Refactor embedding functions and add async query limit

- Separate insert/query embedding funcs
- Add query-specific async limit
- Update storage classes to use new funcs
- Protect vector DB save with lock
- Improve config handling for thresholds

lightrag/kg/nano_vector_db_impl.py

@@ -76,6 +76,8 @@ class NanoVectorDBStorage(BaseVectorStorage):
     cosine_better_than_threshold: float = float(os.getenv("COSINE_THRESHOLD", "0.2"))
 
     def __post_init__(self):
+        # Initialize lock only for file operations
+        self._save_lock = asyncio.Lock()
         # Use global config value if specified, otherwise use default
         config = self.global_config.get("vector_db_storage_cls_kwargs", {})
         self.cosine_better_than_threshold = config.get(
@@ -210,4 +212,6 @@ class NanoVectorDBStorage(BaseVectorStorage):
             logger.error(f"Error deleting relations for {entity_name}: {e}")
 
     async def index_done_callback(self):
-        self._client.save()
+        # Protect file write operation
+        async with self._save_lock:
+            self._client.save()

lightrag/lightrag.py

@@ -154,6 +154,7 @@ class LightRAG:
     embedding_func: EmbeddingFunc = None  # This must be set (we do want to separate llm from the corte, so no more default initialization)
     embedding_batch_num: int = 32
     embedding_func_max_async: int = 16
+    embedding_func_max_async_query: int = 4
 
     # LLM
     llm_model_func: callable = None  # This must be set (we do want to separate llm from the corte, so no more default initialization)
@@ -195,8 +196,11 @@ class LightRAG:
         _print_config = ",\n  ".join([f"{k} = {v}" for k, v in global_config.items()])
         logger.debug(f"LightRAG init with param:\n  {_print_config}\n")
 
-        # Init LLM
+        # Init embedding functions with separate instances for insert and query
-        self.embedding_func = limit_async_func_call(self.embedding_func_max_async)(
+        self.insert_embedding_func = limit_async_func_call(self.embedding_func_max_async)(
+            self.embedding_func
+        )
+        self.query_embedding_func = limit_async_func_call(self.embedding_func_max_async_query)(
             self.embedding_func
         )
 
@@ -238,15 +242,15 @@ class LightRAG:
         ####
         self.full_docs = self.key_string_value_json_storage_cls(
             namespace="full_docs",
-            embedding_func=self.embedding_func,
+            embedding_func=self.insert_embedding_func,
         )
         self.text_chunks = self.key_string_value_json_storage_cls(
             namespace="text_chunks",
-            embedding_func=self.embedding_func,
+            embedding_func=self.insert_embedding_func,
         )
         self.chunk_entity_relation_graph = self.graph_storage_cls(
             namespace="chunk_entity_relation",
-            embedding_func=self.embedding_func,
+            embedding_func=self.insert_embedding_func,
         )
         ####
         # add embedding func by walter over
@@ -254,17 +258,17 @@ class LightRAG:
 
         self.entities_vdb = self.vector_db_storage_cls(
             namespace="entities",
-            embedding_func=self.embedding_func,
+            embedding_func=self.query_embedding_func,
             meta_fields={"entity_name"},
         )
         self.relationships_vdb = self.vector_db_storage_cls(
             namespace="relationships",
-            embedding_func=self.embedding_func,
+            embedding_func=self.query_embedding_func,
             meta_fields={"src_id", "tgt_id"},
         )
         self.chunks_vdb = self.vector_db_storage_cls(
             namespace="chunks",
-            embedding_func=self.embedding_func,
+            embedding_func=self.query_embedding_func,
         )
 
         if self.llm_response_cache and hasattr(