On Aug 21, 2014, at 15:10 , Thomas Sibley <[email protected]> wrote: > The runtime is still dramatically different from my other input, and I wonder > if you have any ideas why? Do you expect it's some property of the data? Or > some pathological edge case? > > I can't help but think the crash and runtime leap are related...
Bingo. After putting together my jstack/strace observations with a reading of the MarkDuplicates source, I wrote the one-line patch attached, recompiled MarkDuplicates.jar, and the runtime dropped to 2-3 minutes. I started a tight loop running and re-running MarkDuplicates on the same problematic input and will see if I can provoke a JVM crash still. My cursory reading of trackOpticalDuplicates(), findOpticalDuplicates(), and related codepaths doesn't reveal anything to me that might be the source of my issue. Perhaps someone more familiar with the JVM/Java/picard can see something?
0001-MarkDuplicates-Comment-out-optical-duplicate-trackin.patch
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