Why Does Similarity Search Fail After Migrating Chroma DB with SQLite Storage?

Below is a possible explanation and solution:

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Why Similarity Search May Fail After Moving the DB

Even though your SQLite metadata (the collection count) appears intact, the HNSW index—used for fast similarity search—is rebuilt in memory and may be tied to the system it was originally created on. In other words, even if the persistent SQLite data is copied over, the vector index may no longer be valid on a new system.

Not Likely a Package Version Issue

Using different versions (chroma-hnswlib==0.7.6 versus 0.7.3 with matching chromadb versions) doesn’t normally cause this problem. Instead, the issue is more about the fact that the HNSW index is built in system RAM and can depend on the host’s CPU architecture and instruction set.

Recommended Solutions

1. Rebuild the Index on the Destination System:
   To ensure that similarity search works, reinsert or reindex the vectors on the target system. This forces the in-memory HNSW index to be rebuilt on the local CPU architecture.

2. Check Your CPU/Compiler Settings (if applicable):
   If you’re seeing errors such as an “illegal instruction” (or a similar runtime failure), it may be that the binary wheel of hnswlib was built for a different CPU instruction set than what is available on your new system. In that case, make sure to rebuild or reinstall the package on the destination machine so that it compiles for your environment.

3. Follow Migration Practices:
   If you’re moving persistent storage between systems, it’s a best practice to treat the SQLite metadata as persistent but reinitialize the in‑memory components. Some CLI tools or scripts (if available for your version) can help with “vacuuming” or rebuilding the database.

By reinitializing the HNSW index on your new system, your similarity searches should work correctly again.

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Feel free to reach out if you need more details on rebuilding the index for your specific setup!