Coalesce and parallelize partial shard reads

changes/3004.feature.rst

@@ -0,0 +1,3 @@
+Optimizes reading more than one, but not all, chunks from a shard. Chunks are now read in parallel
+and reads of nearby chunks within the same shard are combined to reduce the number of calls to the store.
+See :ref:`user-guide-config` for more details.

docs/user-guide/config.rst

@@ -33,6 +33,10 @@ Configuration options include the following:
 - Async and threading options, e.g. ``async.concurrency`` and ``threading.max_workers``
 - Selections of implementations of codecs, codec pipelines and buffers
 - Enabling GPU support with ``zarr.config.enable_gpu()``. See :ref:`user-guide-gpu` for more.
+- Tuning reads from sharded zarrs. When reading less than a complete shard, reads of nearby chunks
+  within the same shard will be combined into a single request if they are less than
+  ``sharding.read.coalesce_max_gap_bytes`` apart and the combined request size is less than
+  ``sharding.read.coalesce_max_bytes``.
 
 For selecting custom implementations of codecs, pipelines, buffers and ndbuffers,
 first register the implementations in the registry and then select them in the config.
@@ -61,4 +65,6 @@ This is the current default configuration::
    'default_zarr_format': 3,
    'json_indent': 2,
    'ndbuffer': 'zarr.buffer.cpu.NDBuffer',
-   'threading': {'max_workers': None}}
+   'sharding': {'read': {'coalesce_max_bytes': 104857600,
+                         'coalesce_max_gap_bytes': 1048576}},
+   'threading': {'max_workers': None}}

pyproject.toml

@@ -352,6 +352,7 @@ ignore = [
 [tool.mypy]
 python_version = "3.11"
 ignore_missing_imports = true
+mypy_path = "src"
 namespace_packages = false
 
 strict = true

src/zarr/codecs/sharding.py

@@ -38,11 +38,13 @@
 from zarr.core.common import (
     ChunkCoords,
     ChunkCoordsLike,
+    concurrent_map,
     parse_enum,
     parse_named_configuration,
     parse_shapelike,
     product,
 )
+from zarr.core.config import config
 from zarr.core.dtype.npy.int import UInt64
 from zarr.core.indexing import (
     BasicIndexer,
@@ -198,7 +200,9 @@ async def from_bytes(
 
     @classmethod
     def create_empty(
-        cls, chunks_per_shard: ChunkCoords, buffer_prototype: BufferPrototype | None = None
+        cls,
+        chunks_per_shard: ChunkCoords,
+        buffer_prototype: BufferPrototype | None = None,
     ) -> _ShardReader:
         if buffer_prototype is None:
             buffer_prototype = default_buffer_prototype()
@@ -248,7 +252,9 @@ def merge_with_morton_order(
 
     @classmethod
     def create_empty(
-        cls, chunks_per_shard: ChunkCoords, buffer_prototype: BufferPrototype | None = None
+        cls,
+        chunks_per_shard: ChunkCoords,
+        buffer_prototype: BufferPrototype | None = None,
     ) -> _ShardBuilder:
         if buffer_prototype is None:
             buffer_prototype = default_buffer_prototype()
@@ -329,9 +335,18 @@ async def finalize(
         return await shard_builder.finalize(index_location, index_encoder)
 
 
+class _ChunkCoordsByteSlice(NamedTuple):
+    """Holds a chunk's coordinates and its byte range in a serialized shard."""
+
+    coords: ChunkCoords
+    byte_slice: slice
+
+
 @dataclass(frozen=True)
 class ShardingCodec(
-    ArrayBytesCodec, ArrayBytesCodecPartialDecodeMixin, ArrayBytesCodecPartialEncodeMixin
+    ArrayBytesCodec,
+    ArrayBytesCodecPartialDecodeMixin,
+    ArrayBytesCodecPartialEncodeMixin,
 ):
     chunk_shape: ChunkCoords
     codecs: tuple[Codec, ...]
@@ -454,7 +469,7 @@ async def _decode_single(
             shape=shard_shape,
             dtype=shard_spec.dtype.to_native_dtype(),
             order=shard_spec.order,
-            fill_value=0,
+            fill_value=shard_spec.fill_value,
         )
         shard_dict = await _ShardReader.from_bytes(shard_bytes, self, chunks_per_shard)
 
@@ -501,39 +516,28 @@ async def _decode_partial_single(
             shape=indexer.shape,
             dtype=shard_spec.dtype.to_native_dtype(),
             order=shard_spec.order,
-            fill_value=0,
+            fill_value=shard_spec.fill_value,
         )
 
         indexed_chunks = list(indexer)
         all_chunk_coords = {chunk_coords for chunk_coords, *_ in indexed_chunks}
 
         # reading bytes of all requested chunks
-        shard_dict: ShardMapping = {}
+        shard_dict_maybe: ShardMapping | None = {}
         if self._is_total_shard(all_chunk_coords, chunks_per_shard):
             # read entire shard
             shard_dict_maybe = await self._load_full_shard_maybe(
-                byte_getter=byte_getter,
-                prototype=chunk_spec.prototype,
-                chunks_per_shard=chunks_per_shard,
+                byte_getter, chunk_spec.prototype, chunks_per_shard
             )
-            if shard_dict_maybe is None:
-                return None
-            shard_dict = shard_dict_maybe
         else:
             # read some chunks within the shard
-            shard_index = await self._load_shard_index_maybe(byte_getter, chunks_per_shard)
-            if shard_index is None:
-                return None
-            shard_dict = {}
-            for chunk_coords in all_chunk_coords:
-                chunk_byte_slice = shard_index.get_chunk_slice(chunk_coords)
-                if chunk_byte_slice:
-                    chunk_bytes = await byte_getter.get(
-                        prototype=chunk_spec.prototype,
-                        byte_range=RangeByteRequest(chunk_byte_slice[0], chunk_byte_slice[1]),
-                    )
-                    if chunk_bytes:
-                        shard_dict[chunk_coords] = chunk_bytes
+            shard_dict_maybe = await self._load_partial_shard_maybe(
+                byte_getter, chunk_spec.prototype, chunks_per_shard, all_chunk_coords
+            )
+
+        if shard_dict_maybe is None:
+            return None
+        shard_dict = shard_dict_maybe
 
         # decoding chunks and writing them into the output buffer
         await self.codec_pipeline.read(
@@ -615,7 +619,9 @@ async def _encode_partial_single(
 
         indexer = list(
             get_indexer(
-                selection, shape=shard_shape, chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape)
+                selection,
+                shape=shard_shape,
+                chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape),
             )
         )
 
@@ -689,7 +695,8 @@ def _shard_index_size(self, chunks_per_shard: ChunkCoords) -> int:
             get_pipeline_class()
             .from_codecs(self.index_codecs)
             .compute_encoded_size(
-                16 * product(chunks_per_shard), self._get_index_chunk_spec(chunks_per_shard)
+                16 * product(chunks_per_shard),
+                self._get_index_chunk_spec(chunks_per_shard),
             )
         )
 
@@ -734,7 +741,8 @@ async def _load_shard_index_maybe(
             )
         else:
             index_bytes = await byte_getter.get(
-                prototype=numpy_buffer_prototype(), byte_range=SuffixByteRequest(shard_index_size)
+                prototype=numpy_buffer_prototype(),
+                byte_range=SuffixByteRequest(shard_index_size),
             )
         if index_bytes is not None:
             return await self._decode_shard_index(index_bytes, chunks_per_shard)
@@ -748,7 +756,10 @@ async def _load_shard_index(
         ) or _ShardIndex.create_empty(chunks_per_shard)
 
     async def _load_full_shard_maybe(
-        self, byte_getter: ByteGetter, prototype: BufferPrototype, chunks_per_shard: ChunkCoords
+        self,
+        byte_getter: ByteGetter,
+        prototype: BufferPrototype,
+        chunks_per_shard: ChunkCoords,
     ) -> _ShardReader | None:
         shard_bytes = await byte_getter.get(prototype=prototype)
 
@@ -758,6 +769,113 @@ async def _load_full_shard_maybe(
             else None
         )
 
+    async def _load_partial_shard_maybe(
+        self,
+        byte_getter: ByteGetter,
+        prototype: BufferPrototype,
+        chunks_per_shard: ChunkCoords,
+        all_chunk_coords: set[ChunkCoords],
+    ) -> ShardMapping | None:
+        """
+        Read chunks from `byte_getter` for the case where the read is less than a full shard.
+        Returns a mapping of chunk coordinates to bytes.
+        """
+        shard_index = await self._load_shard_index_maybe(byte_getter, chunks_per_shard)
+        if shard_index is None:
+            return None
+
+        chunks = [
+            _ChunkCoordsByteSlice(chunk_coords, slice(*chunk_byte_slice))
+            for chunk_coords in all_chunk_coords
+            # Drop chunks where index lookup fails
+            # e.g. when write_empty_chunks = False and the chunk is empty
+            if (chunk_byte_slice := shard_index.get_chunk_slice(chunk_coords))
+        ]
+        if len(chunks) == 0:
+            return None
+
+        groups = self._coalesce_chunks(chunks)
+
+        shard_dicts = await concurrent_map(
+            [(group, byte_getter, prototype) for group in groups],
+            self._get_group_bytes,
+            config.get("async.concurrency"),
+        )
+
+        shard_dict: ShardMutableMapping = {}
+        for d in shard_dicts:
+            if d is None:
+                return None
+            shard_dict.update(d)
+
+        return shard_dict
+
+    def _coalesce_chunks(
+        self,
+        chunks: list[_ChunkCoordsByteSlice],
+    ) -> list[list[_ChunkCoordsByteSlice]]:
+        """
+        Combine chunks from a single shard into groups that should be read together
+        in a single request.
+
+        Respects the following configuration options:
+        - `sharding.read.coalesce_max_gap_bytes`: The maximum gap between
+          chunks to coalesce into a single group.
+        - `sharding.read.coalesce_max_bytes`: The maximum number of bytes in a group.
+        """
+        max_gap_bytes = config.get("sharding.read.coalesce_max_gap_bytes")
+        coalesce_max_bytes = config.get("sharding.read.coalesce_max_bytes")
+
+        sorted_chunks = sorted(chunks, key=lambda c: c.byte_slice.start)
+
+        groups = []
+        current_group = [sorted_chunks[0]]
+
+        for chunk in sorted_chunks[1:]:
+            gap_to_chunk = chunk.byte_slice.start - current_group[-1].byte_slice.stop
+            size_if_coalesced = chunk.byte_slice.stop - current_group[0].byte_slice.start
+            if gap_to_chunk < max_gap_bytes and size_if_coalesced < coalesce_max_bytes:
+                current_group.append(chunk)
+            else:
+                groups.append(current_group)
+                current_group = [chunk]
+
+        groups.append(current_group)
+
+        return groups
+
+    async def _get_group_bytes(
+        self,
+        group: list[_ChunkCoordsByteSlice],
+        byte_getter: ByteGetter,
+        prototype: BufferPrototype,
+    ) -> ShardMapping | None:
+        """
+        Reads a possibly coalesced group of one or more chunks from a shard.
+        Returns a mapping of chunk coordinates to bytes.
+        """
+        group_start = group[0].byte_slice.start
+        group_end = group[-1].byte_slice.stop
+
+        # A single call to retrieve the bytes for the entire group.
+        group_bytes = await byte_getter.get(
+            prototype=prototype,
+            byte_range=RangeByteRequest(group_start, group_end),
+        )
+        if group_bytes is None:
+            return None
+
+        # Extract the bytes corresponding to each chunk in group from group_bytes.
+        shard_dict = {}
+        for chunk in group:
+            chunk_slice = slice(
+                chunk.byte_slice.start - group_start,
+                chunk.byte_slice.stop - group_start,
+            )
+            shard_dict[chunk.coords] = group_bytes[chunk_slice]
+
+        return shard_dict
+
     def compute_encoded_size(self, input_byte_length: int, shard_spec: ArraySpec) -> int:
         chunks_per_shard = self._get_chunks_per_shard(shard_spec)
         return input_byte_length + self._shard_index_size(chunks_per_shard)

src/zarr/core/config.py

@@ -109,6 +109,12 @@ def enable_gpu(self) -> ConfigSet:
             },
             "async": {"concurrency": 10, "timeout": None},
             "threading": {"max_workers": None},
+            "sharding": {
+                "read": {
+                    "coalesce_max_bytes": 100 * 2**20,  # 100MiB
+                    "coalesce_max_gap_bytes": 2**20,  # 1MiB
+                }
+            },
             "json_indent": 2,
             "codec_pipeline": {
                 "path": "zarr.core.codec_pipeline.BatchedCodecPipeline",

src/zarr/core/indexing.py

@@ -1193,7 +1193,7 @@ def __iter__(self) -> Iterator[ChunkProjection]:
             stop = self.chunk_nitems_cumsum[chunk_rix]
             out_selection: slice | npt.NDArray[np.intp]
             if self.sel_sort is None:
-                out_selection = slice(start, stop)
+                out_selection = np.arange(start, stop)
             else:
                 out_selection = self.sel_sort[start:stop]