html_url,issue_url,id,node_id,user,created_at,updated_at,author_association,body,reactions,performed_via_github_app,issue
https://github.com/pydata/xarray/issues/7421#issuecomment-1373697191,https://api.github.com/repos/pydata/xarray/issues/7421,1373697191,IC_kwDOAMm_X85R4PSn,8382834,2023-01-06T14:13:52Z,2023-01-06T14:13:52Z,CONTRIBUTOR,"Creating a conda environment as you suggest, I am fully able to read etc the file, so this solves my issue. Many thanks! Then I guess this means there is some weird issue leading to segfaults on this file with some of the older libnetcdf versions. Closing as using a conda env and a more recent stack fixes things.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373624790,https://api.github.com/repos/pydata/xarray/issues/7421,1373624790,IC_kwDOAMm_X85R39nW,14808389,2023-01-06T13:27:54Z,2023-01-06T13:27:54Z,MEMBER,"> I do not provide a dedicated engine in the open_dataset command, so I guess this is using the netcdf4 engine by default?
Depends on the file format, but in general, I'd recommend passing the engine kwarg explicitly.","{""total_count"": 1, ""+1"": 1, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373600032,https://api.github.com/repos/pydata/xarray/issues/7421,1373600032,IC_kwDOAMm_X85R33kg,8382834,2023-01-06T13:09:29Z,2023-01-06T13:09:29Z,CONTRIBUTOR,"Ok, thanks, this does crash too on my machine. Then likely something to do with my software stack somewhere, I will try with a new mamba / conda environment and check if this fixes things.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373591714,https://api.github.com/repos/pydata/xarray/issues/7421,1373591714,IC_kwDOAMm_X85R31ii,14808389,2023-01-06T13:01:50Z,2023-01-06T13:01:50Z,MEMBER,"This is what I'm doing:
```python
In [1]: import xarray as xr
...:
...: ds = xr.open_dataset(""2018_03_b.nc"", decode_times=False)
...: ds[""accD""].data
Out[1]:
array([[-9.625633e+00, -9.587038e+00, -9.601438e+00, ..., -9.543669e+00,
-9.519094e+00, -9.509479e+00],
[-9.705109e+00, -9.658272e+00, -9.672318e+00, ..., 9.969210e+36,
9.969210e+36, 9.969210e+36]], dtype=float32)
```","{""total_count"": 1, ""+1"": 1, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373587759,https://api.github.com/repos/pydata/xarray/issues/7421,1373587759,IC_kwDOAMm_X85R30kv,8382834,2023-01-06T12:57:38Z,2023-01-06T12:57:38Z,CONTRIBUTOR,"@keewis regarding the engine: I have netcdf4 installed and I do not provide a dedicated engine in the ```open_dataset``` command, so I guess this is using the netcdf4 engine by default? Anyway I can run a command to double check and confirm to you? :)","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373584045,https://api.github.com/repos/pydata/xarray/issues/7421,1373584045,IC_kwDOAMm_X85R3zqt,8382834,2023-01-06T12:53:18Z,2023-01-06T12:53:18Z,CONTRIBUTOR,"@keewis interesting. Just to be sure: I am able to open the dataset just fine too, the issue arises when trying to actually read the field, i.e.:
```python
xr_file = xr.open_dataset(input_file, decode_times=False)
```
is just fine, but
```python
xr_file[""accD""][0, 0:3235893].data
```
is what segfaults; just to be sure there is no misunderstanding, are you actually able to run the last command without isse? :)","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373581179,https://api.github.com/repos/pydata/xarray/issues/7421,1373581179,IC_kwDOAMm_X85R3y97,14808389,2023-01-06T12:49:32Z,2023-01-06T12:49:32Z,MEMBER,"I'm able to open the dataset just fine, so I'd think this has something to do with your environment. Can you try creating a more recent one, using something like:
```
mamba create -n test -c conda-forge python=3.10 xarray netcdf4 ...
```
Also, what engine are you using to read the file? `netcdf4`?","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951
https://github.com/pydata/xarray/issues/7421#issuecomment-1373580808,https://api.github.com/repos/pydata/xarray/issues/7421,1373580808,IC_kwDOAMm_X85R3y4I,8382834,2023-01-06T12:49:05Z,2023-01-06T12:49:05Z,CONTRIBUTOR,"I got help to extract more information in gdb; converting the ipynb to a py file and running it in gdb context:
```
> jupyter nbconvert --to script issue_opening_2018_03_b.ipynb [NbConvertApp] Converting notebook issue_opening_2018_03_b.ipynb to script
[NbConvertApp] Writing 1313 bytes to issue_opening_2018_03_b.py
> gdb --args python3 issue_opening_2018_03_b.py
[...]
(gdb) run
Starting program: /usr/bin/python3 issue_opening_2018_03_b.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library ""/lib/x86_64-linux-gnu/libthread_db.so.1"".
[...]
Thread 1 ""python3"" received signal SIGSEGV, Segmentation fault.
__memmove_sse2_unaligned_erms () at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:314
314 ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S: No such file or directory.
(gdb) bt
#0 __memmove_sse2_unaligned_erms () at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:314
#1 0x00007ffff6af4bdc in NC4_get_vars () from /home/jrmet/.local/lib/python3.8/site-packages/netCDF4/.libs/libnetcdf-5e98d7e6.so.15.0.0
#2 0x00007ffff6af337d in NC4_get_vara () from /home/jrmet/.local/lib/python3.8/site-packages/netCDF4/.libs/libnetcdf-5e98d7e6.so.15.0.0
#3 0x00007ffff6a959aa in NC_get_vara () from /home/jrmet/.local/lib/python3.8/site-packages/netCDF4/.libs/libnetcdf-5e98d7e6.so.15.0.0
#4 0x00007ffff6a96b9b in nc_get_vara () from /home/jrmet/.local/lib/python3.8/site-packages/netCDF4/.libs/libnetcdf-5e98d7e6.so.15.0.0
#5 0x00007ffff6ec24bc in ?? () from /home/jrmet/.local/lib/python3.8/site-packages/netCDF4/_netCDF4.cpython-38-x86_64-linux-gnu.so
#6 0x00000000005f5b39 in PyCFunction_Call ()
```
which seems to be originating in libnetcdf?","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,1520760951