Obscure h5netcdf http serialization issue with python's http.server

What is your issue?

In Pangeo Forge, we try to test our ability to read data over http. This often surfaces edge cases involving xarray and fsspec. This is one such edge case. However, it is kind of important, because it affects our ability to reliably test http-based datasets using python’s built-in http server.

Here is some code that:

• Creates a tiny dataset on disk
• Serves it over http via python -m http.server
• Opens the dataset with fsspec and xarray with the h5netcdf engine
• Pickles the dataset, loads it, and calls .load() to load the data into memory

As you can see, this works with a local file, but not with the http file, with h5py raising a checksum-related error.

import fsspec
import xarray as xr
from pickle import dumps, loads

ds_orig = xr.tutorial.load_dataset('tiny')
ds_orig

fname = 'tiny.nc'
ds_orig.to_netcdf(fname, engine='netcdf4')

# now start an http server in a terminal in the same working directory
# $ python -m http.server

def open_pickle_and_reload(path):
    with fsspec.open(path, mode='rb') as fp:
        with xr.open_dataset(fp, engine='h5netcdf') as ds1:
            pass

    # pickle it and reload it
    ds2 = loads(dumps(ds1))
    ds2.load()

open_pickle_and_reload(fname) # works
url = f'http://127.0.0.1:8000/{fname}'
open_pickle_and_reload(url) # OSError: Unable to open file (incorrect metadata checksum after all read attempts)

full traceback

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/Code/xarray/xarray/backends/file_manager.py in _acquire_with_cache_info(self, needs_lock)
    198             try:
--> 199                 file = self._cache[self._key]
    200             except KeyError:

~/Code/xarray/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 'h5netcdf.core.File'>, (<File-like object HTTPFileSystem, http://127.0.0.1:8000/tiny.nc>,), 'r', (('decode_vlen_strings', True), ('invalid_netcdf', None))]

During handling of the above exception, another exception occurred:

OSError                                   Traceback (most recent call last)
<ipython-input-2-195ac3fcdb43> in <module>
     24 open_pickle_and_reload(fname) # works
     25 url = f'[http://127.0.0.1:8000/{fname}'](http://127.0.0.1:8000/%7Bfname%7D'%3C/span%3E)
---> 26 open_pickle_and_reload(url) # OSError: Unable to open file (incorrect metadata checksum after all read attempts)

<ipython-input-2-195ac3fcdb43> in open_pickle_and_reload(path)
     20     # pickle it and reload it
     21     ds2 = loads(dumps(ds1))
---> 22     ds2.load() # works
     23 
     24 open_pickle_and_reload(fname) # works

~/Code/xarray/xarray/core/dataset.py in load(self, **kwargs)
    687         for k, v in self.variables.items():
    688             if k not in lazy_data:
--> 689                 v.load()
    690 
    691         return self

~/Code/xarray/xarray/core/variable.py in load(self, **kwargs)
    442             self._data = as_compatible_data(self._data.compute(**kwargs))
    443         elif not is_duck_array(self._data):
--> 444             self._data = np.asarray(self._data)
    445         return self
    446 

~/Code/xarray/xarray/core/indexing.py in __array__(self, dtype)
    654 
    655     def __array__(self, dtype=None):
--> 656         self._ensure_cached()
    657         return np.asarray(self.array, dtype=dtype)
    658 

~/Code/xarray/xarray/core/indexing.py in _ensure_cached(self)
    651     def _ensure_cached(self):
    652         if not isinstance(self.array, NumpyIndexingAdapter):
--> 653             self.array = NumpyIndexingAdapter(np.asarray(self.array))
    654 
    655     def __array__(self, dtype=None):

~/Code/xarray/xarray/core/indexing.py in __array__(self, dtype)
    624 
    625     def __array__(self, dtype=None):
--> 626         return np.asarray(self.array, dtype=dtype)
    627 
    628     def __getitem__(self, key):

~/Code/xarray/xarray/core/indexing.py in __array__(self, dtype)
    525     def __array__(self, dtype=None):
    526         array = as_indexable(self.array)
--> 527         return np.asarray(array[self.key], dtype=None)
    528 
    529     def transpose(self, order):

~/Code/xarray/xarray/backends/h5netcdf_.py in __getitem__(self, key)
     49 
     50     def __getitem__(self, key):
---> 51         return indexing.explicit_indexing_adapter(
     52             key, self.shape, indexing.IndexingSupport.OUTER_1VECTOR, self._getitem
     53         )

~/Code/xarray/xarray/core/indexing.py in explicit_indexing_adapter(key, shape, indexing_support, raw_indexing_method)
    814     """
    815     raw_key, numpy_indices = decompose_indexer(key, shape, indexing_support)
--> 816     result = raw_indexing_method(raw_key.tuple)
    817     if numpy_indices.tuple:
    818         # index the loaded np.ndarray

~/Code/xarray/xarray/backends/h5netcdf_.py in _getitem(self, key)
     58         key = tuple(list(k) if isinstance(k, np.ndarray) else k for k in key)
     59         with self.datastore.lock:
---> 60             array = self.get_array(needs_lock=False)
     61             return array[key]
     62 

~/Code/xarray/xarray/backends/h5netcdf_.py in get_array(self, needs_lock)
     45 class H5NetCDFArrayWrapper(BaseNetCDF4Array):
     46     def get_array(self, needs_lock=True):
---> 47         ds = self.datastore._acquire(needs_lock)
     48         return ds.variables[self.variable_name]
     49 

~/Code/xarray/xarray/backends/h5netcdf_.py in _acquire(self, needs_lock)
    180 
    181     def _acquire(self, needs_lock=True):
--> 182         with self._manager.acquire_context(needs_lock) as root:
    183             ds = _nc4_require_group(
    184                 root, self._group, self._mode, create_group=_h5netcdf_create_group

/opt/miniconda3/envs/pangeo-forge-recipes/lib/python3.9/contextlib.py in __enter__(self)
    117         del self.args, self.kwds, self.func
    118         try:
--> 119             return next(self.gen)
    120         except StopIteration:
    121             raise RuntimeError("generator didn't yield") from None

~/Code/xarray/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

~/Code/xarray/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 overridden when opened again

/opt/miniconda3/envs/pangeo-forge-recipes/lib/python3.9/site-packages/h5netcdf/core.py in __init__(self, path, mode, invalid_netcdf, phony_dims, **kwargs)
    719                 else:
    720                     self._preexisting_file = mode in {"r", "r+", "a"}
--> 721                     self._h5file = h5py.File(path, mode, **kwargs)
    722         except Exception:
    723             self._closed = True

/opt/miniconda3/envs/pangeo-forge-recipes/lib/python3.9/site-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, **kwds)
    505                                  fs_persist=fs_persist, fs_threshold=fs_threshold,
    506                                  fs_page_size=fs_page_size)
--> 507                 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
    508 
    509             if isinstance(libver, tuple):

/opt/miniconda3/envs/pangeo-forge-recipes/lib/python3.9/site-packages/h5py/_hl/files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
    218         if swmr and swmr_support:
    219             flags |= h5f.ACC_SWMR_READ
--> 220         fid = h5f.open(name, flags, fapl=fapl)
    221     elif mode == 'r+':
    222         fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5f.pyx in h5py.h5f.open()

OSError: Unable to open file (incorrect metadata checksum after all read attempts)
(external_url)

Strangely, a similar workflow does work with http files hosted elsewhere, e.g.

external_url = 'https://power-datastore.s3.amazonaws.com/v9/climatology/power_901_rolling_zones_utc.nc'
open_pickle_and_reload(external_url)

This suggests there is something peculiar about python’s http.server as compared to other http servers that makes this break.

I would appreciate any thoughts or ideas about what might be going on here (pinging @martindurant and @shoyer)

xref:

• https://github.com/pangeo-forge/pangeo-forge-recipes/pull/373
• https://github.com/pydata/xarray/issues/4242
• https://github.com/google/xarray-beam/issues/49

[martindurant]

Python’s HTTP server does not normally provide content lengths without some extra work, that might be the difference.

[rabernat]

Following up on the suggestion from @shoyer in to not use a context manager, if I redefine my function as

def open_pickle_and_reload(path):
    of = fsspec.open(path, mode='rb').open()
    ds1 = xr.open_dataset(of, engine='h5netcdf')

    # pickle it and reload it
    ds2 = loads(dumps(ds1))
    ds2.load()

…it appears to work fine.