2026-02-03-Enrichment-Progress

Knowledge-RAG Enrichment Progress - 2026-02-03

✅ Checkpoint: 2026-02-03 19:05 CST

Decision: ALL seed data is valid. Full enrichment pipeline resumed.

Key findings:

• “Compromised” label was due to chat model hallucinations (Ollama default), NOT embedding quality
• Embeddings used sentence-transformers/all-MiniLM-L6-v2 on CUDA - verified in log files
• Vector search and retrieval are unaffected
• See Data Integrity Status for details

---

Session Summary

Morning Session (09:09 CST)

Attempted parallel enrichment across 10 ChromaDB collections. Hit ChromaDB Rust bindings segfault due to concurrent access to 17GB monolith database.

Afternoon Session (15:12 CST)

• Investigated “compromised” data concern - determined embeddings are valid
• Switched to sequential enrichment via screen session to avoid segfaults
• Created run_all_enrichment.sh for full queue processing
• Started enrichment on ALL 10 collections

Evening Session (19:05 CST)

• Enrichment queue progressing through collections sequentially
• Currently processing: engineering_corpus (batch 92)
• Multiple collections completed or significantly progressed

Current Status

✅ DATA INTEGRITY - ALL CLEAR

Per Data Integrity Status:

• All collections have valid MiniLM/CUDA embeddings
• Full enrichment pipeline running

Enrichment Progress (updated 19:40 CST)

Collection	Enriched	Total	%	Status
quantum_biology	43,109	378,519	11%	🔄 Partial
science_corpus	1,459	554,335	0%	⏳ Queued
physicists_corpus	1,726	50,642	3%	⏳ Queued
engineering_corpus	6,479	87,746	7%	🔄 RUNNING
math_corpus	7,003	26,311	26%	✅ Partial
knowledgebase	7,100	~7,200	98%	✅ Near Complete
tech_corpus	1,921	1,950	98%	✅ Complete
greek_corpus	1,156	1,156	100%	✅ Complete
esoteric_corpus	846	846	100%	✅ Complete
biohacking_corpus	153	153	100%	✅ Complete

Total remaining: ~1M chunks (~230 hours / ~10 days)
Screen session: enrichment_all (started 15:12)

See Enrichment Status for full details.

Architecture

Multi-DB Config (corpus_config.json)

multi_db:
  enabled: true
  base_path: /mnt/storage/knowledge-rag/corpora
  legacy_monolith: /mnt/storage/knowledge-rag/chroma_db (17GB)

Currently all collections still in monolith. Multi-DB split not yet implemented.

Segfault Issue

Parallel access to monolith causes ChromaDB Rust bindings crash:

chromadb_rust_bindings.abi3.so: segfault at 0

Solution: Sequential processing via run_enrichment_queue.sh

File Locations

• Script: ~/projects/knowledge-rag/qb_enrichment.py
• Queue runner: ~/projects/knowledge-rag/run_enrichment_queue.sh
• Logs: ~/projects/knowledge-rag/{collection}_enrichment.log
• Progress: ~/projects/knowledge-rag/{prefix}_enrichment_progress.json
• Results: ~/projects/knowledge-rag/{prefix}_enrichment_results.jsonl

Resume Instructions

# Check running session
screen -ls
 
# Attach to monitor
screen -r enrichment
 
# If no session, start fresh:
cd ~/projects/knowledge-rag
screen -dmS enrichment bash -c './run_enrichment_queue.sh quantum_biology; exec bash'
 
# Monitor from outside:
tail -f ~/projects/knowledge-rag/quantumbiology_enrichment.log

Next Steps

1. ✅ Complete quantum_biology enrichment (running)
2. ✅ Verify seed data integrity (confirmed valid 2026-02-03)
3. 🔄 Complete enrichment on all 10 collections (IN PROGRESS)
4. 🔲 Implement true multi-DB split for parallel processing (future optimization)

Collections Reference (All Valid ✅)

1. biohacking_corpus (153 chunks) ✅
2. engineering_corpus (87,746 chunks) ✅
3. esoteric_corpus (846 chunks) ✅
4. greek_corpus (1,135 chunks) ✅
5. knowledge_base (~2,100 chunks) ✅
6. math_corpus (26,311 chunks) ✅
7. physicists_corpus (50,642 chunks) ✅
8. quantum_biology (378,519 chunks) ✅
9. science_corpus (554,335 chunks) ✅
10. tech_corpus ✅