Segfault in libjvm.dylib during CreatePanelOfNormalsIntegrationTest

[droazen]

@lbergelson commented on Wed Aug 31 2016

I got a segfault while running CreatePanelOfNormalsIntegrationTest. Subsequent runs were unable to reproduce it.

   18:03:07.573 WARN  TaskSetManager:70 - Stage 181 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB.
Test: Test method testAllTargetsHDF5PoNCreationSpark[0](null, src/test/resources/org/broadinstitute/hellbender/tools/exome/create-pon-control-full.pcov)(org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormalsIntegrationTest) produced standard out/err: 18:03:07.612 WARN  TaskSetManager:70 - Stage 182 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB.

    18:03:07.612 WARN  TaskSetManager:70 - Stage 182 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB.
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000010a5a9401, pid=2425, tid=8963
#
# JRE version: Java(TM) SE Runtime Environment (8.0_91-b14) (build 1.8.0_91-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.91-b14 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.dylib+0x1a9401]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/louisb/Workspace/gatk-protected/hs_err_pid2425.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

hs_err_pid2425.log.txt

@yfarjoun Is this similar to the crash you saw a while back?

---

@yfarjoun commented on Wed Aug 31 2016

no. this is different.

On Wed, Aug 31, 2016 at 3:27 PM, Louis Bergelson notifications@github.com wrote:

I got a segfault while running CreatePanelOfNormalsIntegrationTest. Subsequent runs were unable to reproduce it.

18:03:07.573 WARN TaskSetManager:70 - Stage 181 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB. Test: Test method testAllTargetsHDF5PoNCreationSpark[0](null, src/test/resources/org/broadinstitute/hellbender/tools/exome/create-pon-control-full.pcov)(org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormalsIntegrationTest) produced standard out/err: 18:03:07.612 WARN TaskSetManager:70 - Stage 182 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB.

18:03:07.612 WARN  TaskSetManager:70 - Stage 182 contains a task of very large size (119 KB). The maximum recommended task size is 100 KB.

#

A fatal error has been detected by the Java Runtime Environment:

#

SIGSEGV (0xb) at pc=0x000000010a5a9401, pid=2425, tid=8963

#

JRE version: Java(TM) SE Runtime Environment (8.0_91-b14) (build 1.8.0_91-b14)

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.91-b14 mixed mode bsd-amd64 compressed oops)

Problematic frame:

V [libjvm.dylib+0x1a9401]

#

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

#

An error report file with more information is saved as:

/Users/louisb/Workspace/gatk-protected/hs_err_pid2425.log

#

If you would like to submit a bug report, please visit:

http://bugreport.java.com/bugreport/crash.jsp

#

hs_err_pid2425.log.txt https://github.com/broadinstitute/gatk-protected/files/448383/hs_err_pid2425.log.txt

@yfarjoun https://github.com/yfarjoun Is this similar to the crash you saw a while back?

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[samuelklee]

Not sure if this was reproduced. Deleted in #3935.