issues: 406971782

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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
406971782 MDU6SXNzdWU0MDY5NzE3ODI= 2747 1000x performance regression in transpose from disk between libnetcdf 4.6.1 and 4.6.2 2552981 closed 0     3 2019-02-05T20:59:53Z 2020-08-23T18:53:41Z 2020-08-23T18:53:41Z CONTRIBUTOR      

Having generated test.nc as the two-dimensional array from ```python import numpy as np import xarray as xr

a = np.random.random((1000, 100)) ds = xr.Dataset({'foo': xr.DataArray(a, [('x', np.arange(1000)), ('y', np.arange(100))])}) ds.to_netcdf('test.nc') ```

I am seeing a huge performance regression from libnetcdf=4.6.1 python In [2]: ds = xr.open_dataset('test.nc') ...: %time np.asarray(ds['foo'].transpose('y', 'x')) ...: CPU times: user 2.58 ms, sys: 191 µs, total: 2.77 ms in a conda environment created by conda create -n mwe-fast 'libnetcdf=4.6.1' netcdf4 xarray ipython to the environment created by conda create -n mwe-slow 'libnetcdf=4.6.2' netcdf4 xarray ipython python In [5]: ds = xr.open_dataset('test.nc') ...: %time np.asarray(ds['foo'].transpose('y', 'x')) ...: CPU times: user 4.09 s, sys: 12 ms, total: 4.11 s

Loading into memory mitigates the regression (on mwe-slow): python In [2]: ds = xr.open_dataset('test.nc') ...: %time np.asarray(ds['foo'].load().transpose('y', 'x')) ...: CPU times: user 1.12 ms, sys: 80 µs, total: 1.2 ms

Output of xr.show_versions()

INSTALLED VERSIONS on the working environment `mwe-fast` ------------------ commit: None python: 3.7.1 | packaged by conda-forge | (default, Nov 13 2018, 18:33:04) [GCC 7.3.0] python-bits: 64 OS: Linux OS-release: 4.19.0-2-amd64 machine: x86_64 processor: byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 libhdf5: 1.10.3 libnetcdf: 4.6.1 xarray: 0.11.3 pandas: 0.24.1 numpy: 1.15.4 scipy: None netCDF4: 1.4.2 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.3.4 PseudonetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None cyordereddict: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None setuptools: 40.7.3 pip: 19.0.1 conda: None pytest: None IPython: 7.2.0 sphinx: None INSTALLED VERSIONS on the broken environment `mwe-slow` ------------------ commit: None python: 3.7.1 | packaged by conda-forge | (default, Nov 13 2018, 18:33:04) [GCC 7.3.0] python-bits: 64 OS: Linux OS-release: 4.19.0-2-amd64 machine: x86_64 processor: byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 libhdf5: 1.10.4 libnetcdf: 4.6.2 xarray: 0.11.3 pandas: 0.24.1 numpy: 1.15.4 scipy: None netCDF4: 1.4.2 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.3.4 PseudonetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None cyordereddict: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None setuptools: 40.7.3 pip: 19.0.1 conda: None pytest: None IPython: 7.2.0 sphinx: None 
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