diff --git a/deker/client.py b/deker/client.py index a8fda4f..35fd7f3 100644 --- a/deker/client.py +++ b/deker/client.py @@ -192,6 +192,7 @@ def __init__( write_lock_check_interval: int = 1, loglevel: str = "ERROR", memory_limit: Union[int, str] = 0, + skip_collection_create_memory_check: bool = False, **kwargs: Any, ) -> None: """Deker client constructor. @@ -209,7 +210,7 @@ def __init__( converted into bytes. If result is ``<= 0`` - total RAM + total swap is used .. note:: This parameter is used for early runtime break in case of potential memory overflow - + :param skip_collection_create_memory_check: If we don't want to check size during collection creation :param kwargs: a wildcard, reserved for any extra parameters """ try: @@ -230,6 +231,7 @@ def __init__( write_lock_check_interval=write_lock_check_interval, loglevel=loglevel.upper(), memory_limit=mem_limit, + skip_collection_create_memory_check=skip_collection_create_memory_check, ) self.__uri: Uri = Uri.create(self.__config.uri) self.__is_closed: bool = True diff --git a/deker/collection.py b/deker/collection.py index e4c894d..c63b674 100644 --- a/deker/collection.py +++ b/deker/collection.py @@ -37,7 +37,7 @@ TimeDimensionSchema, VArraySchema, ) -from deker.tools import check_memory, not_deleted +from deker.tools import not_deleted from deker.types import Serializer @@ -278,9 +278,6 @@ def create( :param custom_attributes: ``Array`` or ``VArray`` custom attributes :param id_: ``Array`` or ``VArray`` unique UUID string """ - schema = self.array_schema - shape = schema.arrays_shape if hasattr(schema, "arrays_shape") else schema.shape - check_memory(shape, schema.dtype, self.__adapter.ctx.config.memory_limit) array = self.__manager.create(primary_attributes, custom_attributes, id_) self.logger.debug( f"{array.__class__.__name__} id={array.id} {primary_attributes=}, {custom_attributes=} created" diff --git a/deker/config.py b/deker/config.py index fb4b9d0..d8d7f0e 100644 --- a/deker/config.py +++ b/deker/config.py @@ -43,6 +43,7 @@ class DekerConfig: varray_data_directory: str = "varray_data" array_symlinks_directory: str = "array_symlinks" varray_symlinks_directory: str = "varray_symlinks" + skip_collection_create_memory_check: bool = False @property def as_dict(self) -> dict: diff --git a/docs/deker/fine_tuning.rst b/docs/deker/fine_tuning.rst index 7f5acd9..bbbc6e6 100755 --- a/docs/deker/fine_tuning.rst +++ b/docs/deker/fine_tuning.rst @@ -93,9 +93,12 @@ If you need to change it on the fly, you may use the following function:: set_logging_level("INFO") # now DEKER™ logs starting from "INFO" level + ``memory_limit`` ---------------- +.. _memory_limit: + This parameter is used for the early run time break in case of potential memory overflow. DEKER™ operates big amounts of data, and you may be unaware that your machine will probably run out @@ -142,6 +145,21 @@ suffix is ignored: ``"1024k"``, ``"512m"``, ``"8g"``, ``"1t"`` will work. If you set a memory limit to your container, you'd better limit DEKER™ to the same value. Otherwise your container may be killed because of memory overflow. +``skip_collection_create_memory_check`` +--------------------------------------- +Currently deker has 3 places, where memory check, described in `memory_limit`_: + + * On collection creation via ``client.create_collection()`` + * On getting subset e.g ``array[:]`` + * On reading array as ``XArray`` e.g ``array[:].read_xarray()`` + +While the last two prevent memory overflow and are required, +sometimes you may need to be able to skip the first one + +You can do so by providing +``skip_collection_create_memory_check=True`` as argument to +the :meth:`Client ` constructor + HDF5 Options ============ diff --git a/poetry.lock b/poetry.lock index 47dc925..c744ef9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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[[package]] name = "typing-extensions" -version = "4.11.0" +version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, - {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] [[package]] @@ -2616,13 +2631,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.26.1" +version = "20.26.2" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"}, - 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def test_create_raises_memory_error(self, client, root_path): - """Test create raise MemoryError on too big array.""" - schema = ArraySchema( - dimensions=[ - DimensionSchema(name="x", size=10000), - DimensionSchema(name="y", size=10000), - ], - dtype=float, - ) - col_name = "memory_excess_create" - with Client(embedded_uri(root_path), memory_limit=100, loglevel="CRITICAL") as extra_client: - client.create_collection(col_name, schema) - collection = extra_client.get_collection(col_name) - try: - with pytest.raises(DekerMemoryError): - collection.create() - finally: - collection.delete() - class TestCollectionIterator: def test_adapter_iter_anext(self, array_collection: Collection):