issue_comments: 508772044

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https://github.com/pydata/xarray/issues/2954#issuecomment-508772044 https://api.github.com/repos/pydata/xarray/issues/2954 508772044 MDEyOklzc3VlQ29tbWVudDUwODc3MjA0NA== 500246 2019-07-05T14:13:20Z 2019-07-05T14:14:20Z CONTRIBUTOR

This triggers a segmentation fault (in the .persist() call) on my system, which may be related:

python import xarray import os import subprocess xarray.set_options(file_cache_maxsize=1) f = "/path/to/netcdf/file.nc" ds1 = xarray.open_dataset(f, "/group1", chunks=1024) ds2 = xarray.open_dataset(f, "/group2", chunks=1024) ds_cat = xarray.concat([ds1, ds2]) ds_cat.persist() subprocess.run(fr"lsof | grep {os.getpid():d} | grep '\.nc$'", shell=True)

But there's something with the specific netcdf file going on, for when I create artificial groups, it does not segfault.

``` Fatal Python error: Segmentation fault

Thread 0x00007f542bfff700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 470 in _handle_results File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f5448ff9700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 422 in _handle_tasks File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f54497fa700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 413 in _handle_workers File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f5449ffb700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f544a7fc700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f544affd700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f544b7fe700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f544bfff700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f5458a75700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f5459276700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007f5459a77700 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/multiprocessing/pool.py", line 110 in worker File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 865 in run File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/threading.py", line 885 in _bootstrap

Current thread 0x00007f54731236c0 (most recent call first): File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 244 in open_netcdf4_group File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 173 in acquire File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/backends/netCDF4.py", line 56 in get_array File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/backends/netCDF4_.py", line 74 in getitem File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/indexing.py", line 778 in explicit_indexing_adapter File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/backends/netCDF4.py", line 64 in getitem File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/indexing.py", line 510 in array File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/numpy/core/numeric.py", line 538 in asarray File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/indexing.py", line 604 in array File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/numpy/core/numeric.py", line 538 in asarray File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/variable.py", line 213 in _as_array_or_item File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/variable.py", line 392 in values File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/variable.py", line 297 in data File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/variable.py", line 1204 in set_dims File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/combine.py", line 298 in ensure_common_dims File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/variable.py", line 2085 in concat File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/combine.py", line 305 in _dataset_concat File "/media/nas/x21324/miniconda3/envs/py37d/lib/python3.7/site-packages/xarray/core/combine.py", line 120 in concat File "mwe13.py", line 19 in <module> Segmentation fault (core dumped) ```

 
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   442617907