vectordb-bench 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl

vectordb_bench/__init__.py

@@ -37,23 +37,24 @@ class config:
     K_DEFAULT = 100  # default return top k nearest neighbors during search
     CUSTOM_CONFIG_DIR = pathlib.Path(__file__).parent.joinpath("custom/custom_case.json")
 
-    CAPACITY_TIMEOUT_IN_SECONDS = 24 * 3600 # 24h
-    LOAD_TIMEOUT_DEFAULT        = 2.5 * 3600 # 2.5h
-    LOAD_TIMEOUT_768D_1M        = 2.5 * 3600 # 2.5h
-    LOAD_TIMEOUT_768D_10M       =  25 * 3600 # 25h
-    LOAD_TIMEOUT_768D_100M      = 250 * 3600 # 10.41d
+    CAPACITY_TIMEOUT_IN_SECONDS = 24 * 3600   # 24h
+    LOAD_TIMEOUT_DEFAULT        = 24 * 3600   # 24h
+    LOAD_TIMEOUT_768D_1M        = 24 * 3600   # 24h
+    LOAD_TIMEOUT_768D_10M       = 240 * 3600  # 10d
+    LOAD_TIMEOUT_768D_100M      = 2400 * 3600 # 100d
 
-    LOAD_TIMEOUT_1536D_500K     = 2.5 * 3600 # 2.5h
-    LOAD_TIMEOUT_1536D_5M       =  25 * 3600 # 25h
+    LOAD_TIMEOUT_1536D_500K     = 24 * 3600   # 24h
+    LOAD_TIMEOUT_1536D_5M       = 240 * 3600  # 10d
 
-    OPTIMIZE_TIMEOUT_DEFAULT    = 30 * 60   # 30min
-    OPTIMIZE_TIMEOUT_768D_1M    =  30 * 60   # 30min
-    OPTIMIZE_TIMEOUT_768D_10M   = 5 * 3600 # 5h
-    OPTIMIZE_TIMEOUT_768D_100M  =  50 * 3600 # 50h
+    OPTIMIZE_TIMEOUT_DEFAULT    = 24 * 3600   # 24h
+    OPTIMIZE_TIMEOUT_768D_1M    = 24 * 3600   # 24h
+    OPTIMIZE_TIMEOUT_768D_10M   = 240 * 3600  # 10d
+    OPTIMIZE_TIMEOUT_768D_100M  = 2400 * 3600 # 100d
 
 
-    OPTIMIZE_TIMEOUT_1536D_500K =  15 * 60   # 15min
-    OPTIMIZE_TIMEOUT_1536D_5M   =   2.5 * 3600 # 2.5h
+    OPTIMIZE_TIMEOUT_1536D_500K = 24 * 3600   # 24h
+    OPTIMIZE_TIMEOUT_1536D_5M   = 240 * 3600  # 10d
+    
     def display(self) -> str:
         tmp = [
             i for i in inspect.getmembers(self)

vectordb_bench/backend/clients/__init__.py

@@ -31,6 +31,7 @@ class DB(Enum):
     PgVector = "PgVector"
     PgVectoRS = "PgVectoRS"
     PgVectorScale = "PgVectorScale"
+    PgDiskANN = "PgDiskANN"
     Redis = "Redis"
     MemoryDB = "MemoryDB"
     Chroma = "Chroma"
@@ -77,6 +78,10 @@ class DB(Enum):
             from .pgvectorscale.pgvectorscale import PgVectorScale
             return PgVectorScale
 
+        if self == DB.PgDiskANN:
+            from .pgdiskann.pgdiskann import PgDiskANN
+            return PgDiskANN
+
         if self == DB.Redis:
             from .redis.redis import Redis
             return Redis
@@ -132,6 +137,10 @@ class DB(Enum):
             from .pgvectorscale.config import PgVectorScaleConfig
             return PgVectorScaleConfig
 
+        if self == DB.PgDiskANN:
+            from .pgdiskann.config import PgDiskANNConfig
+            return PgDiskANNConfig
+
         if self == DB.Redis:
             from .redis.config import RedisConfig
             return RedisConfig
@@ -185,6 +194,10 @@ class DB(Enum):
             from .pgvectorscale.config import _pgvectorscale_case_config
             return _pgvectorscale_case_config.get(index_type)
 
+        if self == DB.PgDiskANN:
+            from .pgdiskann.config import _pgdiskann_case_config
+            return _pgdiskann_case_config.get(index_type)
+
         # DB.Pinecone, DB.Chroma, DB.Redis
         return EmptyDBCaseConfig
 

vectordb_bench/backend/clients/api.py

@@ -10,6 +10,8 @@ class MetricType(str, Enum):
     L2 = "L2"
     COSINE = "COSINE"
     IP = "IP"
+    HAMMING = "HAMMING"
+    JACCARD = "JACCARD"
 
 
 class IndexType(str, Enum):

vectordb_bench/backend/clients/pgdiskann/cli.py

@@ -0,0 +1,99 @@
+import click
+import os
+from pydantic import SecretStr
+
+from ....cli.cli import (
+    CommonTypedDict,
+    cli,
+    click_parameter_decorators_from_typed_dict,
+    run,
+)
+from typing import Annotated, Optional, Unpack
+from vectordb_bench.backend.clients import DB
+
+
+class PgDiskAnnTypedDict(CommonTypedDict):
+    user_name: Annotated[
+        str, click.option("--user-name", type=str, help="Db username", required=True)
+    ]
+    password: Annotated[
+        str,
+        click.option("--password",
+                     type=str,
+                     help="Postgres database password",
+                     default=lambda: os.environ.get("POSTGRES_PASSWORD", ""),
+                     show_default="$POSTGRES_PASSWORD",
+                     ),
+    ]
+
+    host: Annotated[
+        str, click.option("--host", type=str, help="Db host", required=True)
+    ]
+    db_name: Annotated[
+        str, click.option("--db-name", type=str, help="Db name", required=True)
+    ]
+    max_neighbors: Annotated[
+        int,
+        click.option(
+            "--max-neighbors", type=int, help="PgDiskAnn max neighbors",
+        ),
+    ]
+    l_value_ib: Annotated[
+        int,
+        click.option(
+            "--l-value-ib", type=int, help="PgDiskAnn l_value_ib",
+        ),
+    ]
+    l_value_is: Annotated[
+        float,
+        click.option(
+            "--l-value-is", type=float, help="PgDiskAnn l_value_is",
+        ),
+    ]
+    maintenance_work_mem: Annotated[
+        Optional[str],
+        click.option(
+            "--maintenance-work-mem",
+            type=str,
+            help="Sets the maximum memory to be used for maintenance operations (index creation). "
+            "Can be entered as string with unit like '64GB' or as an integer number of KB."
+            "This will set the parameters: max_parallel_maintenance_workers,"
+            " max_parallel_workers & table(parallel_workers)",
+            required=False,
+        ),
+    ]
+    max_parallel_workers: Annotated[
+        Optional[int],
+        click.option(
+            "--max-parallel-workers",
+            type=int,
+            help="Sets the maximum number of parallel processes per maintenance operation (index creation)",
+            required=False,
+        ),
+    ]
+
+@cli.command()
+@click_parameter_decorators_from_typed_dict(PgDiskAnnTypedDict)
+def PgDiskAnn(
+    **parameters: Unpack[PgDiskAnnTypedDict],
+):
+    from .config import PgDiskANNConfig, PgDiskANNImplConfig
+
+    run(
+        db=DB.PgDiskANN,
+        db_config=PgDiskANNConfig(
+            db_label=parameters["db_label"],
+            user_name=SecretStr(parameters["user_name"]),
+            password=SecretStr(parameters["password"]),
+            host=parameters["host"],
+            db_name=parameters["db_name"],
+        ),
+        db_case_config=PgDiskANNImplConfig(
+            max_neighbors=parameters["max_neighbors"],
+            l_value_ib=parameters["l_value_ib"],
+            l_value_is=parameters["l_value_is"],
+            max_parallel_workers=parameters["max_parallel_workers"],
+            maintenance_work_mem=parameters["maintenance_work_mem"],
+        ),
+        **parameters,
+    )

vectordb_bench/backend/clients/pgdiskann/config.py

@@ -0,0 +1,145 @@
+from abc import abstractmethod
+from typing import Any, Mapping, Optional, Sequence, TypedDict
+from pydantic import BaseModel, SecretStr
+from typing_extensions import LiteralString
+from ..api import DBCaseConfig, DBConfig, IndexType, MetricType
+
+POSTGRE_URL_PLACEHOLDER = "postgresql://%s:%s@%s/%s"
+
+
+class PgDiskANNConfigDict(TypedDict):
+    """These keys will be directly used as kwargs in psycopg connection string,
+        so the names must match exactly psycopg API"""
+
+    user: str
+    password: str
+    host: str
+    port: int
+    dbname: str
+
+
+class PgDiskANNConfig(DBConfig):
+    user_name: SecretStr = SecretStr("postgres")
+    password: SecretStr
+    host: str = "localhost"
+    port: int = 5432
+    db_name: str
+
+    def to_dict(self) -> PgDiskANNConfigDict:
+        user_str = self.user_name.get_secret_value()
+        pwd_str = self.password.get_secret_value()
+        return {
+            "host": self.host,
+            "port": self.port,
+            "dbname": self.db_name,
+            "user": user_str,
+            "password": pwd_str,
+        }
+
+
+class PgDiskANNIndexConfig(BaseModel, DBCaseConfig):
+    metric_type: MetricType | None = None
+    create_index_before_load: bool = False
+    create_index_after_load: bool = True
+    maintenance_work_mem: Optional[str]
+    max_parallel_workers: Optional[int]
+
+    def parse_metric(self) -> str:
+        if self.metric_type == MetricType.L2:
+            return "vector_l2_ops"
+        elif self.metric_type == MetricType.IP:
+            return "vector_ip_ops"
+        return "vector_cosine_ops"
+
+    def parse_metric_fun_op(self) -> LiteralString:
+        if self.metric_type == MetricType.L2:
+            return "<->"
+        elif self.metric_type == MetricType.IP:
+            return "<#>"
+        return "<=>"
+
+    def parse_metric_fun_str(self) -> str:
+        if self.metric_type == MetricType.L2:
+            return "l2_distance"
+        elif self.metric_type == MetricType.IP:
+            return "max_inner_product"
+        return "cosine_distance"
+    
+    @abstractmethod
+    def index_param(self) -> dict:
+        ...
+
+    @abstractmethod
+    def search_param(self) -> dict:
+        ...
+
+    @abstractmethod
+    def session_param(self) -> dict:
+        ...
+
+    @staticmethod
+    def _optionally_build_with_options(with_options: Mapping[str, Any]) -> Sequence[dict[str, Any]]:
+        """Walk through mappings, creating a List of {key1 = value} pairs. That will be used to build a where clause"""
+        options = []
+        for option_name, value in with_options.items():
+            if value is not None:
+                options.append(
+                    {
+                        "option_name": option_name,
+                        "val": str(value),
+                    }
+                )
+        return options
+
+    @staticmethod
+    def _optionally_build_set_options(
+        set_mapping: Mapping[str, Any]
+    ) -> Sequence[dict[str, Any]]:
+        """Walk through options, creating 'SET 'key1 = "value1";' list"""
+        session_options = []
+        for setting_name, value in set_mapping.items():
+            if value:
+                session_options.append(
+                    {"parameter": {
+                            "setting_name": setting_name,
+                            "val": str(value),
+                        },
+                    }
+                )
+        return session_options
+    
+
+class PgDiskANNImplConfig(PgDiskANNIndexConfig):
+    index: IndexType = IndexType.DISKANN
+    max_neighbors: int | None
+    l_value_ib: int | None
+    l_value_is: float | None
+    maintenance_work_mem: Optional[str] = None
+    max_parallel_workers: Optional[int] = None
+
+    def index_param(self) -> dict:
+        return {
+            "metric": self.parse_metric(),
+            "index_type": self.index.value,
+            "options": {
+                "max_neighbors": self.max_neighbors,
+                "l_value_ib": self.l_value_ib,
+            },
+            "maintenance_work_mem": self.maintenance_work_mem,
+            "max_parallel_workers": self.max_parallel_workers,
+        }
+    
+    def search_param(self) -> dict:
+        return {
+            "metric": self.parse_metric(),
+            "metric_fun_op": self.parse_metric_fun_op(),
+        }
+    
+    def session_param(self) -> dict:
+        return {
+            "diskann.l_value_is": self.l_value_is,
+        }
+    
+_pgdiskann_case_config = {
+    IndexType.DISKANN: PgDiskANNImplConfig,
+}

vectordb_bench/backend/clients/pgdiskann/pgdiskann.py

@@ -0,0 +1,350 @@
+"""Wrapper around the pg_diskann vector database over VectorDB"""
+
+import logging
+import pprint
+from contextlib import contextmanager
+from typing import Any, Generator, Optional, Tuple
+
+import numpy as np
+import psycopg
+from pgvector.psycopg import register_vector
+from psycopg import Connection, Cursor, sql
+
+from ..api import VectorDB
+from .config import PgDiskANNConfigDict, PgDiskANNIndexConfig
+
+log = logging.getLogger(__name__)
+
+
+class PgDiskANN(VectorDB):
+    """Use psycopg instructions"""
+
+    conn: psycopg.Connection[Any] | None = None
+    coursor: psycopg.Cursor[Any] | None = None
+
+    _filtered_search: sql.Composed
+    _unfiltered_search: sql.Composed
+
+    def __init__(
+        self,
+        dim: int,
+        db_config: PgDiskANNConfigDict,
+        db_case_config: PgDiskANNIndexConfig,
+        collection_name: str = "pg_diskann_collection",
+        drop_old: bool = False,
+        **kwargs,
+    ):
+        self.name = "PgDiskANN"
+        self.db_config = db_config
+        self.case_config = db_case_config
+        self.table_name = collection_name
+        self.dim = dim
+
+        self._index_name = "pgdiskann_index"
+        self._primary_field = "id"
+        self._vector_field = "embedding"
+
+        self.conn, self.cursor = self._create_connection(**self.db_config)        
+
+        log.info(f"{self.name} config values: {self.db_config}\n{self.case_config}")
+        if not any(
+            (
+                self.case_config.create_index_before_load,
+                self.case_config.create_index_after_load,
+            )
+        ):
+            err = f"{self.name} config must create an index using create_index_before_load or create_index_after_load"
+            log.error(err)
+            raise RuntimeError(
+                f"{err}\n{pprint.pformat(self.db_config)}\n{pprint.pformat(self.case_config)}"
+            )
+
+        if drop_old:
+            self._drop_index()
+            self._drop_table()
+            self._create_table(dim)
+            if self.case_config.create_index_before_load:
+                self._create_index()
+
+        self.cursor.close()
+        self.conn.close()
+        self.cursor = None
+        self.conn = None
+
+    @staticmethod
+    def _create_connection(**kwargs) -> Tuple[Connection, Cursor]:
+        conn = psycopg.connect(**kwargs)
+        conn.cursor().execute("CREATE EXTENSION IF NOT EXISTS pg_diskann CASCADE")
+        conn.commit()
+        register_vector(conn)
+        conn.autocommit = False
+        cursor = conn.cursor()
+
+        assert conn is not None, "Connection is not initialized"
+        assert cursor is not None, "Cursor is not initialized"
+
+        return conn, cursor
+
+    @contextmanager
+    def init(self) -> Generator[None, None, None]:
+        self.conn, self.cursor = self._create_connection(**self.db_config)
+
+        # index configuration may have commands defined that we should set during each client session
+        session_options: dict[str, Any] = self.case_config.session_param()
+
+        if len(session_options) > 0:
+            for setting_name, setting_val in session_options.items():
+                command = sql.SQL("SET {setting_name} " + "= {setting_val};").format(
+                    setting_name=sql.Identifier(setting_name),
+                    setting_val=sql.Identifier(str(setting_val)),
+                )
+                log.debug(command.as_string(self.cursor))
+                self.cursor.execute(command)
+            self.conn.commit()
+        
+        self._filtered_search = sql.Composed(
+            [
+                sql.SQL(
+                    "SELECT id FROM public.{table_name} WHERE id >= %s ORDER BY embedding "
+                    ).format(table_name=sql.Identifier(self.table_name)),
+                sql.SQL(self.case_config.search_param()["metric_fun_op"]),
+                sql.SQL(" %s::vector LIMIT %s::int"),
+            ]
+        )
+
+        self._unfiltered_search = sql.Composed(
+            [
+                sql.SQL("SELECT id FROM public.{} ORDER BY embedding ").format(
+                    sql.Identifier(self.table_name)
+                ),
+                sql.SQL(self.case_config.search_param()["metric_fun_op"]),
+                sql.SQL(" %s::vector LIMIT %s::int"),
+            ]
+        )
+
+        try:
+            yield
+        finally:
+            self.cursor.close()
+            self.conn.close()
+            self.cursor = None
+            self.conn = None
+
+    def _drop_table(self):
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+        log.info(f"{self.name} client drop table : {self.table_name}")
+
+        self.cursor.execute(
+            sql.SQL("DROP TABLE IF EXISTS public.{table_name}").format(
+                table_name=sql.Identifier(self.table_name)
+            )
+        )
+        self.conn.commit()
+
+    def ready_to_load(self):
+        pass
+
+    def optimize(self):
+        self._post_insert()
+
+    def _post_insert(self):
+        log.info(f"{self.name} post insert before optimize")
+        if self.case_config.create_index_after_load:
+            self._drop_index()
+            self._create_index()
+
+    def _drop_index(self):
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+        log.info(f"{self.name} client drop index : {self._index_name}")
+
+        drop_index_sql = sql.SQL("DROP INDEX IF EXISTS {index_name}").format(
+            index_name=sql.Identifier(self._index_name)
+        )
+        log.debug(drop_index_sql.as_string(self.cursor))
+        self.cursor.execute(drop_index_sql)
+        self.conn.commit()
+
+    def _set_parallel_index_build_param(self):
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+
+        index_param = self.case_config.index_param()
+
+        if index_param["maintenance_work_mem"] is not None:
+            self.cursor.execute(
+                sql.SQL("SET maintenance_work_mem TO {};").format(
+                    index_param["maintenance_work_mem"]
+                )
+            )
+            self.cursor.execute(
+                sql.SQL("ALTER USER {} SET maintenance_work_mem TO {};").format(
+                    sql.Identifier(self.db_config["user"]),
+                    index_param["maintenance_work_mem"],
+                )
+            )
+            self.conn.commit()
+
+        if index_param["max_parallel_workers"] is not None:
+            self.cursor.execute(
+                sql.SQL("SET max_parallel_maintenance_workers TO '{}';").format(
+                    index_param["max_parallel_workers"]
+                )
+            )
+            self.cursor.execute(
+                sql.SQL(
+                    "ALTER USER {} SET max_parallel_maintenance_workers TO '{}';"
+                ).format(
+                    sql.Identifier(self.db_config["user"]),
+                    index_param["max_parallel_workers"],
+                )
+            )
+            self.cursor.execute(
+                sql.SQL("SET max_parallel_workers TO '{}';").format(
+                    index_param["max_parallel_workers"]
+                )
+            )
+            self.cursor.execute(
+                sql.SQL(
+                    "ALTER USER {} SET max_parallel_workers TO '{}';"
+                ).format(
+                    sql.Identifier(self.db_config["user"]),
+                    index_param["max_parallel_workers"],
+                )
+            )
+            self.cursor.execute(
+                sql.SQL(
+                    "ALTER TABLE {} SET (parallel_workers = {});"
+                ).format(
+                    sql.Identifier(self.table_name),
+                    index_param["max_parallel_workers"],
+                )
+            )
+            self.conn.commit()
+
+        results = self.cursor.execute(
+            sql.SQL("SHOW max_parallel_maintenance_workers;")
+        ).fetchall()
+        results.extend(
+            self.cursor.execute(sql.SQL("SHOW max_parallel_workers;")).fetchall()
+        )
+        results.extend(
+            self.cursor.execute(sql.SQL("SHOW maintenance_work_mem;")).fetchall()
+        )
+        log.info(f"{self.name} parallel index creation parameters: {results}")
+    def _create_index(self):
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+        log.info(f"{self.name} client create index : {self._index_name}")
+
+        index_param: dict[str, Any] = self.case_config.index_param()
+        self._set_parallel_index_build_param()
+
+        options = []
+        for option_name, option_val in index_param["options"].items():
+            if option_val is not None:
+                options.append(
+                    sql.SQL("{option_name} = {val}").format(
+                        option_name=sql.Identifier(option_name),
+                        val=sql.Identifier(str(option_val)),
+                    )
+                )
+        
+        if any(options):
+            with_clause = sql.SQL("WITH ({});").format(sql.SQL(", ").join(options))
+        else:
+            with_clause = sql.Composed(())
+
+        index_create_sql = sql.SQL(
+            """
+            CREATE INDEX IF NOT EXISTS {index_name} ON public.{table_name} 
+            USING {index_type} (embedding {embedding_metric})
+            """
+        ).format(
+            index_name=sql.Identifier(self._index_name),
+            table_name=sql.Identifier(self.table_name),
+            index_type=sql.Identifier(index_param["index_type"].lower()),
+            embedding_metric=sql.Identifier(index_param["metric"]),
+        )
+        index_create_sql_with_with_clause = (
+            index_create_sql + with_clause
+        ).join(" ")
+        log.debug(index_create_sql_with_with_clause.as_string(self.cursor))
+        self.cursor.execute(index_create_sql_with_with_clause)
+        self.conn.commit()
+
+    def _create_table(self, dim: int):
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+
+        try:
+            log.info(f"{self.name} client create table : {self.table_name}")
+
+            self.cursor.execute(
+                sql.SQL(
+                    "CREATE TABLE IF NOT EXISTS public.{table_name} (id BIGINT PRIMARY KEY, embedding vector({dim}));"
+                ).format(table_name=sql.Identifier(self.table_name), dim=dim)
+            )
+            self.conn.commit()
+        except Exception as e:
+            log.warning(
+                f"Failed to create pgdiskann table: {self.table_name} error: {e}"
+            )
+            raise e from None
+
+    def insert_embeddings(
+        self,
+        embeddings: list[list[float]],
+        metadata: list[int],
+        **kwargs: Any,
+    ) -> Tuple[int, Optional[Exception]]:
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+
+        try:
+            metadata_arr = np.array(metadata)
+            embeddings_arr = np.array(embeddings)
+
+            with self.cursor.copy(
+                sql.SQL("COPY public.{table_name} FROM STDIN (FORMAT BINARY)").format(
+                    table_name=sql.Identifier(self.table_name)
+                )
+            ) as copy:
+                copy.set_types(["bigint", "vector"])
+                for i, row in enumerate(metadata_arr):
+                    copy.write_row((row, embeddings_arr[i]))
+            self.conn.commit()
+
+            if kwargs.get("last_batch"):
+                self._post_insert()
+
+            return len(metadata), None
+        except Exception as e:
+            log.warning(
+                f"Failed to insert data into table ({self.table_name}), error: {e}"
+            )
+            return 0, e
+
+    def search_embedding(
+        self,
+        query: list[float],
+        k: int = 100,
+        filters: dict | None = None,
+        timeout: int | None = None,
+    ) -> list[int]:
+        assert self.conn is not None, "Connection is not initialized"
+        assert self.cursor is not None, "Cursor is not initialized"
+
+        q = np.asarray(query)
+        if filters:
+            gt = filters.get("id")
+            result = self.cursor.execute(
+                    self._filtered_search, (gt, q, k), prepare=True, binary=True
+                    )
+        else:
+            result = self.cursor.execute(
+                    self._unfiltered_search, (q, k), prepare=True, binary=True
+                    )
+
+        return [int(i[0]) for i in result.fetchall()]