On Aug 20, 2014, at 15:58 , Thomas Sibley <trsib...@uw.edu> wrote: > On Aug 20, 2014, at 14:25 , Thomas Sibley <trsib...@uw.edu> wrote: >> I'm running into problems using Picard's MarkDuplicates utility. Sometimes >> I get a JVM crash, sometimes the process just seems to hang. After the >> initial startup, strace shows nothing but sched_yield() and futex() calls. >> While the input data which hangs has ~900k reads, MarkDuplicates runs in >> about 1min on ~400k reads from a different input file. >> >> Example informational output from both crashing and hanging runs are >> attached, as well as the crash log of the JVM. >> >> $ java -version >> java version "1.7.0_67" >> Java(TM) SE Runtime Environment (build 1.7.0_67-b01) >> Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode) > > Additional information: jconsole never connects to the java process and > jstack -F produces the attached thread trace.
The process I ran jstack on just completed without error, after 130 minutes. It took a few retry attempts to get a run all the way through without a JVM crash. Attached is the informational output from the MarkDuplicates command. I'm still interested in tracking down the reason for the JVM crashes, if anyone has pointers or ideas. I'd also like to know more about what affects the runtime of MarkDuplicates. It's a little wild to me that a ~2 fold increase in read number alone might produce a runtime difference from 1 minute to 130 minutes. Are there other properties of the input data that would affect this? Thanks, Thomas
MarkDuplicates-success-900k.log
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