Remove global access in fv3core and physics tests #60

elynnwu · 2021-12-10T19:15:03Z

This PR is a prerequisite to moving namelist to driver. The goal for this PR is to 1) remove global config access, 2) share translate class infrastructure, 3) remove dependencies to fv3core in physics tests.

Changes:

Move grid, global_config, and corners from fv3core.utils to pace.util.testing and pace.util: global_config is removed from most places and can be deleted soon-ish
Move translate and parallel_translate to pace.util.testing: they are shared in dycore and physics
Move NamelistDefaults to pace.util.namelist
Add PhysicsConfig class: when namelist is moved to the driver, we should add a method to return physics config
Add filter in physics savepoint test to only check for physics tests: since the logic checks for every serialized savepoint, pytest also tries to run dycore tests (with no matching test in the physics folder). Adding this avoid checking all serialized savepoints, but future physics test needs to be included here.
Pass namelist and stencil_factory down to each savepoint class
Remove stencil_facotry from Grid class

…ics namelist defaults to the _config

… into stencil externals rather than constants

…variables externals

…nly constants into microphysics

…o shared-constants

elynnwu · 2021-12-11T01:43:29Z

fv3gfs-physics/fv3gfs/physics/testing/translate.py

+                    backend=self.backend,
+                )
+
+    def python_grid(self):


All fv3core import in physics test have been removed except for Grid here. Should we make a new classmethod in GridData that makes the class with serialized data? Or should we retain Grid? We also need a new location for either of them.

Grid's main responsibility is to convert serialized data, which may or may not include some number of halos and may or may not be staggered, into standardized storages that all have 3 halos and a compute origin at (3, 3). For this reason, Grid should continue to be used in the test code, and should probably live with the translate infrastructure.

This makes sense, I had thought that we wanted to get rid of Grid all together. If the plan is to keep it alive within the translate infrastructure, I'll go ahead and reshuffle some things.

mcgibbon · 2021-12-13T23:00:18Z

fv3gfs-physics/fv3gfs/physics/_config.py

+def namelist_to_flatish_dict(nml_input):
+    nml = dict(nml_input)
+    for name, value in nml.items():
+        if isinstance(value, f90nml.Namelist):
+            nml[name] = namelist_to_flatish_dict(value)
+    flatter_namelist = {}
+    for key, value in nml.items():
+        if isinstance(value, dict):
+            for subkey, subvalue in value.items():
+                if subkey in flatter_namelist:
+                    raise ValueError(
+                        "Cannot flatten this namelist, duplicate keys: " + subkey
+                    )
+                flatter_namelist[subkey] = subvalue
+        else:
+            flatter_namelist[key] = value
+    return flatter_namelist


namelist_to_flatish_dict should probably go to util since it's used identically in the dycore. This can also live in pace.util.namelist.

Moved to pace.util.namelist

mcgibbon · 2021-12-13T23:03:02Z

fv3gfs-physics/fv3gfs/physics/testing/translate.py

+                    backend=self.backend,
+                )
+
+    def python_grid(self):


Grid's main responsibility is to convert serialized data, which may or may not include some number of halos and may or may not be staggered, into standardized storages that all have 3 halos and a compute origin at (3, 3). For this reason, Grid should continue to be used in the test code, and should probably live with the translate infrastructure.

fv3gfs-physics/tests/savepoint/translate/translate_fv_update_phys.py

fv3gfs-physics/tests/savepoint/conftest.py

mcgibbon · 2021-12-13T23:12:50Z

fv3gfs-physics/tests/savepoint/conftest.py

-def process_grid_savepoint(serializer, grid_savepoint, rank, *, backend: str):
-    grid = make_grid(grid_savepoint, serializer, rank, backend=backend)
-    fv3core._config.set_grid(grid)
+def Grid(serializer, grid_savepoint, rank, layout, *, backend: str):


Please use a lowercase name, since this isn't returning a class.

Changed to upper_grid

mcgibbon · 2021-12-13T23:14:15Z

fv3gfs-physics/tests/savepoint/conftest.py

+    grid_rank0 = Grid(
+        serializer, grid_savepoint, 0, physics_config.layout, backend=backend
+    )


This variable is unused, you should be able to delete it.

mcgibbon · 2021-12-13T23:18:29Z

I’m a little worried that if we duplicate the base translate classes and make small changes, these classes are very complex and may be hard to merge later. Would it be possible to put these in pace.util.testing in a way that both physics and dycore continue to use the same code?

rheacangeo

Epic. As discussed, there are some known circular dependencies that come about from this. But we agree, this PR is large enough, and if everything works, we should merge this and make a new story to address those smaller cycles.

rheacangeo · 2021-12-17T21:55:15Z

fv3core/examples/standalone/runfile/dynamics.py


-        fv3core.set_backend(args.backend)
-        fv3core.set_rebuild(False)
-        fv3core.set_validate_args(False)


Is validate_args False when this script runs now?

great catch, changed to False

rheacangeo · 2021-12-17T21:56:07Z

fv3core/examples/standalone/runfile/dynamics.py

 from datetime import datetime
 from typing import Any, Dict, List, Tuple

+import f90nml


please before merging make sure you run run_standalone (either login to daint, or do it through the performance test jenkins plan on your branch) so we know it still works.

rheacangeo · 2021-12-17T21:59:08Z

fv3core/examples/standalone/runfile/dynamics.py

        # references it is updated or removed
-        grid = spec.make_grid_from_namelist(namelist, rank)
-
+        grid = spec.make_grid_from_namelist(dycore_config, rank, args.backend)


if this is only referenced by reading serialized input, this could be moved to inside the read_serialized_initial_state method

stencil_factory is needed for the baroclinic test case too, so can't be inside read_serialized_initial_state only

rheacangeo · 2021-12-17T22:02:26Z

fv3core/tests/main/test_config.py

+# def test_set_backend():
+#     start_backend = fv3core.get_backend()
+#     new_backend = "new_backend"
+#     assert new_backend != start_backend
+#     fv3core.set_backend(new_backend)
+#     assert fv3core.get_backend() == new_backend


this can be deleted now?

rheacangeo · 2021-12-17T22:06:16Z

fv3core/tests/main/test_grid.py

    domain_compute: Index3D,
 ):
-    grid = fv3core.utils.grid.GridIndexing(
+    grid = pace.stencils.testing.grid.GridIndexing(


is GridIndexing in pace.dsl or pace.stencils.testing.grid?

It is pace.dsl, updated here and elsewhere

mcgibbon

Very nice seeing the test code make direct use of namelist and stencil_factory instead of relying on Grid for everything.

You can leave refactoring pace.stencils.testing.grid for a follow-on PR, but please make a Jira task. It's not great having every stencil file import from testing, since the idea of putting things there is to indicate the stencil code shouldn't be importing from it.

Very few comments for how much you've updated. Great job!

.pre-commit-config.yaml

mcgibbon · 2021-12-17T21:47:17Z

examples/dyn_phy.py

 import time

 import click
+import f90nml


I don't know how to evaluate changes to example scripts like this that aren't in CI. We should consider CI-testing all our examples. For now I'll trust you've run this and it works.

Yes, we should add a plan for this. This script was actually broken for a while and we didn't notice.

mcgibbon · 2021-12-17T21:48:02Z

fv3core/examples/standalone/runfile/acoustics.py



-def set_up_namelist(data_directory: str) -> None:
+def set_up_namelist(data_directory: str) -> DynamicalCoreConfig:


Can you update this function's name and docstring now that it's returning a config and not a namelist? You could name it dycore_config_from_namelist.

mcgibbon · 2021-12-17T21:54:21Z

fv3core/examples/wrapped/runfiles/baroclinic_test.py

+    turbulent_kinetic_energy.metadata.gt4py_backend = backend
+    cloud_fraction.metadata.gt4py_backend = backend
+    u_tendency.metadata.gt4py_backend = backend
+    v_tendency.metadata.gt4py_backend = backend


You can pass the gt4py_backend argument when calling Quantity.from_data_array above, instead of overriding it here.

mcgibbon · 2021-12-17T21:55:58Z

fv3core/fv3core/_config.py

    n_sponge: int = NamelistDefaults.n_sponge

+    @classmethod
+    def from_f90nml(cls, namelist: f90nml.Namelist):


Return value type hints for constructors are particularly important/helpful, because they provide type hinting in the place where they're used. For example, this will make mypy check for any typos in attribute accesses on DynamicalCoreConfig in our untested runfiles.

Suggested change

n_sponge: int = NamelistDefaults.n_sponge

@classmethod

def from_f90nml(cls, namelist: f90nml.Namelist):

n_sponge: int = NamelistDefaults.n_sponge

@classmethod

def from_f90nml(cls, namelist: f90nml.Namelist) -> "DynamicalCoreConfig":

mcgibbon · 2021-12-17T22:24:06Z

fv3core/tests/main/test_dycore_call.py

+    with unittest.mock.patch("pace.util.global_config.get_backend", new=error_func):
        with unittest.mock.patch(
-            "fv3core.utils.global_config.is_gpu_backend", new=error_func
+            "pace.util.global_config.is_gpu_backend", new=error_func


Make sure there's a Jira task to delete pace.util.global_config, if we're no longer using it.

It's being used in two spots in the main tests. Once we get rid of those, we can delete global_config

mcgibbon · 2021-12-17T22:26:54Z

fv3core/tests/savepoint/conftest.py

-def process_grid_savepoint(serializer, grid_savepoint, rank, *, backend: str):
-    grid = make_grid(grid_savepoint, serializer, rank, backend=backend)
-    fv3core._config.set_grid(grid)
+def upper_grid(serializer, grid_savepoint, rank, layout, *, backend: str):


What is an "upper" grid? Is there a reason for this function when you can directly call make_grid?

It was originally going to be a pytest fixture, but you're right we can just call make_grid directly. Changing this.

mcgibbon · 2021-12-17T22:31:07Z

fv3gfs-physics/fv3gfs/physics/testing/__init__.py

@@ -1,2 +0,0 @@
-from . import translate_physics
-from .translate_physics import TranslatePhysicsFortranData2Py


Why were these removed?

Since we no longer need to carry separate translate class infrastructure, we don't need this in physics anymore. If we decide to add TranslatePhysics, it will go here.

fv3gfs-physics/tests/savepoint/conftest.py

mcgibbon · 2021-12-17T22:32:49Z

fv3gfs-physics/tests/savepoint/conftest.py

+def upper_grid(serializer, grid_savepoint, rank, layout, *, backend: str):
+    grid = make_grid(grid_savepoint, serializer, rank, layout, backend=backend)


Can you call make_grid directly?

I'm a little confused by this network of functions (grid_data, grid_indexing, physics_config, etc.). Instead of calling grid_data(grid), should you directly use grid.grid_data in whatever function is calling these?

They were supposed to be pytest fixtures, but it's easier to make them instead. I forgot to clean up, deleting all these now.

rheacangeo · 2021-12-17T22:53:33Z

fv3core/examples/standalone/runfile/dynamics.py

+        stencil_config = pace.dsl.stencil.StencilConfig(
+            backend=args.backend,
+            rebuild=False,
+            validate_args=True,


change to False please

rheacangeo

Wahoo! I think the Grid object served us well, but good to finalize the shift away from it by untangling the objects we were grabbing from it as an interim step. Lots going on here and this will make many things possible!

mcgibbon

Make sure there are the 2 Jira tasks for removing global_config and for moving utilities out of pace.stencils.testing.grid, otherwise looks good to me!

* pace-physics -> pySHiELD * Removed pySHiELD locally * Added pySHiELD as submodule * Updating branch to current versions of NDSL and pyFV3 * Updating pyFV3 and pySHiELD for changes to their setup.py files * Updated constraints.txt to match new pySHiELD submodule * Removed local references in constraints.txt * Update pySHiELD * lint * Remove unused mypy * Bad driver `setup,py` * Regenerate `constraints.txt` * Remove local constraints * Lint --------- Co-authored-by: Florian Deconinck <[email protected]>

elynnwu and others added 27 commits December 7, 2021 11:38

delete shared link

f55fcdc

move gt4py util to pace.dsl

a166c79

update dependencies

1a7805c

move get_stencils_with_varied_bounds to pace.dsl

a4390cc

moving fv3core global_costants to pace.util.constants and adding phys…

3f74522

…ics namelist defaults to the _config

linting

784a29f

physics uses pace.util.constants and namelist constants are converted…

d7f4817

… into stencil externals rather than constants

add do_sedi_w to namelist, and make a couple pf microphysics runtime …

6d48843

…variables externals

remove the physics global constants file

bfbc678

moved to stencil

ac40e7d

fixed stencil varied bounds unit test

5373260

move more constants to namelist as discovered and move microphysics-o…

118cfe9

…nly constants into microphysics

Merge remote-tracking branch 'origin/feature/move-gt4py-pace-dsl' int…

e2ed9bb

…o shared-constants

remove comment that might become untrue very easily

7baefb7

remove duplicate CV_AIR entry

d71f88b

irain_f is an int

0685419

remapping uses the localc CONSV_MIN

b9d7530

Merge branch 'main' into feature/move-gt4py-pace-dsl

323d20f

Merge branch 'main' into feature/move-gt4py-pace-

bcd8684

Merge remote-tracking branch 'origin/feature/move-gt4py-pace-dsl' int…

f01bc67

…o shared-constants

add physics config

138ee4f

c12 6 ranks passing

0fd784b

physics test no fv3core import except set_backend

ccc85f6

Merge branch 'main' into feature

b7e7db3

no fv3core import in conftest

c126b33

cleanup

5858ddc

Merge branch 'main' into feature/remove-fv3core-from-physics-test

9d6594a

elynnwu commented Dec 11, 2021

View reviewed changes

elynnwu marked this pull request as ready for review December 13, 2021 17:54

mcgibbon reviewed Dec 13, 2021

View reviewed changes

elynnwu added 4 commits December 14, 2021 12:41

clean up function and type hint

3661492

physics translate class to pace.util.testing

fbf764f

fv3core tests passing

773e9d9

Merge branch 'main' into feature/remove-fv3core-from-physics-test

d91e4e4

elynnwu changed the title ~~Remove fv3core from physics tests~~ Remove global access in fv3core and physics tests Dec 15, 2021

elynnwu added 7 commits December 15, 2021 13:27

remove stencil_factory from Grid

75c0857

force skip mypy inside fv_subgridz

009b483

Merge branch 'main' into feature/remove-fv3core-from-physics-test

799b21a

translate to pace stecil testing

d3e5149

Merge branch 'main' into feature/remove-fv3core-from-physics-test

0499232

remove global namelist

bf4c859

fix dyn_phy run script

c181e62

rheacangeo reviewed Dec 17, 2021

View reviewed changes

mcgibbon reviewed Dec 17, 2021

View reviewed changes

rheacangeo reviewed Dec 17, 2021

View reviewed changes

PR cleanup

9b07de6

rheacangeo approved these changes Dec 18, 2021

View reviewed changes

mcgibbon approved these changes Dec 20, 2021

View reviewed changes

elynnwu merged commit 309408b into main Dec 20, 2021

elynnwu deleted the feature/remove-fv3core-from-physics-test branch December 20, 2021 18:33



		def set_up_namelist(data_directory: str) -> None:
		def set_up_namelist(data_directory: str) -> DynamicalCoreConfig:

		@@ -1,2 +0,0 @@
		from . import translate_physics
		from .translate_physics import TranslatePhysicsFortranData2Py

		def upper_grid(serializer, grid_savepoint, rank, layout, *, backend: str):
		grid = make_grid(grid_savepoint, serializer, rank, layout, backend=backend)

Remove global access in fv3core and physics tests #60

Remove global access in fv3core and physics tests #60

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elynnwu commented Dec 10, 2021 •

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