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HDF5 Corruption

HDF5 corruption occurs when files are not properly closed, written from multiple processes, or have incompatible versions.

Quick answer

HDF5 corruption occurs when files are not properly closed, written from multiple processes, or have incompatible versions.

Reliability#hdf5#corruption#h5py#storage#reliability

What this failure is

HDF5 Corruption is a Reliability failure seen during ML training runs. HDF5 corruption occurs when files are not properly closed, written from multiple processes, or have incompatible versions. Common tags: Hdf5, Corruption, H5py, Storage.

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Why it happens (the mechanism)

HDF5 file not closed properly. Concurrent writes to same file. HDF5 library version mismatch. File truncation from disk full. 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

  • HDF5 read fails
  • OSError: Unable to open file
  • HDF5 file is corrupted

Common symptoms and what they mean

SymptomWhy it happens
OSError: Unable to open file (Unable to truncate file)HDF5 file not closed properly
h5py.H5ErrorConcurrent writes to same file
HDF5 file header corruptionHDF5 library version mismatch

Which systems are affected

  • Training with HDF5 datasets
  • Storing features in HDF5
  • Multi-process HDF5 writing

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: OSError: Unable to open file (Unable to truncate file)
  • ✓Verified signal present: h5py.H5Error
  • ✓Verified signal present: HDF5 file header corruption
  • ✓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

Bytedance Sequence Length Straggler often co-occurs with this failure because both share underlying assumptions about reliability; if you fix this entry but still see drift, validate the related primary cause next. bytedance sequence length straggler →
Training Checkpoint Corruption On Write often co-occurs with this failure because both share underlying assumptions about reliability; if you fix this entry but still see drift, validate the related neighboring cause next. training checkpoint corruption on write →
Checkpoint Partial Save often co-occurs with this failure because both share underlying assumptions about reliability; if you fix this entry but still see drift, validate the related neighboring cause next. checkpoint partial save →

Root cause

  • HDF5 file not closed properly
  • Concurrent writes to same file
  • HDF5 library version mismatch
  • File truncation from disk full

The fix and how to prevent it

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References

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