Load esmvalcore.dataset.Dataset objects in parallel using Dask
#2517
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this is brilliant, bud! I've been meaning to get delayed in places in Core for some time. Got one possible nagging comment through - from https://docs.dask.org/en/stable/delayed-best-practices.html they say "Every delayed task has an overhead of a few hundred microseconds. Usually this is ok, but it can become a problem if you apply dask.delayed too finely. In this case, it’s often best to break up your many tasks into batches or use one of the Dask collections to help you." - I am guessing this applies to O(millions) (at least) but can we maybe run a test with one of those mega recipes that loads hundreds of datasets?
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oh and maybe a line or two in the documentation perhaps? Bit of an advanced topic, so maybe a very short reference |
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This may need a bit more testing. The recipe below fails with the distributed scheduler and the iris # ESMValTool
# recipe_python.yml
#
# See https://docs.esmvaltool.org/en/latest/recipes/recipe_examples.html
# for a description of this recipe.
#
# See https://docs.esmvaltool.org/projects/esmvalcore/en/latest/recipe/overview.html
# for a description of the recipe format.
---
documentation:
description: |
Example recipe that plots a map and timeseries of temperature.
title: Recipe that runs an example diagnostic written in Python.
authors:
- andela_bouwe
- righi_mattia
maintainer:
- schlund_manuel
references:
- acknow_project
projects:
- esmval
- c3s-magic
datasets:
- {dataset: FGOALS-f3-L, ensemble: 'r1i1p1f1', grid: gn}
preprocessors:
# See https://docs.esmvaltool.org/projects/esmvalcore/en/latest/recipe/preprocessor.html
# for a description of the preprocessor functions.
annual_mean_global:
area_statistics:
operator: mean
annual_statistics:
operator: mean
convert_units:
units: degrees_C
diagnostics:
timeseries:
description: Annual mean temperature in Amsterdam and global mean since 1850.
themes:
- phys
realms:
- atmos
variables:
tos_global:
short_name: tos
mip: Omon
project: CMIP6
exp: [historical, ssp585]
preprocessor: annual_mean_global
timerange: 1850/2100
caption: Annual global mean {long_name} according to {dataset}.
scripts:
script1:
script: examples/diagnostic.py
quickplot:
plot_type: plot |
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This issue mentioned above is fixed by SciTools/iris#6187. |
| @@ -765,6 +798,51 @@ def _load(self) -> Cube: | |||
| **self.facets, | |||
| } | |||
| settings["concatenate"] = {"check_level": self.session["check_level"]} | |||
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| 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.
Thanks for reviewing @schlunma! As far as I can see it does not change the preprocessing pipeline, but maybe you can find a case where it does? Maybe you could run a recipe that you think could potentially be broken as a test and report back the result? |
Description
Load the individual files in a dataset in parallel using Dask and add the option to get a
dask.delayed.Delayedback fromesmvalcore.dataset.Datasetthat can be fed todask.computeto get aniris.cube.Cube. This can considerably speed up loading datasets that consist of many files or, when used with the delayed option, speed up loading multiple datasets.Related to #2300 and #2316
Link to documentation: https://esmvaltool--2517.org.readthedocs.build/projects/ESMValCore/en/2517/api/esmvalcore.dataset.html#esmvalcore.dataset.Dataset.load
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Changes are backward compatibleThe preprocessor functionfix_metadatano longer groups by the attribute"source_file".To help with the number pull requests: