Fixes from integration with SRW's make_orog (#603)

A set of changes to the drivers run as part of SRW's make_orog task.

- Run commands seemed not to work as expected, so changed them to use config files.
- More information was needed in the UW YAML in a couple of instances.

Also ordered the tests in each of the drivers.

docs/sections/user_guide/cli/drivers/filter_topo/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    filtered_output_file
+      The filtered output file staged from raw input
     input_grid_file
       The input grid file
     namelist_file

docs/sections/user_guide/cli/drivers/filter_topo/show-schema.out

@@ -6,7 +6,7 @@
         "config": {
           "additionalProperties": false,
           "properties": {
-            "input_grid_file": {
+            "filtered_orog": {
               "type": "string"
 ...
         "rundir"

docs/sections/user_guide/cli/drivers/orog_gsl/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    input_config_file
+      The input config file
     input_grid_file
       The input grid file
     provisioned_rundir

docs/sections/user_guide/cli/drivers/shave/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    input_config_file
+      The input config file
     provisioned_rundir
       Run directory provisioned with all required content
     run

docs/sections/user_guide/yaml/components/filter_topo.rst

@@ -20,10 +20,18 @@ config:
 
 Configuration parameters for the ``orog_gsl`` component.
 
+  **filtered_orog:**
+
+  Name of the filtered output file.
+
   **input_grid_file:**
 
   Path to the tiled input grid file.
 
+  **input_raw_orog:**
+
+  Path to the raw orography file. The output of the ``orog`` driver.
+
 namelist:
 ^^^^^^^^^
 

docs/sections/user_guide/yaml/components/shave.rst

@@ -27,7 +27,7 @@ Describes the required parameters to run a ``shave`` configuration.
 
   Name of the grid file with extra points to be shaved.
 
-  **nh4:**
+  **nhalo:**
 
   The number of halo rows/columns.
 
@@ -39,6 +39,10 @@ Describes the required parameters to run a ``shave`` configuration.
 
   The j/y dimensions of the compute domain (not including halo)
 
+  **output_grid_file:**
+
+  The path to the output file.
+
 rundir:
 ^^^^^^^
 

docs/shared/filter_topo.yaml

@@ -1,6 +1,8 @@
 filter_topo:
   config:
+    filtered_orog: C403_filtered_orog.tile7.nc
     input_grid_file: /path/to/C403_grid.tile7.halo6.nc
+    input_raw_orog: /path/to/out.oro.nc
   execution:
     batchargs:
       cores: 1

docs/shared/orog.yaml

@@ -4,12 +4,12 @@ orog:
       cores: 1
       walltime: 00:05:00
     executable: /path/to/orog
-    files_to_link:
-      fort.15: /path/to/fix/thirty.second.antarctic.new.bin
-      landcover30.fixed: /path/to/fix/landcover30.fixed
-      fort.235: /path/to/fix/gmted2010.30sec.int
-    grid_file: /path/to/netcdf/grid/file
-    rundir: /path/to/run/dir
+  files_to_link:
+    fort.15: /path/to/fix/thirty.second.antarctic.new.bin
+    landcover30.fixed: /path/to/fix/landcover30.fixed
+    fort.235: /path/to/fix/gmted2010.30sec.int
+  grid_file: /path/to/netcdf/grid/file
+  rundir: /path/to/run/dir
 platform:
   account: me
   scheduler: slurm

docs/shared/shave.yaml

@@ -1,9 +1,10 @@
 shave:
   config:
     input_grid_file: /path/to/input/grid/file
-    nh4: 1
+    nhalo: 0
     nx: 214
     ny: 128
+    output_grid_file: /path/to/C403_oro_data.tile7.halo0.nc
   execution:
     batchargs:
       cores: 1

src/uwtools/drivers/filter_topo.py

@@ -10,7 +10,7 @@
 from uwtools.drivers.driver import DriverTimeInvariant
 from uwtools.drivers.support import set_driver_docstring
 from uwtools.strings import STR
-from uwtools.utils.tasks import symlink
+from uwtools.utils.tasks import filecopy, symlink
 
 
 class FilterTopo(DriverTimeInvariant):
@@ -27,10 +27,21 @@ def input_grid_file(self):
         """
         src = Path(self.config["config"]["input_grid_file"])
         dst = Path(self.config[STR.rundir], src.name)
-        yield self.taskname("Input grid")
+        yield self.taskname(f"Input grid {str(src)}")
         yield asset(dst, dst.is_file)
         yield symlink(target=src, linkname=dst)
 
+    @task
+    def filtered_output_file(self):
+        """
+        The filtered output file staged from raw input.
+        """
+        src = Path(self.config["config"]["input_raw_orog"])
+        dst = self.rundir / self.config["config"]["filtered_orog"]
+        yield self.taskname(f"Raw orog input {str(dst)}")
+        yield asset(dst, dst.is_file)
+        yield filecopy(src=src, dst=dst)
+
     @task
     def namelist_file(self):
         """
@@ -56,6 +67,7 @@ def provisioned_rundir(self):
         yield self.taskname("provisioned run directory")
         yield [
             self.input_grid_file(),
+            self.filtered_output_file(),
             self.namelist_file(),
             self.runscript(),
         ]

src/uwtools/drivers/orog.py

@@ -37,7 +37,7 @@ def grid_file(self):
         The input grid file.
         """
         grid_file = Path(self.config["grid_file"])
-        yield self.taskname("Input grid file")
+        yield self.taskname(f"Input grid file {grid_file}")
         yield asset(grid_file, grid_file.is_file) if str(grid_file) != "none" else None
 
     @task
@@ -62,8 +62,9 @@ def input_config_file(self):
                 "blat",
             ]
             inputs = " ".join([str(inputs[i]) for i in ordered_entries])
-        outgrid = self.config["grid_file"]
-        orogfile = self.config.get("orog_file")
+        outgrid = "'{}'".format(self.config["grid_file"])
+        if orogfile := self.config.get("orog_file"):
+            orogfile = "'{}'".format(orogfile)
         mask_only = ".true." if self.config.get("mask") else ".false."
         merge_file = self.config.get("merge", "none")  # string none is intentional
         content = [i for i in [inputs, outgrid, orogfile, mask_only, merge_file] if i is not None]
@@ -82,6 +83,22 @@ def provisioned_rundir(self):
             self.runscript(),
         ]
 
+    @task
+    def runscript(self):
+        """
+        The runscript.
+        """
+        path = self._runscript_path
+        yield self.taskname(path.name)
+        yield asset(path, path.is_file)
+        yield None
+        envvars = {
+            "KMP_AFFINITY": "disabled",
+            "OMP_NUM_THREADS": self.config.get(STR.execution, {}).get(STR.threads, 1),
+            "OMP_STACKSIZE": "2048m",
+        }
+        self._write_runscript(path=path, envvars=envvars)
+
     # Public helper methods
 
     @classmethod

src/uwtools/drivers/orog_gsl.py

@@ -9,6 +9,7 @@
 from uwtools.drivers.driver import DriverTimeInvariant
 from uwtools.drivers.support import set_driver_docstring
 from uwtools.strings import STR
+from uwtools.utils.file import writable
 from uwtools.utils.tasks import symlink
 
 
@@ -19,6 +20,19 @@ class OrogGSL(DriverTimeInvariant):
 
     # Workflow tasks
 
+    @task
+    def input_config_file(self):
+        """
+        The input config file.
+        """
+        path = self._input_config_path
+        yield self.taskname(str(path))
+        yield asset(path, path.is_file)
+        yield None
+        inputs = [str(self.config["config"][k]) for k in ("tile", "resolution", "halo")]
+        with writable(path) as f:
+            print("\n".join(inputs), file=f)
+
     @task
     def input_grid_file(self):
         """
@@ -40,6 +54,7 @@ def provisioned_rundir(self):
         """
         yield self.taskname("provisioned run directory")
         yield [
+            self.input_config_file(),
             self.input_grid_file(),
             self.runscript(),
             self.topo_data_2p5m(),
@@ -81,14 +96,20 @@ def driver_name(cls) -> str:
 
     # Private helper methods
 
+    @property
+    def _input_config_path(self) -> Path:
+        """
+        Path to the input config file.
+        """
+        return self.rundir / "orog_gsl.cfg"
+
     @property
     def _runcmd(self):
         """
         The full command-line component invocation.
         """
-        inputs = [str(self.config["config"][k]) for k in ("tile", "resolution", "halo")]
         executable = self.config[STR.execution][STR.executable]
-        return "echo '%s' | %s" % ("\n".join(inputs), executable)
+        return "%s < %s" % (executable, self._input_config_path.name)
 
 
 set_driver_docstring(OrogGSL)

src/uwtools/drivers/shave.py

@@ -2,11 +2,15 @@
 A driver for shave.
 """
 
-from iotaa import tasks
+from pathlib import Path
+
+from iotaa import asset, task, tasks
 
 from uwtools.drivers.driver import DriverTimeInvariant
 from uwtools.drivers.support import set_driver_docstring
 from uwtools.strings import STR
+from uwtools.utils.file import writable
+from uwtools.utils.tasks import file
 
 
 class Shave(DriverTimeInvariant):
@@ -16,13 +20,34 @@ class Shave(DriverTimeInvariant):
 
     # Workflow tasks
 
+    @task
+    def input_config_file(self):
+        """
+        The input config file.
+        """
+        path = self._input_config_path
+        yield self.taskname(str(path))
+        yield asset(path, path.is_file)
+        config = self.config["config"]
+        input_file = Path(config["input_grid_file"])
+        yield file(path=input_file)
+        flags = [
+            config[key] for key in ["nx", "ny", "nhalo", "input_grid_file", "output_grid_file"]
+        ]
+        content = "{} {} {} '{}' '{}'".format(*flags)
+        with writable(path) as f:
+            print(content, file=f)
+
     @tasks
     def provisioned_rundir(self):
         """
         Run directory provisioned with all required content.
         """
         yield self.taskname("provisioned run directory")
-        yield self.runscript()
+        yield [
+            self.input_config_file(),
+            self.runscript(),
+        ]
 
     # Public helper methods
 
@@ -35,18 +60,20 @@ def driver_name(cls) -> str:
 
     # Private helper methods
 
+    @property
+    def _input_config_path(self) -> Path:
+        """
+        Path to the input config file.
+        """
+        return self.rundir / "shave.cfg"
+
     @property
     def _runcmd(self):
         """
         The full command-line component invocation.
         """
         executable = self.config[STR.execution][STR.executable]
-        config = self.config["config"]
-        input_file = config["input_grid_file"]
-        output_file = input_file.replace(".nc", "_NH0.nc")
-        flags = [config[key] for key in ["nx", "ny", "nh4", "input_grid_file"]]
-        flags.append(output_file)
-        return f"{executable} {' '.join(str(flag) for flag in flags)}"
+        return "%s < %s" % (executable, self._input_config_path.name)
 
 
 set_driver_docstring(Shave)

src/uwtools/resources/jsonschema/filter-topo.jsonschema

@@ -6,12 +6,20 @@
         "config": {
           "additionalProperties": false,
           "properties": {
+            "filtered_orog": {
+              "type": "string"
+            },
             "input_grid_file": {
               "type": "string"
+            },
+            "input_raw_orog": {
+              "type": "string"
             }
           },
           "required": [
-            "input_grid_file"
+            "filtered_orog",
+            "input_grid_file",
+            "input_raw_orog"
           ]
         },
         "execution": {

src/uwtools/resources/jsonschema/orog.jsonschema

@@ -4,7 +4,7 @@
       "additionalProperties": false,
       "properties": {
         "execution": {
-          "$ref": "urn:uwtools:execution-serial"
+          "$ref": "urn:uwtools:execution"
         },
         "files_to_link": {
           "$ref": "urn:uwtools:files-to-stage"

src/uwtools/resources/jsonschema/shave.jsonschema

@@ -9,8 +9,8 @@
             "input_grid_file": {
               "type": "string"
             },
-            "nh4": {
-              "minimum": 1,
+            "nhalo": {
+              "minimum": 0,
               "type": "integer"
             },
             "nx": {
@@ -20,13 +20,17 @@
             "ny": {
               "minimum": 1,
               "type": "integer"
+            },
+            "output_grid_file": {
+              "type": "string"
             }
           },
           "required": [
             "input_grid_file",
-            "nh4",
+            "nhalo",
             "nx",
-            "ny"
+            "ny",
+            "output_grid_file"
           ]
         },
         "execution": {