TSPS-239 get wdl running on 500k sample ref panel #1373
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added 2 commits
September 12, 2024 08:21
increase gap between command memory and machine memory so machines dont crash
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Can one of the admins verify this patch? |
jsotobroad
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Description
When runnign the wdl on the 500k sample simluated reference panel we ran in to some issues where things were getting fuly preempted and then fully retried so i removed the retries and lowered the preemptible number. I think we can probably up the preemptible number back up but we should leave the maxRetries removed cuz tehy dont really make sense for our workflow.
CountVariantsInSampleBeagle was also runnign out of memory for the larger chromosomes so I upped the memory for that.
I increased the gap between the machine memory and the command memory for java commands because i was seeing machines fall over because the machine wasnt getting enough memory to do what it needed. this made things more consistent
Run before changes -https://bvdp-saturn-dev.appspot.com/#workspaces/teaspoons-imputation-
dev/teaspoons_imputation_dev_control_workspace_20240726/job_history/6981ff6e-8acf-4769-9109-192e794741ce
Run after changes - https://bvdp-saturn-dev.appspot.com/#workspaces/teaspoons-imputation-dev/teaspoons_imputation_dev_control_workspace_20240726/job_history/67c74355-5ec2-4ee4-87e1-905d5c77596c
Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.