issues: 786347954
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| id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
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| 786347954 | MDU6SXNzdWU3ODYzNDc5NTQ= | 4814 | Error while loading an HDF file | 5797727 | closed | 0 | 2 | 2021-01-14T21:19:34Z | 2023-08-14T08:42:46Z | 2021-01-22T19:30:48Z | NONE | What happened: I am trying to read a HDF file from MODIS satellite product. Source of the file: https://ladsweb.modaps.eosdis.nasa.gov/archive/allData/61/MOD06_L2/2015/012/MOD06_L2.A2015012.1510.061.2017318235218.hdf and
returns Error log``` --------------------------------------------------------------------------- KeyError Traceback (most recent call last) ~/.local/lib/python3.6/site-packages/xarray/backends/file_manager.py in _acquire_with_cache_info(self, needs_lock) 198 try: --> 199 file = self._cache[self._key] 200 except KeyError: ~/.local/lib/python3.6/site-packages/xarray/backends/lru_cache.py in __getitem__(self, key) 52 with self._lock: ---> 53 value = self._cache[key] 54 self._cache.move_to_end(key) KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/project/umd_amit_tandon/iury/data/coldpools/modis/MOD06_L2/2015/001/MOD06_L2.A2015001.0000.061.2017318203346.hdf',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False))] During handling of the above exception, another exception occurred: OSError Traceback (most recent call last) <ipython-input-3-3a318c45af2b> in <module>() ----> 1 xr.open_dataset(fnames[0]) ~/.local/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs, use_cftime, decode_timedelta) 507 if engine == "netcdf4": 508 store = backends.NetCDF4DataStore.open( --> 509 filename_or_obj, group=group, lock=lock, **backend_kwargs 510 ) 511 elif engine == "scipy": ~/.local/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in open(cls, filename, mode, format, group, clobber, diskless, persist, lock, lock_maker, autoclose) 356 netCDF4.Dataset, filename, mode=mode, kwargs=kwargs 357 ) --> 358 return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose) 359 360 def _acquire(self, needs_lock=True): ~/.local/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in __init__(self, manager, group, mode, lock, autoclose) 312 self._group = group 313 self._mode = mode --> 314 self.format = self.ds.data_model 315 self._filename = self.ds.filepath() 316 self.is_remote = is_remote_uri(self._filename) ~/.local/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in ds(self) 365 @property 366 def ds(self): --> 367 return self._acquire() 368 369 def open_store_variable(self, name, var): ~/.local/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in _acquire(self, needs_lock) 359 360 def _acquire(self, needs_lock=True): --> 361 with self._manager.acquire_context(needs_lock) as root: 362 ds = _nc4_require_group(root, self._group, self._mode) 363 return ds /opt/conda/lib/python3.6/contextlib.py in __enter__(self) 79 def __enter__(self): 80 try: ---> 81 return next(self.gen) 82 except StopIteration: 83 raise RuntimeError("generator didn't yield") from None ~/.local/lib/python3.6/site-packages/xarray/backends/file_manager.py in acquire_context(self, needs_lock) 185 def acquire_context(self, needs_lock=True): 186 """Context manager for acquiring a file.""" --> 187 file, cached = self._acquire_with_cache_info(needs_lock) 188 try: 189 yield file ~/.local/lib/python3.6/site-packages/xarray/backends/file_manager.py in _acquire_with_cache_info(self, needs_lock) 203 kwargs = kwargs.copy() 204 kwargs["mode"] = self._mode --> 205 file = self._opener(*self._args, **kwargs) 206 if self._mode == "w": 207 # ensure file doesn't get overriden when opened again netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Dataset.__init__() netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success() OSError: [Errno -51] NetCDF: Unknown file format: b'/project/umd_amit_tandon/iury/data/coldpools/modis/MOD06_L2/2015/001/MOD06_L2.A2015001.0000.061.2017318203346.hdf' ``` What you expected to happen: Read the HDF file normally. Minimal Complete Verifiable Example: Just
Anything else we need to know?: Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19) [GCC 7.2.0] python-bits: 64 OS: Linux OS-release: 2.6.32-754.35.1.el6.x86_64 machine: x86_64 processor: byteorder: little LC_ALL: C.UTF-8 LANG: C.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.5 libnetcdf: 4.6.3 xarray: 0.16.1 pandas: 1.1.4 numpy: 1.16.4 scipy: 1.2.0 netCDF4: 1.5.4 pydap: None h5netcdf: 0.8.1 h5py: 2.7.1 Nio: None zarr: None cftime: 1.2.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: 1.2.1 dask: 0.16.1 distributed: 1.20.2 matplotlib: 3.2.2 cartopy: None seaborn: 0.8.1 numbagg: None pint: None setuptools: 38.4.0 pip: 20.2.4 conda: 4.4.10 pytest: 3.3.2 IPython: 6.2.1 sphinx: 1.6.6 |
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completed | 13221727 | issue |