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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
474247717 MDU6SXNzdWU0NzQyNDc3MTc= 3168 apply_ufunc erroneously operating on an empty array when dask used TomNicholas 35968931 closed 0     3 2019-07-29T20:44:23Z 2020-03-30T15:08:16Z 2020-03-30T15:08:15Z MEMBER      

Problem description

apply_ufunc with dask='parallelized' appears to be trying to act on an empty numpy array when the computation is specified, but before .compute() is called. In other words, a ufunc which just prints the shape of its argument will print (0,0) then print the correct shape once .compute() is called.

Minimum working example

```python import numpy as np import xarray as xr

def example_ufunc(x): print(x.shape) return np.mean(x, axis=-1)

def new_mean(da, dim): result = xr.apply_ufunc(example_ufunc, da, input_core_dims=[[dim]], dask='parallelized', output_dtypes=[da.dtype]) return result

shape = {'t': 2, 'x':3} data = xr.DataArray(data=np.random.rand(*shape.values()), dims=shape.keys()) unchunked = data chunked = data.chunk(shape)

actual = new_mean(chunked, dim='x') # raises the warning print(actual)

print(actual.compute()) # does the computation correctly ```

Result

(0, 0) /home/tnichol/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/fromnumeric.py:3118: RuntimeWarning: Mean of empty slice. out=out, **kwargs) <xarray.DataArray (t: 2)> dask.array<shape=(2,), dtype=float64, chunksize=(2,)> Dimensions without coordinates: t (2, 3) <xarray.DataArray (t: 2)> array([0.147205, 0.402913]) Dimensions without coordinates: t

Expected result

Same thing without the (0,0) or the numpy warning.

Output of xr.show_versions()

(my xarray is up-to-date with master)

INSTALLED VERSIONS ------------------ commit: None python: 3.6.6 |Anaconda, Inc.| (default, Oct 9 2018, 12:34:16) [GCC 7.3.0] python-bits: 64 OS: Linux OS-release: 3.10.0-862.14.4.el7.x86_64 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 libhdf5: 1.10.2 libnetcdf: 4.6.1 xarray: 0.12.3+23.g1d7bcbd pandas: 0.24.2 numpy: 1.16.4 scipy: 1.3.0 netCDF4: 1.4.2 pydap: None h5netcdf: None h5py: 2.8.0 Nio: None zarr: None cftime: 1.0.3.4 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: 1.2.1 dask: 2.1.0 distributed: 2.1.0 matplotlib: 3.1.0 cartopy: None seaborn: 0.9.0 numbagg: None setuptools: 40.6.2 pip: 18.1 conda: None pytest: 4.0.0 IPython: 7.1.1 sphinx: 1.8.2 
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   completed xarray 13221727 issue

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