Improve safe chunk validation (#9559)

* fix safe chunks validation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix safe chunks validation * Update xarray/tests/test_backends.py Co-authored-by: Maximilian Roos <[email protected]> * The validation of the chunks now is able to detect full or partial chunk and raise a proper error based on the mode selected, it is also possible to use the auto region detection with the mode "a" * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * The test_extract_zarr_variable_encoding does not need to use the region parameter * Inline the code of the allow_partial_chunks and end, document the parameter in order on the extract_zarr_variable_encoding method, raise the correct error if the border size is smaller than the zchunk on mode equal to r+ * Inline the code of the allow_partial_chunks and end, document the parameter in order on the extract_zarr_variable_encoding method, raise the correct error if the border size is smaller than the zchunk on mode equal to r+ * Now the mode r+ is able to update the last chunk of Zarr even if it is not "complete" * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Now the mode r+ is able to update the last chunk of Zarr even if it is not "complete" * Add a typehint to the modes to avoid issues with mypy * Fix the detection of the last chunk * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix the whats-new and add mode="w" to the new test case * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Maximilian Roos <[email protected]> Co-authored-by: Maximilian Roos <[email protected]>
pydata · Sep 30, 2024 · 095d47f · 095d47f
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diff --git a/doc/whats-new.rst b/doc/whats-new.rst
@@ -61,7 +61,9 @@ Bug fixes
   <https://github.com/spencerkclark>`_.
 - Fix a few bugs affecting groupby reductions with `flox`. (:issue:`8090`, :issue:`9398`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
-
+- Fix the safe_chunks validation option on the to_zarr method
+  (:issue:`5511`, :pull:`9559`). By `Joseph Nowak
+  <https://github.com/josephnowak>`_.
 
 Documentation
 ~~~~~~~~~~~~~

diff --git a/xarray/backends/zarr.py b/xarray/backends/zarr.py
@@ -112,7 +112,9 @@ def __getitem__(self, key):
         # could possibly have a work-around for 0d data here
 
 
-def _determine_zarr_chunks(enc_chunks, var_chunks, ndim, name, safe_chunks):
+def _determine_zarr_chunks(
+    enc_chunks, var_chunks, ndim, name, safe_chunks, region, mode, shape
+):
     """
     Given encoding chunks (possibly None or []) and variable chunks
     (possibly None or []).
@@ -163,7 +165,9 @@ def _determine_zarr_chunks(enc_chunks, var_chunks, ndim, name, safe_chunks):
 
     if len(enc_chunks_tuple) != ndim:
         # throw away encoding chunks, start over
-        return _determine_zarr_chunks(None, var_chunks, ndim, name, safe_chunks)
+        return _determine_zarr_chunks(
+            None, var_chunks, ndim, name, safe_chunks, region, mode, shape
+        )
 
     for x in enc_chunks_tuple:
         if not isinstance(x, int):
@@ -189,20 +193,58 @@ def _determine_zarr_chunks(enc_chunks, var_chunks, ndim, name, safe_chunks):
     # TODO: incorporate synchronizer to allow writes from multiple dask
     # threads
     if var_chunks and enc_chunks_tuple:
-        for zchunk, dchunks in zip(enc_chunks_tuple, var_chunks, strict=True):
-            for dchunk in dchunks[:-1]:
+        # If it is possible to write on partial chunks then it is not necessary to check
+        # the last one contained on the region
+        allow_partial_chunks = mode != "r+"
+
+        base_error = (
+            f"Specified zarr chunks encoding['chunks']={enc_chunks_tuple!r} for "
+            f"variable named {name!r} would overlap multiple dask chunks {var_chunks!r} "
+            f"on the region {region}. "
+            f"Writing this array in parallel with dask could lead to corrupted data."
+            f"Consider either rechunking using `chunk()`, deleting "
+            f"or modifying `encoding['chunks']`, or specify `safe_chunks=False`."
+        )
+
+        for zchunk, dchunks, interval, size in zip(
+            enc_chunks_tuple, var_chunks, region, shape, strict=True
+        ):
+            if not safe_chunks:
+                continue
+
+            for dchunk in dchunks[1:-1]:
                 if dchunk % zchunk:
-                    base_error = (
-                        f"Specified zarr chunks encoding['chunks']={enc_chunks_tuple!r} for "
-                        f"variable named {name!r} would overlap multiple dask chunks {var_chunks!r}. "
-                        f"Writing this array in parallel with dask could lead to corrupted data."
-                    )
-                    if safe_chunks:
-                        raise ValueError(
-                            base_error
-                            + " Consider either rechunking using `chunk()`, deleting "
-                            "or modifying `encoding['chunks']`, or specify `safe_chunks=False`."
-                        )
+                    raise ValueError(base_error)
+
+            region_start = interval.start if interval.start else 0
+
+            if len(dchunks) > 1:
+                # The first border size is the amount of data that needs to be updated on the
+                # first chunk taking into account the region slice.
+                first_border_size = zchunk
+                if allow_partial_chunks:
+                    first_border_size = zchunk - region_start % zchunk
+
+                if (dchunks[0] - first_border_size) % zchunk:
+                    raise ValueError(base_error)
+
+            if not allow_partial_chunks:
+                region_stop = interval.stop if interval.stop else size
+
+                if region_start % zchunk:
+                    # The last chunk which can also be the only one is a partial chunk
+                    # if it is not aligned at the beginning
+                    raise ValueError(base_error)
+
+                if np.ceil(region_stop / zchunk) == np.ceil(size / zchunk):
+                    # If the region is covering the last chunk then check
+                    # if the reminder with the default chunk size
+                    # is equal to the size of the last chunk
+                    if dchunks[-1] % zchunk != size % zchunk:
+                        raise ValueError(base_error)
+                elif dchunks[-1] % zchunk:
+                    raise ValueError(base_error)
+
         return enc_chunks_tuple
 
     raise AssertionError("We should never get here. Function logic must be wrong.")
@@ -243,7 +285,14 @@ def _get_zarr_dims_and_attrs(zarr_obj, dimension_key, try_nczarr):
 
 
 def extract_zarr_variable_encoding(
-    variable, raise_on_invalid=False, name=None, safe_chunks=True
+    variable,
+    raise_on_invalid=False,
+    name=None,
+    *,
+    safe_chunks=True,
+    region=None,
+    mode=None,
+    shape=None,
 ):
     """
     Extract zarr encoding dictionary from xarray Variable
@@ -252,12 +301,18 @@ def extract_zarr_variable_encoding(
     ----------
     variable : Variable
     raise_on_invalid : bool, optional
-
+    name: str | Hashable, optional
+    safe_chunks: bool, optional
+    region: tuple[slice, ...], optional
+    mode: str, optional
+    shape: tuple[int, ...], optional
     Returns
     -------
     encoding : dict
         Zarr encoding for `variable`
     """
+
+    shape = shape if shape else variable.shape
     encoding = variable.encoding.copy()
 
     safe_to_drop = {"source", "original_shape"}
@@ -285,7 +340,14 @@ def extract_zarr_variable_encoding(
                 del encoding[k]
 
     chunks = _determine_zarr_chunks(
-        encoding.get("chunks"), variable.chunks, variable.ndim, name, safe_chunks
+        enc_chunks=encoding.get("chunks"),
+        var_chunks=variable.chunks,
+        ndim=variable.ndim,
+        name=name,
+        safe_chunks=safe_chunks,
+        region=region,
+        mode=mode,
+        shape=shape,
     )
     encoding["chunks"] = chunks
     return encoding
@@ -762,16 +824,10 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No
             if v.encoding == {"_FillValue": None} and fill_value is None:
                 v.encoding = {}
 
-            # We need to do this for both new and existing variables to ensure we're not
-            # writing to a partial chunk, even though we don't use the `encoding` value
-            # when writing to an existing variable. See
-            # https://github.com/pydata/xarray/issues/8371 for details.
-            encoding = extract_zarr_variable_encoding(
-                v,
-                raise_on_invalid=vn in check_encoding_set,
-                name=vn,
-                safe_chunks=self._safe_chunks,
-            )
+            zarr_array = None
+            zarr_shape = None
+            write_region = self._write_region if self._write_region is not None else {}
+            write_region = {dim: write_region.get(dim, slice(None)) for dim in dims}
 
             if name in existing_keys:
                 # existing variable
@@ -801,7 +857,40 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No
                     )
                 else:
                     zarr_array = self.zarr_group[name]
-            else:
+
+                if self._append_dim is not None and self._append_dim in dims:
+                    # resize existing variable
+                    append_axis = dims.index(self._append_dim)
+                    assert write_region[self._append_dim] == slice(None)
+                    write_region[self._append_dim] = slice(
+                        zarr_array.shape[append_axis], None
+                    )
+
+                    new_shape = list(zarr_array.shape)
+                    new_shape[append_axis] += v.shape[append_axis]
+                    zarr_array.resize(new_shape)
+
+                zarr_shape = zarr_array.shape
+
+            region = tuple(write_region[dim] for dim in dims)
+
+            # We need to do this for both new and existing variables to ensure we're not
+            # writing to a partial chunk, even though we don't use the `encoding` value
+            # when writing to an existing variable. See
+            # https://github.com/pydata/xarray/issues/8371 for details.
+            # Note: Ideally there should be two functions, one for validating the chunks and
+            # another one for extracting the encoding.
+            encoding = extract_zarr_variable_encoding(
+                v,
+                raise_on_invalid=vn in check_encoding_set,
+                name=vn,
+                safe_chunks=self._safe_chunks,
+                region=region,
+                mode=self._mode,
+                shape=zarr_shape,
+            )
+
+            if name not in existing_keys:
                 # new variable
                 encoded_attrs = {}
                 # the magic for storing the hidden dimension data
@@ -833,22 +922,6 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No
                 )
                 zarr_array = _put_attrs(zarr_array, encoded_attrs)
 
-            write_region = self._write_region if self._write_region is not None else {}
-            write_region = {dim: write_region.get(dim, slice(None)) for dim in dims}
-
-            if self._append_dim is not None and self._append_dim in dims:
-                # resize existing variable
-                append_axis = dims.index(self._append_dim)
-                assert write_region[self._append_dim] == slice(None)
-                write_region[self._append_dim] = slice(
-                    zarr_array.shape[append_axis], None
-                )
-
-                new_shape = list(zarr_array.shape)
-                new_shape[append_axis] += v.shape[append_axis]
-                zarr_array.resize(new_shape)
-
-            region = tuple(write_region[dim] for dim in dims)
             writer.add(v.data, zarr_array, region)
 
     def close(self) -> None:
@@ -897,9 +970,9 @@ def _validate_and_autodetect_region(self, ds) -> None:
         if not isinstance(region, dict):
             raise TypeError(f"``region`` must be a dict, got {type(region)}")
         if any(v == "auto" for v in region.values()):
-            if self._mode != "r+":
+            if self._mode not in ["r+", "a"]:
                 raise ValueError(
-                    f"``mode`` must be 'r+' when using ``region='auto'``, got {self._mode!r}"
+                    f"``mode`` must be 'r+' or 'a' when using ``region='auto'``, got {self._mode!r}"
                 )
             region = self._auto_detect_regions(ds, region)
 

diff --git a/xarray/core/dataarray.py b/xarray/core/dataarray.py
@@ -4316,6 +4316,14 @@ def to_zarr(
             if Zarr arrays are written in parallel. This option may be useful in combination
             with ``compute=False`` to initialize a Zarr store from an existing
             DataArray with arbitrary chunk structure.
+            In addition to the many-to-one relationship validation, it also detects partial
+            chunks writes when using the region parameter,
+            these partial chunks are considered unsafe in the mode "r+" but safe in
+            the mode "a".
+            Note: Even with these validations it can still be unsafe to write
+            two or more chunked arrays in the same location in parallel if they are
+            not writing in independent regions, for those cases it is better to use
+            a synchronizer.
         storage_options : dict, optional
             Any additional parameters for the storage backend (ignored for local
             paths).

diff --git a/xarray/core/dataset.py b/xarray/core/dataset.py
@@ -2509,6 +2509,14 @@ def to_zarr(
             if Zarr arrays are written in parallel. This option may be useful in combination
             with ``compute=False`` to initialize a Zarr from an existing
             Dataset with arbitrary chunk structure.
+            In addition to the many-to-one relationship validation, it also detects partial
+            chunks writes when using the region parameter,
+            these partial chunks are considered unsafe in the mode "r+" but safe in
+            the mode "a".
+            Note: Even with these validations it can still be unsafe to write
+            two or more chunked arrays in the same location in parallel if they are
+            not writing in independent regions, for those cases it is better to use
+            a synchronizer.
         storage_options : dict, optional
             Any additional parameters for the storage backend (ignored for local
             paths).