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  • jnhansen · 2 ✖

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  • Concatenate across multiple dimensions with open_mfdataset · 2 ✖

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410361639 https://github.com/pydata/xarray/issues/2159#issuecomment-410361639 https://api.github.com/repos/pydata/xarray/issues/2159 MDEyOklzc3VlQ29tbWVudDQxMDM2MTYzOQ== jnhansen 2622379 2018-08-03T20:03:21Z 2018-08-03T20:14:17Z NONE

Yes, xarray should support that very easily -- assuming you have dask installed: python ds = auto_merge('*.nc') ds.to_netcdf('larger_than_memory.nc') auto_merge conserves the chunk sizes resulting from the individual files. If the single files are still too large to fit into memory individually you can rechunk to smaller chunk sizes. The same goes of course for the original xarray.open_mfdataset.

I tested it on a ~25 GB dataset (on a machine with less memory than that).

Note: ds = auto_merge('*.nc') actually runs in a matter of milliseconds, as it merely provides a view of the merged dataset. Only once you call ds.to_netcdf('larger_than_memory.nc') all the disk I/O happens.

 
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   Concatenate across multiple dimensions with open_mfdataset 324350248
410348249 https://github.com/pydata/xarray/issues/2159#issuecomment-410348249 https://api.github.com/repos/pydata/xarray/issues/2159 MDEyOklzc3VlQ29tbWVudDQxMDM0ODI0OQ== jnhansen 2622379 2018-08-03T19:07:10Z 2018-08-03T19:12:21Z NONE

I just had the exact same problem, and while I didn't yet have time to dig into the source code of xarray.open_mfdataset, I wrote my own function to achieve this:

https://gist.github.com/jnhansen/fa474a536201561653f60ea33045f4e2

Maybe it's helpful to some of you.

Note that I make the following assumptions (which are reasonable for my use case): * the data variables in each part are identical * equality of the first element of two coordinate arrays is sufficient to assume equality of the two coordinate arrays

 
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   Concatenate across multiple dimensions with open_mfdataset 324350248

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