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Auto rechunk to enable blockwise reduction #380

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48 changes: 43 additions & 5 deletions flox/core.py
Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,12 @@
# _simple_combine.
DUMMY_AXIS = -2

# Thresholds below which we will automatically rechunk to blockwise if it makes sense
# 1. Fractional change in number of chunks after rechunking
BLOCKWISE_RECHUNK_NUM_CHUNKS_THRESHOLD = 0.25
# 2. Fractional change in max chunk size after rechunking
BLOCKWISE_RECHUNK_CHUNK_SIZE_THRESHOLD = 0.15

logger = logging.getLogger("flox")


Expand Down Expand Up @@ -151,8 +157,11 @@ def identity(x: T) -> T:
return x


def _issorted(arr: np.ndarray) -> bool:
return bool((arr[:-1] <= arr[1:]).all())
def _issorted(arr: np.ndarray, ascending=True) -> bool:
if ascending:
return bool((arr[:-1] <= arr[1:]).all())
else:
return bool((arr[:-1] >= arr[1:]).all())


def _is_arg_reduction(func: T_Agg) -> bool:
Expand Down Expand Up @@ -230,6 +239,8 @@ def _get_optimal_chunks_for_groups(chunks, labels):
Δl = abs(c - l)
if c == 0 or newchunkidx[-1] > l:
continue
f = f.item() # noqa
l = l.item() # noqa
if Δf < Δl and f > newchunkidx[-1]:
newchunkidx.append(f)
else:
Expand Down Expand Up @@ -628,7 +639,9 @@ def rechunk_for_cohorts(
return array.rechunk({axis: newchunks})


def rechunk_for_blockwise(array: DaskArray, axis: T_Axis, labels: np.ndarray) -> DaskArray:
def rechunk_for_blockwise(
array: DaskArray, axis: T_Axis, labels: np.ndarray, *, force: bool = True
) -> DaskArray:
"""
Rechunks array so that group boundaries line up with chunk boundaries, allowing
embarrassingly parallel group reductions.
Expand All @@ -651,13 +664,27 @@ def rechunk_for_blockwise(array: DaskArray, axis: T_Axis, labels: np.ndarray) ->
DaskArray
Rechunked array
"""
labels = factorize_((labels,), axes=())[0]
chunks = array.chunks[axis]
if len(chunks) == 1:
return array

labels = factorize_((labels,), axes=())[0]
newchunks = _get_optimal_chunks_for_groups(chunks, labels)
if newchunks == chunks:
return array
else:

Δn = abs(len(newchunks) - len(chunks))
if force or (
(Δn / len(chunks) < BLOCKWISE_RECHUNK_NUM_CHUNKS_THRESHOLD)
and (
abs(max(newchunks) - max(chunks)) / max(chunks) < BLOCKWISE_RECHUNK_CHUNK_SIZE_THRESHOLD
)
):
logger.debug("Rechunking to enable blockwise.")
# Less than 25% change in number of chunks, let's do it
return array.rechunk({axis: newchunks})
else:
return array


def reindex_(
Expand Down Expand Up @@ -2468,6 +2495,17 @@ def groupby_reduce(
has_dask = is_duck_dask_array(array) or is_duck_dask_array(by_)
has_cubed = is_duck_cubed_array(array) or is_duck_cubed_array(by_)

if (
method is None
and is_duck_dask_array(array)
and not any_by_dask
and by_.ndim == 1
and _issorted(by_, ascending=True)
):
# Let's try rechunking for sorted 1D by.
(single_axis,) = axis_
array = rechunk_for_blockwise(array, single_axis, by_, force=False)

if _is_first_last_reduction(func):
if has_dask and nax != 1:
raise ValueError(
Expand Down
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