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.
jstack
Description: Binary data
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