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- Loading datasets of numpy string arrays leads to error and/or segfault · 3 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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1012204673 | https://github.com/pydata/xarray/issues/5706#issuecomment-1012204673 | https://api.github.com/repos/pydata/xarray/issues/5706 | IC_kwDOAMm_X848VQSB | scottstanie 8291800 | 2022-01-13T14:48:08Z | 2022-01-13T14:48:08Z | CONTRIBUTOR | Sounds good, but it seems like you're correct that it's a netcdf/netcdf4-python problem here, so I'll defer to others as to what the best changes to default settings would be to avoid the segfaults |
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Loading datasets of numpy string arrays leads to error and/or segfault 970619131 | |
1012132794 | https://github.com/pydata/xarray/issues/5706#issuecomment-1012132794 | https://api.github.com/repos/pydata/xarray/issues/5706 | IC_kwDOAMm_X848U-u6 | scottstanie 8291800 | 2022-01-13T13:23:45Z | 2022-01-13T13:23:45Z | CONTRIBUTOR | ah sorry, didn't see the request for ``` $ ncdump test_str_list.h5 netcdf test_str_list { dimensions: phony_dim_0 = 2 ; phony_dim_1 = 2 ; variables: string pairs(phony_dim_0, phony_dim_1) ; data: pairs =
"2020010120200201 ", NIL,
"2020010120200301 ", NIL ;
}
``` netcdf test_str_list_attr { // global attributes: string :NULLPAD = "20200101�<T��\007", "20200201", "20200101�=T��\007", "20200301" ; string :NULLTERM = "20200101", "20200201", "20200101", "20200301" ; string :numpy_S = "20200101", "20200201\1775T��\007", "20200101", "20200301�3T��\007" ; string :numpy_O = "20200101", "20200201", "20200101", "20200301" ; } ``` |
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Loading datasets of numpy string arrays leads to error and/or segfault 970619131 | |
1011556328 | https://github.com/pydata/xarray/issues/5706#issuecomment-1011556328 | https://api.github.com/repos/pydata/xarray/issues/5706 | IC_kwDOAMm_X848Sx_o | scottstanie 8291800 | 2022-01-12T23:51:07Z | 2022-01-12T23:53:01Z | CONTRIBUTOR | sure! here it is:
(and just to include the specific traceback that hapened now, in case my versions are different from what I showed):
In [4]: import h5py
...: import xarray as xr
...:
...: with h5py.File("test_str_list.h5", "w") as hf:
...: hf["pairs"] = np.array([["20200101", "20200201"], ["20200101", "20200301"]]).astype("S")
...:
...: ds = xr.load_dataset("test_str_list.h5")
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/xarray/backends/plugins.py:68: RuntimeWarning: Engine 'cfgrib' loading failed:
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/gribapi/_bindings.cpython-38-x86_64-linux-gnu.so: undefined symbol: codes_bufr_key_is_header
warnings.warn(f"Engine {name!r} loading failed:\n{ex}", RuntimeWarning)
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/fsspec/implementations/local.py:29: FutureWarning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release.
warnings.warn(
*** Error in `/home/scott/miniconda3/envs/mapping/bin/python': free(): invalid next size (fast): 0x00005564b64622a0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81679)[0x7f56e752b679]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/netCDF4/../../../libnetcdf.so.18(nc_free_string+0x25)[0x7f54cf53d1a5]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/netCDF4/_netCDF4.cpython-38-x86_64-linux-gnu.so(+0xcf3c8)[0x7f54cf7313c8]
/home/scott/miniconda3/envs/mapping/bin/python(PyCFunction_Call+0x54)[0x5564b397df44]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/netCDF4/_netCDF4.cpython-38-x86_64-linux-gnu.so(+0x224fd)[0x7f54cf6844fd]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/netCDF4/_netCDF4.cpython-38-x86_64-linux-gnu.so(+0x559d9)[0x7f54cf6b79d9]
/home/scott/miniconda3/envs/mapping/bin/python(PyObject_GetItem+0x45)[0x5564b39d7935]
/home/scott/miniconda3/envs/mapping/bin/python(+0x128e0b)[0x5564b397ae0b]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0x947)[0x5564b3a1ec77]
/home/scott/miniconda3/envs/mapping/bin/python(+0x1b0736)[0x5564b3a02736]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0x947)[0x5564b3a1ec77]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x1a6)[0x5564b3a01fc6]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0x4e03)[0x5564b3a23133]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x1a6)[0x5564b3a01fc6]
/home/scott/miniconda3/envs/mapping/bin/python(+0x1800cd)[0x5564b39d20cd]
/home/scott/miniconda3/envs/mapping/bin/python(PyObject_GetItem+0x45)[0x5564b39d7935]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0xd53)[0x5564b3a1f083]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalCodeWithName+0x2c3)[0x5564b3a00db3]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x378)[0x5564b3a02198]
/home/scott/miniconda3/envs/mapping/bin/python(+0x1b0841)[0x5564b3a02841]
/home/scott/miniconda3/envs/mapping/bin/python(+0x12404d)[0x5564b397604d]
/home/scott/miniconda3/envs/mapping/bin/python(_PyObject_CallFunction_SizeT+0x99)[0x5564b39761f9]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa11fd)[0x7f56dddfe1fd]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa54d7)[0x7f56dde024d7]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x8a2d5)[0x7f56ddde72d5]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x8adc4)[0x7f56ddde7dc4]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa559a)[0x7f56dde0259a]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa5ac9)[0x7f56dde02ac9]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x13f2b7)[0x7f56dde9c2b7]
/home/scott/miniconda3/envs/mapping/bin/python(+0x129082)[0x5564b397b082]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0x181e)[0x5564b3a1fb4e]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalCodeWithName+0x2c3)[0x5564b3a00db3]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x378)[0x5564b3a02198]
/home/scott/miniconda3/envs/mapping/bin/python(+0x1b0841)[0x5564b3a02841]
/home/scott/miniconda3/envs/mapping/bin/python(+0x12404d)[0x5564b397604d]
/home/scott/miniconda3/envs/mapping/bin/python(_PyObject_CallFunction_SizeT+0x99)[0x5564b39761f9]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa11fd)[0x7f56dddfe1fd]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa54d7)[0x7f56dde024d7]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x8a2d5)[0x7f56ddde72d5]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x8adc4)[0x7f56ddde7dc4]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa559a)[0x7f56dde0259a]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa5ac9)[0x7f56dde02ac9]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x13f2b7)[0x7f56dde9c2b7]
/home/scott/miniconda3/envs/mapping/bin/python(+0x129082)[0x5564b397b082]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0x4e03)[0x5564b3a23133]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x1a6)[0x5564b3a01fc6]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalFrameDefault+0xa63)[0x5564b3a1ed93]
/home/scott/miniconda3/envs/mapping/bin/python(_PyEval_EvalCodeWithName+0x2c3)[0x5564b3a00db3]
/home/scott/miniconda3/envs/mapping/bin/python(_PyFunction_Vectorcall+0x378)[0x5564b3a02198]
/home/scott/miniconda3/envs/mapping/bin/python(+0x1b0841)[0x5564b3a02841]
/home/scott/miniconda3/envs/mapping/bin/python(+0x12404d)[0x5564b397604d]
/home/scott/miniconda3/envs/mapping/bin/python(_PyObject_CallFunction_SizeT+0x99)[0x5564b39761f9]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa11fd)[0x7f56dddfe1fd]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0xa54d7)[0x7f56dde024d7]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so(+0x8a2d5)[0x7f56ddde72d5]
/home/scott/miniconda3/envs/mapping/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so
Aborted (core dumped)
xr.show_versions
In [2]: xr.show_versions()
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: 3.10.0-1062.4.1.el7.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.10.6
libnetcdf: 4.7.4
xarray: 0.20.2
pandas: 1.1.0
numpy: 1.21.2
scipy: 1.5.3
netCDF4: 1.5.4
pydap: None
h5netcdf: 0.11.0
h5py: 3.2.1
Nio: None
zarr: 2.8.3
cftime: 1.2.1
nc_time_axis: None
PseudoNetCDF: None
rasterio: 1.2.6
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2021.01.0
distributed: 2.20.0
matplotlib: 3.3.1
cartopy: 0.19.0.post1
seaborn: None
numbagg: None
fsspec: 0.6.3
cupy: 9.0.0
pint: 0.17
sparse: None
setuptools: 50.3.2
pip: 21.2.4
conda: 4.8.4
pytest: 6.2.4
IPython: 7.18.1
sphinx: 4.0.2
|
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Loading datasets of numpy string arrays leads to error and/or segfault 970619131 |
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