I'm curious whether you're using openjdk or oracle jdk. I've seen strange behavior from open jdk.
Please excuse the brevity. Sent from my Zack Morris phone. > On Aug 21, 2014, at 6:02 PM, Thomas Sibley <[email protected]> wrote: > >> On Aug 21, 2014, at 15:29 , Thomas Sibley <[email protected]> wrote: >>> 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. > > 100 runs later, doing 4 at a time, and I haven't provoked a JVM crash with my > patched MarkDuplicates. I also tried with the IntelDeflater re-enabled and > did not trigger a crash. Average run times of 1.38 minutes. > > _Something_ is bogging down in findOpticalDuplicates and going off the deep > end. I'd guess the Collection.sort call since I saw mention of the sort > implementation guts in the crash logs, but again, I'm no expert on the JVM. > > Thomas > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
