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  • Import hangs when matplotlib installed but no display available · 3 ✖
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992878363 https://github.com/pydata/xarray/issues/6062#issuecomment-992878363 https://api.github.com/repos/pydata/xarray/issues/6062 IC_kwDOAMm_X847Lh8b jaicher 4666753 2021-12-13T20:38:37Z 2021-12-14T04:43:21Z CONTRIBUTOR

I have matplotlib installed.

Here's the output of xr.show_versions() (after rolling back to 0.19):

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:59:51) [GCC 9.4.0] python-bits: 64 OS: Linux OS-release: 5.4.72-microsoft-standard-WSL2 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: C.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.1 libnetcdf: 4.8.1 xarray: 0.19.0 pandas: 1.3.4 numpy: 1.21.4 scipy: 1.7.3 netCDF4: 1.5.8 pydap: None h5netcdf: None h5py: 2.10.0 Nio: None zarr: 2.10.3 cftime: 1.5.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: 1.3.2 dask: 2021.11.2 distributed: 2021.11.2 matplotlib: 3.5.1 cartopy: None seaborn: 0.11.2 numbagg: None pint: None setuptools: 59.4.0 pip: 21.3.1 conda: None pytest: None IPython: 7.30.1 sphinx: 4.3.1

By "no display available", I meant on a headless server (e.g. WSL2, compute node on slurm cluster).

Digging more into this, this is related to matplotlib/matplotlib#17396 (matplotlib >= 3.4):

  • matplotlib tries to automatically select the plotting backend, especially whether or not there is a display to use.
  • On Linux, matplotlib < 3.4, this was effectively done by checking if DISPLAY environment variable was set.
  • For matplotlib >= 3.4, matplotlib/matplotlib#17396 added additional check to call XOpenDisplay(NULL) to see if X11 is able to connect to the DISPLAY environment variable.
  • This was to fix instances where DISPLAY was set but no longer valid. A common example is on slurm (or some other cluster managers) opening a compute node which by default copies all environment variables, including DISPLAY, to a new node.

I experience hanging because my WSL2 setup sets DISPLAY to reference an X11 server that isn't always running. Since the X11 server is on Windows, the DISPLAY refers to a remote address. Apparently, X11 doesn't give up when it isn't able to connect to a remote X11 server, and, so it hangs on that command.

That is for matplotlib >= 3.4. For matplotlib = 3.3 (which is still less than a year old) and xarray=0.20, I get:

  • (RedHat on cluster, selects TkAgg backend): is able to import, but fails to plot afterwards
  • (WSL2, attempts to select QtAgg backend): fails import (and exits Python!) with message:

``` qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, minimal, minimalegl, offscreen, vnc, webgl, xcb.

Aborted ```

This will become a little bit less of an issue when we set the minimum version of matplotlib to 3.4. However, I still think we should revert PR #5794 (PR #6064). It doesn't fix any bug. Before matplotlib >= 3.4, the common-knowledge I had previously seen from writing scripts with headless-use of matplotlib was that we shouldn't import matplotlib.pyplot until we needed it. This was consistent with the previous imports in the plotting functions. Reverting will make it so that errors related to how the plotting environment is set up only take place when users explicitly want to make plots, rather than for all imports of xarray, many of which do not involve any plotting whatsoever.

 
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   Import hangs when matplotlib installed but no display available 1076377174
990970627 https://github.com/pydata/xarray/issues/6062#issuecomment-990970627 https://api.github.com/repos/pydata/xarray/issues/6062 IC_kwDOAMm_X847EQMD mathause 10194086 2021-12-10T13:23:23Z 2021-12-10T13:23:23Z MEMBER

Can you let us know your OS and xr.show_versions().

Could be a bug of the "MacOSX" backend: matplotlib/matplotlib#19197 & matplotlib/matplotlib#19268. (However, we test on macos in our CI.)

 
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   Import hangs when matplotlib installed but no display available 1076377174
990668637 https://github.com/pydata/xarray/issues/6062#issuecomment-990668637 https://api.github.com/repos/pydata/xarray/issues/6062 IC_kwDOAMm_X847DGdd Illviljan 14371165 2021-12-10T07:03:23Z 2021-12-10T07:03:23Z MEMBER

What do you mean with "no display available"? You haven't installed matplotlib? The CI runs without mpl as well and works fine there.

 
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   Import hangs when matplotlib installed but no display available 1076377174

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