Set allow_rechunk=True in apply_ufunc

[dcherian]

What happened:

blockwise calls unify_chunks by default but apply_gufunc does not; so we have a regression in apply_ufunc now that we've switched from blockwise to apply_gufunc.

Minimal Complete Verifiable Example:

import operator

a = xr.DataArray(np.arange(10), dims=("a")).chunk({"a": 2})
b = xr.DataArray(np.arange(10), dims=("a")).chunk({"a": 4})

xr.apply_ufunc(operator.add, a, b, dask="parallelized", output_dtypes=[a.dtype]).compute()

raises

ValueError: Dimension `'__loopdim0__'` with different chunksize present

on master but works with 0.16.0

I think we need to do dask_gufunc_kwargs.setdefault("allow_rechunk", True)

If we want to avoid that, we'll need to go through a deprecation cycle.

[dcherian]

(this is causing downstream test failures: NCAR/pop-tools#59; thanks @mnlevy1981)

[kmuehlbauer]

The behaviour changed in #4060 (commit a7fb5a9). Please see discussion with regard to allow_rechunk over there. Reason to not handle/set allow_rechunk=True was @shoyer's comment.

[dcherian]

Copying over that comment...

I am pretty confident that existing behavior of xarray.apply_ufunc with un-equal chunks along non-core dimensions is entirely broken. I am OK with just erroring for now.

@shoyer could you please clarify what you meant?

For example, this works with v0.16.0 but fails on master

import operator

import numpy as np

import xarray as xr

a = xr.DataArray(np.ones((10, 10)), dims=("a", "b")).chunk({"a": 2, "b": 1})
b = xr.DataArray(np.ones((10, 10)), dims=("a", "b")).chunk({"a": -1, "b": 4})

xr.apply_ufunc(
    operator.add, a, b, dask="parallelized", output_dtypes=[a.dtype],
).compute().equals(a.compute() + b.compute())

[kmuehlbauer]

One solution would be to catch this ValueError, issue a FutureWarning and add allow_rechunk=True to dask_gufunc_kwargs here:

xarray/xarray/core/computation.py

Lines 646 to 657 in 9c85dd5

	def func(*arrays):
	import dask.array as da
	res = da.apply_gufunc(
	numpy_func,
	signature.to_gufunc_string(exclude_dims),
	*arrays,
	vectorize=vectorize,
	output_dtypes=output_dtypes,
	**dask_gufunc_kwargs,
	)

        def func(*arrays):
            import dask.array as da

            gufunc = functools.partial(
                da.apply_gufunc,
                numpy_func,
                signature.to_gufunc_string(exclude_dims),
                *arrays,
                vectorize=vectorize,
                output_dtypes=output_dtypes,
            )

            try:
                res = gufunc(**dask_gufunc_kwargs)
            except ValueError as exc:
                if "with different chunksize present" in str(exc):
                    warnings.warn(
                        f"``allow_rechunk=True`` need to be explicitely set in the "
                        f"``dask_gufunc_kwargs`` parameter. Not setting will raise dask "
                        f"ValueError ``{str(exc)}`` in a future version.",
                        FutureWarning,
                        stacklevel=2,
                    )
                    dask_gufunc_kwargs["allow_rechunk"] = True
                    res = gufunc(**dask_gufunc_kwargs)
                else:
                    raise

I could make a PR out of this. The message wording can surely be improved. WDYT @dcherian and @shoyer?

[shoyer]

Maybe we do want to set allow_rechunk=True? It seems that I was just mistaken about the current behavior.

[kmuehlbauer]

@shoyer In this case: Should we warn the user, that data might be loaded into memory?

Another questions are, why does this kwarg exist in dask and why do they not rechunk per default?

[kmuehlbauer]

From the dask apply_gufunc docstring:

"""
allow_rechunk: Optional, bool, keyword only

    Allows rechunking, otherwise chunk sizes need to match and core dimensions are to consist only of one chunk. 
    Warning: enabling this can increase memory usage significantly. Defaults to False
"""

Current code handling in dask:

https://github.com/dask/dask/blob/42873f27ce11ce35652dda344dae5c47b742bef2/dask/array/gufunc.py#L398-L417

         if not allow_rechunk:
            chunksizes = chunksizess[dim]
            #### Check if core dimensions consist of only one chunk
            if (dim in core_shapes) and (chunksizes[0][0] < core_shapes[dim]):
                raise ValueError(
                    "Core dimension `'{}'` consists of multiple chunks. To fix, rechunk into a single \
chunk along this dimension or set `allow_rechunk=True`, but beware that this may increase memory usage \
significantly.".format(
                        dim
                    )
                )
            #### Check if loop dimensions consist of same chunksizes, when they have sizes > 1
            relevant_chunksizes = list(
                unique(c for s, c in zip(sizes, chunksizes) if s > 1)
            )
            if len(relevant_chunksizes) > 1:
                raise ValueError(
                    "Dimension `'{}'` with different chunksize present".format(dim)
                )

IIUTC, this not only rechunks non-core dimensions but also fixes core dimensions with more than one chunk. Would this be intended from the xarray-side? Before #4060 core dimension chunks>1 was catched and errored:

            # core dimensions cannot span multiple chunks
            for axis, dim in enumerate(core_dims, start=-len(core_dims)):
                if len(data.chunks[axis]) != 1:
                    raise ValueError(
                        "dimension {!r} on {}th function argument to "
                        "apply_ufunc with dask='parallelized' consists of "
                        "multiple chunks, but is also a core dimension. To "
                        "fix, rechunk into a single dask array chunk along "
                        "this dimension, i.e., ``.chunk({})``, but beware "
                        "that this may significantly increase memory usage.".format(
                            dim, n, {dim: -1}
                        )
                    )

Explicit rechunk was recommended to the user, though.

That means setting allow_rechunk=True per default alone will not give us same behaviour as before #4060. I'm unsure how to proceed.

[kmuehlbauer]

Another questions are, why does this kwarg exist in dask and why do they not rechunk per default?

Trying to answer this from looking at the dask code.

• allow_rechunk=False: catch chunking problems in core and non-core-dimensions and raise an error.
  This helps to prevent users running into loading huge dask arrays into memory without further notice.
• allow_rechunk=True: blockwise is called with align_arrays=True per default which means automatic rechunking for all arrays (core and non-core dimensions). Users can use this, if they are sure the system can handle possible large amounts of data.

[dcherian]

So to maintain backward compatibility, we should add that same check

            # core dimensions cannot span multiple chunks
            for axis, dim in enumerate(core_dims, start=-len(core_dims)):
                if len(data.chunks[axis]) != 1:
                    raise ValueError(
                        "dimension {!r} on {}th function argument to "
                        "apply_ufunc with dask='parallelized' consists of "
                        "multiple chunks, but is also a core dimension. To "
                        "fix, rechunk into a single dask array chunk along "
                        "this dimension, i.e., ``.chunk({})``, but beware "
                        "that this may significantly increase memory usage.".format(
                            dim, n, {dim: -1}
                        )
                    )

and set allow_rechunk=True.

We could deprecate and remove this check in a couple of versions but I don't know if it's worth the effort...

[kmuehlbauer]

@dcherian @shoyer

In #4392 I've tried to get around this bug. I found it easier to just catch the dask ValueError's and not add more code checks. I'll add more information in that PR.