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  • Abnormal process termination when using bottleneck function on xarray data after transposing and having a dimension with length 1 · 2 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
973971543 https://github.com/pydata/xarray/issues/6002#issuecomment-973971543 https://api.github.com/repos/pydata/xarray/issues/6002 IC_kwDOAMm_X846DaBX keewis 14808389 2021-11-19T10:56:32Z 2021-11-19T10:56:32Z MEMBER

It's just a simple numpy.ndarray.transpose: python In [1]: import numpy as np ...: import bottleneck as bn ...: ...: n_time = 1 ...: spec_data = np.random.random(size=(n_time,192,121)) ...: ...: bn.nanmax(spec_data.transpose(0, 2, 1)) Segmentation fault numpy.transpose returns a view, so I guess that's what causes bottleneck to segfault? Not sure, though, especially since changing the order does not trigger the segfault: spec_data.transpose(1, 0, 2)... maybe bottleneck doesn't like views with a first dimension of size 1?

 
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   Abnormal process termination when using bottleneck function on xarray data after transposing and having a dimension with length 1 1057335460
973229567 https://github.com/pydata/xarray/issues/6002#issuecomment-973229567 https://api.github.com/repos/pydata/xarray/issues/6002 IC_kwDOAMm_X846Ak3_ max-sixty 5635139 2021-11-18T20:19:59Z 2021-11-18T20:19:59Z MEMBER

Thanks for the detail @RubendeBruin . I'm guessing this a bottleneck issue — would you be up for trying to run bottleneck's nanmax function on the underlying numpy array (xdata.data), and seeing whether that has the same effect?

 
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   Abnormal process termination when using bottleneck function on xarray data after transposing and having a dimension with length 1 1057335460

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