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LMDB Corruption

LMDB corruption occurs when LMDB files are not properly closed, transactions interrupted, or map_size exceeded.

Quick answer

LMDB corruption occurs when LMDB files are not properly closed, transactions interrupted, or map_size exceeded.

Data Pipeline#lmdb#corruption#map-size#data-pipeline#storage

What this failure is

LMDB Corruption is a Data Pipeline failure seen during ML training runs. LMDB corruption occurs when LMDB files are not properly closed, transactions interrupted, or map_size exceeded. Common tags: Lmdb, Corruption, Map Size, Data Pipeline.

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Why it happens (the mechanism)

LMDB map_size too small for data. LMDB file corruption from interrupted write. Concurrent write to same LMDB. LMDB not properly closed. Taken together, these mechanisms explain why the failure is reproducible, why it tends to surface on specific workloads or scales, and why generic mitigation attempts often fall short without addressing the underlying cause.

What you'll observe

  • LMDB read fails
  • LMDB: mdb_env_open failed
  • LMDB transaction fails to commit

Common symptoms and what they mean

SymptomWhy it happens
lmdb.MapFullError: Environment map_size limit reachedLMDB map_size too small for data
lmdb.CorruptedError: mdb_page_getLMDB file corruption from interrupted write
mdb_txn_commit: Invalid argumentConcurrent write to same LMDB

Which systems are affected

  • Training with LMDB datasets
  • Fast data loading with LMDB
  • Image storage in LMDB

How to confirm this is the problem

Use this checklist to test the hypothesis against a small reproduction. No single line proves the root cause, so preserve the preceding events and compare one variable at a time.

  • ✓Reproduce the failure from a clean checkpoint/seed: the symptom must appear without warm-up state from a previous run.
  • ✓Verified signal present: lmdb.MapFullError: Environment map_size limit reached
  • ✓Verified signal present: lmdb.CorruptedError: mdb_page_get
  • ✓Verified signal present: mdb_txn_commit: Invalid argument
  • ✓A targeted fix from the "How to fix it" section eliminates or substantially reduces the symptom within one validation pass.

The fix and the prevention pattern

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Related failures to investigate next

Augmentation Pipeline Error often co-occurs with this failure because both share underlying assumptions about data pipeline; if you fix this entry but still see drift, validate the related primary cause next. augmentation pipeline error →
Rag Embedding Mismatch often co-occurs with this failure because both share underlying assumptions about data pipeline; if you fix this entry but still see drift, validate the related neighboring cause next. rag embedding mismatch →
Tokenization Error often co-occurs with this failure because both share underlying assumptions about data pipeline; if you fix this entry but still see drift, validate the related neighboring cause next. tokenization error →

Root cause

  • LMDB map_size too small for data
  • LMDB file corruption from interrupted write
  • Concurrent write to same LMDB
  • LMDB not properly closed

The fix and how to prevent it

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References

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