Path(os.environ["PHYSICS_ROOT"]).exists()
-    ):
-        temp_dep = tempdir / dependency
-        temp_dep.mkdir(parents=True)
-        clone_dependency(values, temp_dep)
-    else:
-        temp_dep = Path(os.environ["PHYSICS_ROOT"]) / dependency
-
-    working_dep = working / dependency
-
-    # make the working directory location
-    working_dep.mkdir(parents=True)
-
-    for extract_file in files:
-        source_file = temp_dep / extract_file
-        dest_file = working_dep / extract_file
-        run_command(f"mkdir -p {dest_file.parents[0]}")
-        copy_command = f"cp -r {source_file} {dest_file}"
+    mirror_loc = os.getenv("MIRROR_LOC", "")
+    use_mirrors = bool(mirror_loc)
+    mirror_loc = Path(mirror_loc)
+
+    for dependency, sources in dependencies.items():
+        if dependency not in extract_lists:
+            continue
+        files = extract_lists[dependency]
+
+        # If the PHYSICS_ROOT environment variable is provided, then use sources there
+        if "PHYSICS_ROOT" in os.environ and Path(os.environ["PHYSICS_ROOT"]).exists():
+            clone_loc = Path(os.environ["PHYSICS_ROOT"]) / dependency
+        else:
+            clone_loc = working.parent / "scratch" / dependency
+            clone_and_merge(dependency, sources, clone_loc, use_mirrors, mirror_loc)
+
+        # make the working directory location
+        working_dir = working / dependency
+        working_dir.mkdir(parents=True, exist_ok=True)
+
+        # rsync extract files from clone loc to the working directory
+        copy_command = "rsync --include='**/' "
+        for extract_file in files:
+            if not extract_file:
+                continue
+            if Path(clone_loc / extract_file).is_dir():
+                extract_file = extract_file.rstrip("/")
+                extract_file += "/**"
+            copy_command += f"--include='{extract_file}' "
+        copy_command += f"--exclude='*' -avmq {clone_loc}/ {working_dir}"
         run_command(copy_command)
 
-    rmtree(tempdir)
-
 
 def parse_args() -> argparse.Namespace:
     """
@@ -101,34 +67,30 @@ def parse_args() -> argparse.Namespace:
         "-d",
         "--dependencies",
         default="./dependencies.yaml",
-        help="The dependencies file for the apps working copy.",
-    )
-    parser.add_argument(
-        "-w", "--working", default=".", help="Location to perform extract steps in."
+        help="The dependencies file for the apps working copy",
     )
+    parser.add_argument("-w", "--working", default=".", help="Build location")
     parser.add_argument(
         "-e",
         "--extract",
         default="./extract.yaml",
         help="Path to file containing extract lists",
     )
-    return parser.parse_args()
+
+    args = parser.parse_args()
+    args.working = Path(args.working)
+    return args
 
 
 def main():
     args: argparse.Namespace = parse_args()
 
-    extract_lists: Dict = load_yaml(args.extract)
-    dependencies: Dict = load_yaml(args.dependencies)
-
-    for dependency in dependencies:
-        if dependency in extract_lists:
-            extract_files(
-                dependency,
-                dependencies[dependency],
-                extract_lists[dependency],
-                Path(args.working),
-            )
+    logging.basicConfig(level=logging.INFO)
+
+    extract_lists: dict = load_yaml(args.extract)
+    dependencies: dict = load_yaml(args.dependencies)
+
+    extract_files(dependencies, extract_lists, args.working)
 
 
 if __name__ == "__main__":