Exceeding target memory

luntergroup / octopus

Bayesian haplotype-based mutation calling

MIT License

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Exceeding target memory #113

Closed hpoisner closed 4 years ago

hpoisner commented 4 years ago

Describe the bug I tried to run Octopus with --target-working-memory 32GB and my job was killed when it exceeded 36GB. The octopus version is 0.5.2. Is there a way to limit the absolute memory use?

dancooke commented 4 years ago

You cannot set a strict upper bound on memory consumption, but there are several options - including --target-working-memory that influence the maximum memory footprint. Note that --target-working-memory only sets the target maximum memory for the calling models working memory, and does not include the read and reference buffer.

dancooke commented 4 years ago

Closing due to inactivity. Please re-open if needed.