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  • martindurant · 7 ✖

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  • Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) · 7 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
739959248 https://github.com/pydata/xarray/issues/4478#issuecomment-739959248 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDczOTk1OTI0OA== martindurant 6042212 2020-12-07T14:39:57Z 2020-12-07T14:39:57Z CONTRIBUTOR

Please try with fsspec master.

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
704353239 https://github.com/pydata/xarray/issues/4478#issuecomment-704353239 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwNDM1MzIzOQ== martindurant 6042212 2020-10-06T15:30:50Z 2020-10-06T15:30:50Z CONTRIBUTOR

That's a lot of data!

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
704285976 https://github.com/pydata/xarray/issues/4478#issuecomment-704285976 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwNDI4NTk3Ng== martindurant 6042212 2020-10-06T13:55:34Z 2020-10-06T13:55:34Z CONTRIBUTOR

Can you confirm that this works ok with fsspec and s3fs master?

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
702846089 https://github.com/pydata/xarray/issues/4478#issuecomment-702846089 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwMjg0NjA4OQ== martindurant 6042212 2020-10-02T16:59:45Z 2020-10-02T16:59:45Z CONTRIBUTOR

I have reproduced it locally (also with moto). Indeed, many threads are trying to stall the event loop at once. This will take a little finesse.

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
702816676 https://github.com/pydata/xarray/issues/4478#issuecomment-702816676 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwMjgxNjY3Ng== martindurant 6042212 2020-10-02T15:59:59Z 2020-10-02T15:59:59Z CONTRIBUTOR

Thanks for the digging, I'll look into it

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
702213899 https://github.com/pydata/xarray/issues/4478#issuecomment-702213899 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwMjIxMzg5OQ== martindurant 6042212 2020-10-01T15:27:00Z 2020-10-01T15:27:00Z CONTRIBUTOR

File "/usr/local/lib/python3.7/asyncio/base_events.py", line 1771, in _run_once handle = self._ready.popleft()

This looks like it may be a race conditions where multiple threads are calling the event loop at once. I wonder if you could list the event loops in use and the threads (perhaps best run with base python than ipython/jupyter).

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711
702124268 https://github.com/pydata/xarray/issues/4478#issuecomment-702124268 https://api.github.com/repos/pydata/xarray/issues/4478 MDEyOklzc3VlQ29tbWVudDcwMjEyNDI2OA== martindurant 6042212 2020-10-01T13:11:32Z 2020-10-01T13:11:32Z CONTRIBUTOR

The following code, modified to the style of the s3fs test suite, works OK: ```python def test_with_xzarr(s3): da = pytest.importorskip("dask.array") xr = pytest.importorskip("xarray") name = "sample"

nana = xr.DataArray(da.zeros((1023, 1023, 3)))

s3_path = f"{test_bucket_name}/{name}"
s3store = s3.get_mapper(s3_path)

print("Storing")
nana.to_dataset().to_zarr(store=s3store, mode="w", consolidated=True, compute=True)

```

 
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   Dataset to zarr not working with newest s3fs Storage (s3fs > 0.5.0) 712782711

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