Debugging tool memory errors

Often the tool output contains one of:

MemoryError                 # Python
what():  std::bad_alloc     # C++
Segmentation Fault          # C - but could be other problems too
Killed                      # Linux OOM Killer


  • Change input sizes or params
    • Map/reduce?
  • Decrease the amount of memory the tool needs
  • Increase the amount of memory available to the job
    • Request more memory from cluster scheduler
    • Use job resubmission to automatically rerun with a larger memory allocation
  • Cross your fingers and rerun the job
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