issues: 252358450
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id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
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252358450 | MDExOlB1bGxSZXF1ZXN0MTM3Mjc0Nzgx | 1517 | Automatic parallelization for dask arrays in apply_ufunc | 1217238 | closed | 0 | 22 | 2017-08-23T17:27:36Z | 2017-10-09T23:28:52Z | 2017-10-09T23:26:06Z | MEMBER | 0 | pydata/xarray/pulls/1517 | This lets you parallelize a function designed for numpy inputs just by adding a few keyword arguments to Example usage, to calculate rank correlation between two variables (this will probably turn into an example for the docs): ```python import numpy as np import xarray as xr import bottleneck def covariance_gufunc(x, y): return ((x - x.mean(axis=-1, keepdims=True)) * (y - y.mean(axis=-1, keepdims=True))).mean(axis=-1) def correlation_gufunc(x, y): return covariance_gufunc(x, y) / (x.std(axis=-1) * y.std(axis=-1)) def spearman_correlation_gufunc(x, y): x_ranks = bottleneck.rankdata(x, axis=-1) y_ranks = bottleneck.rankdata(y, axis=-1) return correlation_gufunc(x_ranks, y_ranks) def spearman_correlation(x, y, dim):
return xr.core.compuation.apply_ufunc(
spearman_correlation_gufunc, x, y,
input_core_dims=[[dim], [dim]],
dask='parallelized',
output_dtypes=[float])
In [57]: array1 = xr.DataArray(rs.randn(1000, 100000), dims=['place', 'time']) # 800MB In [58]: array2 = array1 + 0.5 * rs.randn(1000, 100000) using one core, on numpy arraysIn [61]: %time _ = spearman_correlation(array1, array2, 'time') CPU times: user 21.6 s, sys: 2.84 s, total: 24.5 s Wall time: 24.9 s using all my laptop's cores, with daskIn [63]: r = spearman_correlation(array1.chunk({'place': 10}), array2.chunk({'place': 10}), 'time') In [64]: %time _ = r.compute() CPU times: user 30.9 s, sys: 1.74 s, total: 32.6 s Wall time: 4.59 s ``` Still needs examples in the documentation. The next step is finally expose
cc @mrocklin |
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13221727 | pull |