issue_comments: 1011556328

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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/5706#issuecomment-1011556328 https://api.github.com/repos/pydata/xarray/issues/5706 1011556328 IC_kwDOAMm_X848Sx_o 8291800 2022-01-12T23:51:07Z 2022-01-12T23:53:01Z CONTRIBUTOR

sure! here it is:

bash $ h5dump test_str_list.h5 HDF5 "test_str_list.h5" { GROUP "/" { DATASET "pairs" { DATATYPE H5T_STRING { STRSIZE 8; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } DATA { (0,0): "20200101", "20200201", (1,0): "20200101", "20200301" } } } }

(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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