Add Global Subset Grids#
Step 1.1: Horizontal Grid#
Extract a subgrid from a global grid using the subgrid_from_supergrid method:
from CrocoDash.grid import Grid
grid = Grid.subgrid_from_supergrid(
path = "s3://crocodile-cesm/CrocoDash/data/grids/ocean_hgrid_trimmed.nc", # supergrid
llc = (16.0, 192.0), # (l)ower (l)eft (c)orner coords
urc = (27.0, 209.0), # (u)pper (r)ight (c)orner coords
name = "hawaii_2"
)
syntax error, unexpected WORD_WORD, expecting SCAN_ATTR or SCAN_DATASET or SCAN_ERROR
context: <?xml^ version="1.0" encoding="UTF-8"?><Error><Code>AccessDenied</Code><Message>Access Denied</Message><RequestId>EZDBQD557KRH6R81</RequestId><HostId>QfodkXjoEJLl/aftGGgLUc8gnqltpwUVYFe9SdsMDfztr0a6FIjWi/maeB8Uzlkx4lV57DMj5x4=</HostId></Error>
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/file_manager.py:211, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
210 try:
--> 211 file = self._cache[self._key]
212 except KeyError:
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/lru_cache.py:56, in LRUCache.__getitem__(self, key)
55 with self._lock:
---> 56 value = self._cache[key]
57 self._cache.move_to_end(key)
KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('s3://crocodile-cesm/CrocoDash/data/grids/ocean_hgrid_trimmed.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '902317f9-1c3d-4a95-94dd-b2760296281c']
During handling of the above exception, another exception occurred:
OSError Traceback (most recent call last)
Input In [1], in <cell line: 0>()
1 from CrocoDash.grid import Grid
----> 3 grid = Grid.subgrid_from_supergrid(
4 path = "s3://crocodile-cesm/CrocoDash/data/grids/ocean_hgrid_trimmed.nc", # supergrid
5 llc = (16.0, 192.0), # (l)ower (l)eft (c)orner coords
6 urc = (27.0, 209.0), # (u)pper (r)ight (c)orner coords
7 name = "hawaii_2"
8 )
File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/visualCaseGen/external/mom6_bathy/mom6_bathy/grid.py:432, in Grid.subgrid_from_supergrid(cls, path, llc, urc, name)
411 @classmethod
412 def subgrid_from_supergrid(cls, path: str, llc: tuple[float, float], urc: tuple[float, float], name: str) -> "Grid":
413 """Create a Grid instance from a subset of a supergrid file.
414
415 Parameters
(...)
429 The Grid instance created from the supergrid file.
430 """
--> 432 full_grid = cls.from_supergrid(path)
434 assert len(llc) == 2, "llc must be a tuple of two floats"
435 assert len(urc) == 2, "urc must be a tuple of two floats"
File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/visualCaseGen/external/mom6_bathy/mom6_bathy/grid.py:376, in Grid.from_supergrid(cls, path, name)
359 """Create a Grid instance from a supergrid file.
360
361 Parameters
(...)
372 The Grid instance created from the supergrid file.
373 """
375 # read supergrid dataset
--> 376 ds = xr.open_dataset(path)
377 assert (
378 ds.x.units == ds.y.units and "degree" in ds.x.units
379 ), "Only degrees units are supported in supergrid files"
381 # check supergrid
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/api.py:572, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
560 decoders = _resolve_decoders_kwargs(
561 decode_cf,
562 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...)
568 decode_coords=decode_coords,
569 )
571 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 572 backend_ds = backend.open_dataset(
573 filename_or_obj,
574 drop_variables=drop_variables,
575 **decoders,
576 **kwargs,
577 )
578 ds = _dataset_from_backend_dataset(
579 backend_ds,
580 filename_or_obj,
(...)
590 **kwargs,
591 )
592 return ds
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:593, in NetCDF4BackendEntrypoint.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, group, mode, format, clobber, diskless, persist, lock, autoclose)
572 def open_dataset( # type: ignore[override] # allow LSP violation, not supporting **kwargs
573 self,
574 filename_or_obj: str | os.PathLike[Any] | BufferedIOBase | AbstractDataStore,
(...)
590 autoclose=False,
591 ) -> Dataset:
592 filename_or_obj = _normalize_path(filename_or_obj)
--> 593 store = NetCDF4DataStore.open(
594 filename_or_obj,
595 mode=mode,
596 format=format,
597 group=group,
598 clobber=clobber,
599 diskless=diskless,
600 persist=persist,
601 lock=lock,
602 autoclose=autoclose,
603 )
605 store_entrypoint = StoreBackendEntrypoint()
606 with close_on_error(store):
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:400, in NetCDF4DataStore.open(cls, filename, mode, format, group, clobber, diskless, persist, lock, lock_maker, autoclose)
394 kwargs = dict(
395 clobber=clobber, diskless=diskless, persist=persist, format=format
396 )
397 manager = CachingFileManager(
398 netCDF4.Dataset, filename, mode=mode, kwargs=kwargs
399 )
--> 400 return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:347, in NetCDF4DataStore.__init__(self, manager, group, mode, lock, autoclose)
345 self._group = group
346 self._mode = mode
--> 347 self.format = self.ds.data_model
348 self._filename = self.ds.filepath()
349 self.is_remote = is_remote_uri(self._filename)
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:409, in NetCDF4DataStore.ds(self)
407 @property
408 def ds(self):
--> 409 return self._acquire()
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/netCDF4_.py:403, in NetCDF4DataStore._acquire(self, needs_lock)
402 def _acquire(self, needs_lock=True):
--> 403 with self._manager.acquire_context(needs_lock) as root:
404 ds = _nc4_require_group(root, self._group, self._mode)
405 return ds
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/contextlib.py:137, in _GeneratorContextManager.__enter__(self)
135 del self.args, self.kwds, self.func
136 try:
--> 137 return next(self.gen)
138 except StopIteration:
139 raise RuntimeError("generator didn't yield") from None
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/file_manager.py:199, in CachingFileManager.acquire_context(self, needs_lock)
196 @contextlib.contextmanager
197 def acquire_context(self, needs_lock=True):
198 """Context manager for acquiring a file."""
--> 199 file, cached = self._acquire_with_cache_info(needs_lock)
200 try:
201 yield file
File /usr/share/miniconda/envs/CrocoDash/lib/python3.11/site-packages/xarray/backends/file_manager.py:217, in CachingFileManager._acquire_with_cache_info(self, needs_lock)
215 kwargs = kwargs.copy()
216 kwargs["mode"] = self._mode
--> 217 file = self._opener(*self._args, **kwargs)
218 if self._mode == "w":
219 # ensure file doesn't get overridden when opened again
220 self._mode = "a"
File src/netCDF4/_netCDF4.pyx:2469, in netCDF4._netCDF4.Dataset.__init__()
File src/netCDF4/_netCDF4.pyx:2028, in netCDF4._netCDF4._ensure_nc_success()
OSError: [Errno -78] NetCDF: Authorization failure: 's3://crocodile-cesm/CrocoDash/data/grids/ocean_hgrid_trimmed.nc'
Step 1.2: Topography#
from CrocoDash.topo import Topo
topo = Topo(
grid = grid,
min_depth = 9.5,
)
bathymetry_path='s3://crocodile-cesm/CrocoDash/data/gebco/GEBCO_2024.zarr/'
topo.interpolate_from_file(
file_path = bathymetry_path,
longitude_coordinate_name="lon",
latitude_coordinate_name="lat",
vertical_coordinate_name="elevation"
)
Begin regridding bathymetry...
Original bathymetry size: 6.26 Mb
Regridded size: 0.70 Mb
Automatic regridding may fail if your domain is too big! If this process hangs or crashes,open a terminal with appropriate computational and resources try calling ESMF directly in the input directory None via
`mpirun -np NUMBER_OF_CPUS ESMF_Regrid -s bathymetry_original.nc -d bathymetry_unfinished.nc -m bilinear --src_var depth --dst_var depth --netcdf4 --src_regional --dst_regional`
For details see https://xesmf.readthedocs.io/en/latest/large_problems_on_HPC.html
Afterwards, run the 'expt.tidy_bathymetry' method to skip the expensive interpolation step, and finishing metadata, encoding and cleanup.
Regridding successful! Now calling `tidy_bathymetry` method for some finishing touches...
Tidy bathymetry: Reading in regridded bathymetry to fix up metadata...done. Filling in inland lakes and channels... done.
setup bathymetry has finished successfully.
topo.depth.plot()
<matplotlib.collections.QuadMesh at 0x15051e88a930>
