Slight AoU docs adjustment [VS-1366] #8955
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gbggrant
reviewed
Aug 15, 2024
| - If re-running the extract workflow with call caching enabled, it may be necessary to increase memory in the `ExtractTask` / `PgenExtractTask` tasks. Due to the way call caching works in Cromwell (i.e. the `memory` attribute is not part of the call caching hashes), it is possible to edit the value of the `memory` runtime attribute of a task without breaking call caching. However, do *not* alter the value of the `memory_gib` input parameter as changing that absolutely will break call caching and will cause tens of thousands of shards to re-run needlessly! | ||
| - For Echo ACAF VCF extract, the VCF extract workflow was call-caching re-run with `ExtractTask` memory hard-coded to 100 GiB. 9/9 extract shards which did not complete on the initial run of the workflow succeeded on their first (non-preempted) attempt in the second run of the workflow. | ||
| - For Echo ACAF PGEN extract, the PGEN extract workflow was call-caching re-run with `PgenExtractTask` memory hard-coded to 50 GiB. 20/24 extract shards which did not complete on the initial run of the workflow succeeded on their first (non-preempted) attempt in the second run of the workflow. The remaining 4 shards hit `OutOfMemoryErrors` on their first attempt but succeeded on the second attempt with 50 GiB * 1.5 = 75 GiB of memory thanks to "retry with more memory". | ||
| - When re-running the extract workflow with call caching enabled, it will be necessary to increase memory in the `ExtractTask` / `PgenExtractTask` tasks. Due to the way call caching works in Cromwell (i.e. the `memory` runtime attribute is not part of the call caching hashes), it is possible to edit the value of the `memory` runtime attribute of a task without breaking call caching. However, do *not* alter the value of the `memory_gib` input parameter as changing that absolutely will break call caching and will cause tens of thousands of shards to re-run needlessly! Both VCF and PGEN extracts can have their memory set to `"50 GiB"` for the call-caching re-run. Most extract shards should finish on the first re-run attempt, but a few stragglers will likely OOM and automatically re-run with more memory. |
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I'm confused. Are you suggesting to edit the WDL to change the value of the memory runtime attribute? Wouldn't that break caching? I must be missing something.
rsasch
approved these changes
Aug 16, 2024
gbggrant
reviewed
Aug 19, 2024
gbggrant
reviewed
Aug 19, 2024
Co-authored-by: George Grant <[email protected]>
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