muninn-troubleshoot

name	muninn-troubleshoot
description	Diagnoses muninn build failures, extension-loading errors, platform-specific pitfalls, and runtime issues across SQLite CLI, C, Python, Node.js, and WASM. Covers SQLITE_OMIT_LOAD_EXTENSION on macOS system Python, CMake hangs on Apple Silicon (GGML_NATIVE), Metal GPU toggles (MUNINN_GPU_LAYERS), llama.cpp log verbosity (MUNINN_LOG_LEVEL), ASan-built dylibs failing in Python, GGUF model resolution, and wasm32 vs wasm64 linkage. Use when the user mentions "unable to open shared library", "not authorized", "SQLITE_OMIT_LOAD_EXTENSION", "enable_load_extension fails", "muninn build failed", "CMake hangs", "Segmentation fault muninn", "model not registered", "MUNINN_GPU_LAYERS", "WASM muninn fails", "muninn troubleshooting", or hits a muninn load / build error.
license	MIT

muninn-troubleshoot — Diagnose build and runtime failures

Every issue below is something that has actually broken in development or user-reported. Work through the symptom → diagnosis → fix pattern rather than rewriting the user's code blindly.

Extension fails to load

Python: enable_load_extension raises or returns not authorized

Symptom

AttributeError: 'sqlite3.Connection' object has no attribute 'enable_load_extension'
# or
sqlite3.OperationalError: not authorized

Diagnosis — macOS system Python (/usr/bin/python3) and some Linux distro Pythons are compiled with SQLITE_OMIT_LOAD_EXTENSION. Check:

import sqlite3
print(sqlite3.sqlite_version)
db = sqlite3.connect(":memory:")
print(hasattr(db, "enable_load_extension"))   # False → system Python blocked

Fix — one of:

# Option A: Homebrew Python
brew install python
/opt/homebrew/bin/python3 -m pip install sqlite-muninn

# Option B: pysqlite3-binary (drop-in replacement with a bundled non-OMIT SQLite)
pip install pysqlite3-binary

# If using pysqlite3-binary
import pysqlite3 as sqlite3

SQLite CLI: Error: unable to open shared library

Symptom

sqlite> .load ./muninn
Error: unable to open shared library ./muninn

Diagnosis — one of:

1. File doesn't exist at that path — check with ls ./muninn*
2. Architecture mismatch (arm64 binary on x86_64 or vice versa) — check file ./muninn.dylib
3. SIP / notarization on macOS — xattr -l ./muninn.dylib shows quarantine flag

Fix

# Remove quarantine on macOS
xattr -d com.apple.quarantine ./muninn.dylib

# Rebuild for current architecture
make clean && make all

Do not drop the file extension in the Bash-visible path: .load ./muninn is correct, .load ./muninn.dylib also works. Both resolve to the same file.

Node.js: Cannot open shared library or undefined load export

Diagnosis — either better-sqlite3 is missing, or you installed sqlite-muninn without native binaries (CI slim image, Alpine musl without glibc).

Fix

# Ensure both packages; rebuild bindings if on odd glibc
npm install sqlite-muninn better-sqlite3
npm rebuild better-sqlite3

On Alpine (musl) the prebuilt binaries may not match — build from source:

apk add build-base python3 cmake
npm install --build-from-source sqlite-muninn

Build fails

CMake hangs on Apple Silicon during first make all

Symptom — make all sits at -- Detecting CXX compiler features for 10+ minutes.

Diagnosis — llama.cpp defaults to GGML_NATIVE=ON, which runs check_cxx_source_runs() for SVE/SME CPU features. On Apple Silicon, this probe hangs indefinitely.

Fix — the project's Makefile already passes -DGGML_NATIVE=OFF. If you are bypassing the Makefile (calling CMake directly), pass the flag manually:

cmake -S vendor/llama.cpp -B vendor/llama.cpp/build \
  -DGGML_NATIVE=OFF \
  -DGGML_METAL=ON \
  -DGGML_METAL_EMBED_LIBRARY=ON

Linux: linker errors on libstdc++ or libpthread

Symptom

undefined reference to `__pthread_create`
undefined reference to `std::basic_string`

Diagnosis — llama.cpp is C++, so the muninn extension needs to pull C++ runtime and pthreads when statically linked.

Fix — ensure these flags are in the link step (the Makefile handles this automatically):

-lstdc++ -lpthread

macOS equivalent: -lc++ -framework Accelerate -framework Metal -framework MetalKit -framework Foundation.

WASM: invalid wasm64 objects

Symptom — llama.cpp produces .o files that the final link rejects as "not a wasm32 object."

Diagnosis — recent llama.cpp defaults to LLAMA_WASM_MEM64=ON, producing wasm64 objects. muninn targets wasm32 for compatibility with @sqlite.org/sqlite-wasm.

Fix — pass -DLLAMA_WASM_MEM64=OFF when configuring. The Makefile handles this for make wasm.

Runtime errors

Error: no such function: muninn_embed

Diagnosis — extension loaded but no embedding model registered. The function exists; the failure is from the model lookup inside it.

Fix

INSERT INTO temp.muninn_models(name, model)
  SELECT 'MiniLM', muninn_embed_model('models/all-MiniLM-L6-v2.Q8_0.gguf');

If the error is literally "no such function" (not "model not registered"), the extension failed to load — debug that first.

Error: model not registered: 'X'

Diagnosis — model name mismatch, or the model was registered on a different connection.

Fix — list registered models:

SELECT name, dim FROM temp.muninn_models;
SELECT name FROM temp.muninn_chat_models;

Models are session-scoped. Reconnecting drops them. Re-register after sqlite3.connect(...).

Segmentation fault in Python tests

Diagnosis — you're loading muninn built with AddressSanitizer into a non-ASan Python interpreter. ASan must be present on both sides or neither.

Fix

make clean
make all           # not `make debug`

Use make debug only for the C test runner, never for integration from Python.

Metal GPU disabled on macOS

Diagnosis — MUNINN_GPU_LAYERS=0 was set, or the binary was built without Metal.

Fix

unset MUNINN_GPU_LAYERS                  # reverts to compile-time default (99 on macOS)
export MUNINN_LOG_LEVEL=warn              # surface llama.cpp warnings if still slow

# Verify at build time:
make clean
grep -r "GGML_METAL=ON" scripts/generate_build.py

On Linux there is no CUDA support in the current build; GPU layers are always 0.

llama.cpp is silent (can't see warnings)

Fix

export MUNINN_LOG_LEVEL=verbose   # all logs
export MUNINN_LOG_LEVEL=warn      # warnings + errors
export MUNINN_LOG_LEVEL=error     # errors only (default is silent)

WASM-specific pitfalls

Model file cannot be found

WASM reads from the virtual filesystem, not HTTP. Preload:

const response = await fetch("/models/miniLM.gguf");
const bytes = new Uint8Array(await response.arrayBuffer());
sqlite3.FS.writeFile("/models/miniLM.gguf", bytes);

db.exec(`
  INSERT INTO temp.muninn_models(name, model)
  SELECT 'MiniLM', muninn_embed_model('/models/miniLM.gguf');
`);

For persistence across page reloads, use OPFS (sqlite3.oo1.OpfsDb) and preload models into OPFS once.

Slow embedding / chat in the browser

Expected — WASM is CPU-only with no Metal. For interactive demos, use a small model (MiniLM 384d) and keep batch size 1. For production quality, run the native build behind an API instead.

Diagnostic snippets

-- Confirm each subsystem registered
SELECT name FROM pragma_function_list WHERE name LIKE 'muninn_%';
SELECT name FROM pragma_module_list   WHERE name LIKE 'hnsw_%' OR name LIKE 'graph_%' OR name = 'muninn_models' OR name = 'muninn_chat_models';

-- Check loaded extension compile options
SELECT sqlite_version();
SELECT sqlite_compileoption_used('ENABLE_LOAD_EXTENSION');   -- must be 1

# Show which shared library SQLite loaded (macOS)
sqlite3 -cmd ".load ./muninn" ":memory:" "SELECT 1;" 2>&1
lsof -p $$ | grep muninn

When to escalate

If none of the above applies:

1. Capture MUNINN_LOG_LEVEL=verbose output.
2. Run make test — if C tests fail, the issue is in the extension itself.
3. Run make test-python — if Python tests fail but C passes, the issue is the binding layer.
4. Open an issue at https://github.com/neozenith/sqlite-muninn/issues with platform + architecture + log tail.

See also

• muninn-setup — original install/load paths
• getting-started.md § Common pitfalls — authoritative list
• Project Makefile — canonical build flags