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  • Writing netcdf after running xarray.dataset.reindex to fill gaps in a time series fails due to memory allocation error · 3 ✖

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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
1248550900 https://github.com/pydata/xarray/issues/7018#issuecomment-1248550900 https://api.github.com/repos/pydata/xarray/issues/7018 IC_kwDOAMm_X85Ka1_0 lassiterdc 64621312 2022-09-15T19:59:39Z 2022-09-15T19:59:39Z NONE

I tried your suggestion and still ran into a memory allocation error, but it sounds like you're onto something. I also found this other thread about reindex causing memory allocation errors but it doesn't look like a solution was discovered there either. https://github.com/pydata/xarray/issues/2745

 
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   Writing netcdf after running xarray.dataset.reindex to fill gaps in a time series fails due to memory allocation error 1368696980
1245425482 https://github.com/pydata/xarray/issues/7018#issuecomment-1245425482 https://api.github.com/repos/pydata/xarray/issues/7018 IC_kwDOAMm_X85KO69K JamiePringle 12818667 2022-09-13T13:36:40Z 2022-09-13T13:36:40Z NONE

I think #7028 might help you -- I was running into a similar problem. In short, try keeping your time variables as float64 instead of as date time (or converting before you try to save). 

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   Writing netcdf after running xarray.dataset.reindex to fill gaps in a time series fails due to memory allocation error 1368696980
1242793638 https://github.com/pydata/xarray/issues/7018#issuecomment-1242793638 https://api.github.com/repos/pydata/xarray/issues/7018 IC_kwDOAMm_X85KE4am lassiterdc 64621312 2022-09-10T19:34:26Z 2022-09-10T19:34:26Z NONE

I found a functional workaround is to chunk by one of the spatial dimensions instead. I'd still like to know why the code above fails though. I'm assuming there's a scheduled task with dask the occurs before to_netcdf but I haven't been able to figure out what that is.

python ds = xr.open_dataset(fldr_in_grib, engine="cfgrib", chunks={"latitude":875}, backend_kwargs={'indexpath': ''})

 
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   Writing netcdf after running xarray.dataset.reindex to fill gaps in a time series fails due to memory allocation error 1368696980

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