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Load esmvalcore.dataset.Dataset objects in parallel using Dask #2517

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103 changes: 88 additions & 15 deletions esmvalcore/dataset.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,15 @@
import re
import textwrap
import uuid
from collections.abc import Iterable
from copy import deepcopy
from fnmatch import fnmatchcase
from itertools import groupby
from pathlib import Path
from typing import Any, Iterator, Sequence, Union
from typing import Any, Iterator, Sequence, TypeVar, Union

import dask
from dask.delayed import Delayed
from iris.cube import Cube

from esmvalcore import esgf, local
Expand Down Expand Up @@ -84,6 +87,14 @@ def _ismatch(facet_value: FacetValue, pattern: FacetValue) -> bool:
)


T = TypeVar("T")


def _first(elems: Iterable[T]) -> T:
"""Return the first element."""
return next(iter(elems))


class Dataset:
"""Define datasets, find the related files, and load them.

Expand Down Expand Up @@ -693,9 +704,19 @@ def files(self) -> Sequence[File]:
def files(self, value):
self._files = value

def load(self) -> Cube:
def load(self, compute: bool = True) -> Cube | Delayed:
"""Load dataset.

Parameters
----------
compute:
If :obj:`True`, return the :class:`~iris.cube.Cube` immediately.
If :obj:`False`, return a :class:`~dask.delayed.Delayed` object
that can be used to load the cube by calling its
:meth:`~dask.delayed.Delayed.compute` method. Multiple datasets
can be loaded in parallel by passing a list of such delayeds
to :func:`dask.compute`.

Raises
------
InputFilesNotFound
Expand All @@ -718,7 +739,7 @@ def load(self) -> Cube:
supplementary_cubes.append(supplementary_cube)

output_file = _get_output_file(self.facets, self.session.preproc_dir)
cubes = preprocess(
cubes = dask.delayed(preprocess)(
[cube],
"add_supplementary_variables",
input_files=input_files,
Expand All @@ -727,7 +748,10 @@ def load(self) -> Cube:
supplementary_cubes=supplementary_cubes,
)

return cubes[0]
cube = dask.delayed(_first)(cubes)
if compute:
return cube.compute()
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return cube

def _load(self) -> Cube:
"""Load self.files into an iris cube and return it."""
Expand All @@ -742,7 +766,16 @@ def _load(self) -> Cube:
msg = "\n".join(lines)
raise InputFilesNotFound(msg)

input_files = [
file.local_file(self.session["download_dir"])
if isinstance(file, esgf.ESGFFile)
else file
for file in self.files
]
output_file = _get_output_file(self.facets, self.session.preproc_dir)
debug = self.session["save_intermediary_cubes"]

# Load all input files and concatenate them.
fix_dir_prefix = Path(
self.session._fixed_file_dir,
self._get_joined_summary_facets("_", join_lists=True) + "_",
Expand All @@ -765,6 +798,51 @@ def _load(self) -> Cube:
**self.facets,
}
settings["concatenate"] = {"check_level": self.session["check_level"]}

result = []
for input_file in input_files:
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This changes how data is passed through the different preprocessor functions, doesn't it?

Right now, for example, fix_metadata will get ALL cubes from ALL files as input. With this change here, it will only get the cubes from one file, right?

I know that fix_metadata itself groups by file, but this is already very problematic (see #1806 and #2551).

I also fear that this might have other undesired side effects. Why do you need to treat these first preprocessor functions differently in the new code?

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Why do you need to treat these first preprocessor functions differently in the new code?

To improve parallelism. Like this, each input file can be loaded and preprocessed up to the concatenate step in parallel.

This changes how data is passed through the different preprocessor functions, doesn't it?

No, it just takes the grouping out of fix_metadata and implements it in the function calling fix_metadata to enable additional parallelism. If this pull request is merged, #2551 would need to be updated to do the grouping here instead of inside fix_metadata.

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Okay, I think I misunderstood the code in the first place. The function preprocess is not at all straightforward when it comes to handling of input and output types...I agree that the behavior has not changed.

I will test this with a couple of recipes once Levante is running again next week. In the meantime, would it make sense to remove the grouping of files in fix_metadata? It would be confusing to have this in two places of the code. I know that this wouldn't be strictly backwards-compatible, but the grouping was only enabled if the cubes have a source_file attribute (which is probably only the case when used within ESMValTool). I highly doubt that this function would be very useful outside of ESMValTool anyway.

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I removed the grouping in d5a39af, but where would you suggest we remove the "source_file" attribute now? Apart from grouping, it is also used to generate error messages from the cmor checkers. Should it be removed after cmor_check_data?

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Good question. I would either remove it after cmor_check_data or remove it altogether from the code. The preprocessors log all filenames anyway now, so its not as important anymore as it used to be.

files = dask.delayed(preprocess)(
[input_file],
"fix_file",
input_files=[input_file],
output_file=output_file,
debug=debug,
**settings["fix_file"],
)
# Multiple cubes may be present in a file.
cubes = dask.delayed(preprocess)(
files,
"load",
input_files=[input_file],
output_file=output_file,
debug=debug,
**settings["load"],
)
# Combine the cubes into a single cube per file.
cubes = dask.delayed(preprocess, pure=False)(
cubes,
"fix_metadata",
input_files=[input_file],
output_file=output_file,
debug=debug,
**settings["fix_metadata"],
)
cube = dask.delayed(_first)(cubes)
result.append(cube)

# Concatenate the cubes from all files.
result = dask.delayed(preprocess, pure=False)(
result,
"concatenate",
input_files=input_files,
output_file=output_file,
debug=debug,
**settings["concatenate"],
)

# At this point `result` is a list containing a single cube. Apply the
# remaining preprocessor functions to this cube.
settings.clear()
settings["cmor_check_metadata"] = {
"check_level": self.session["check_level"],
"cmor_table": self.facets["project"],
Expand All @@ -777,6 +855,7 @@ def _load(self) -> Cube:
"timerange": self.facets["timerange"],
}
settings["fix_data"] = {
"pure": False,
"session": self.session,
**self.facets,
}
Expand All @@ -787,24 +866,18 @@ def _load(self) -> Cube:
"frequency": self.facets["frequency"],
"short_name": self.facets["short_name"],
}

result = [
file.local_file(self.session["download_dir"])
if isinstance(file, esgf.ESGFFile)
else file
for file in self.files
]
for step, kwargs in settings.items():
result = preprocess(
pure = settings.pop("pure", True)
result = dask.delayed(preprocess, pure=pure)(
result,
step,
input_files=self.files,
input_files=input_files,
output_file=output_file,
debug=self.session["save_intermediary_cubes"],
debug=debug,
**kwargs,
)

cube = result[0]
cube = dask.delayed(_first)(result)
return cube

def from_ranges(self) -> list["Dataset"]:
Expand Down
12 changes: 9 additions & 3 deletions tests/integration/dataset/test_dataset.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import iris.coords
import iris.cube
import pytest
from dask.delayed import Delayed

from esmvalcore.config import CFG
from esmvalcore.dataset import Dataset
Expand Down Expand Up @@ -55,7 +56,8 @@ def example_data(tmp_path, monkeypatch):
monkeypatch.setitem(CFG, "output_dir", tmp_path / "output_dir")


def test_load(example_data):
@pytest.mark.parametrize("lazy", [True, False])
def test_load(example_data, lazy):
tas = Dataset(
short_name="tas",
mip="Amon",
Expand All @@ -72,7 +74,11 @@ def test_load(example_data):
tas.find_files()
print(tas.files)

cube = tas.load()

if lazy:
result = tas.load(compute=False)
assert isinstance(result, Delayed)
cube = result.compute()
else:
cube = tas.load()
assert isinstance(cube, iris.cube.Cube)
assert cube.cell_measures()