[Swift-user] Bus Error

Thu Sep 4 14:52:56 CDT 2014

Hi Mihael,

This was on Blues, java version “1.7.0_55”.

Theres a ~4GB core-java-7-5702-3026-108521-1409822206 core dump file that was generated. (Actually there were two, the other one is ~1.3GB.)
Following this (http://www.javacodegeeks.com/2013/02/analysing-a-java-core-dump.html), this is the error:
Program terminated with signal 7, Bus error.
#0  0x00002b873a0fe6e0 in signalHandler(int, siginfo*, void*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so

And this is where it happened:
(gdb) where
#0  0x00002b873a0fe6e0 in signalHandler(int, siginfo*, void*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#1  <signal handler called>
#2  0x00002b873a102428 in os::PlatformEvent::park(long) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#3  0x00002b873a0f12eb in ObjectMonitor::wait(long, bool, Thread*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#4  0x00002b8739f63148 in JVM_MonitorWait ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#5  0x00002b87402b1608 in ?? ()
#6  0x00000007c7208000 in ?? ()
#7  0x0000000000000000 in ?? ()

Does this help at all?

Jonathan

On Sep 4, 2014, at 2:28 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:

> Hi Jonathan,
> 
> It's a bus error, which is just slightly worse than a segfault. both of
> which would reflect bugs in the JVM.
> 
> Was there a hs_err_pid???.log produced? It might help.
> 
> Also, it might help to know the exact version of java as well as the
> hardware details.
> 
> Mihael
> 
> On Thu, 2014-09-04 at 10:44 -0500, Jonathan Ozik wrote:
>> Hi all,
>> 
>> I’m trying to launch a large number of runs, 16807 to be precise, and am running into a couple of issues.
>> The first issue was a Java heap out of memory exception. I looked around to see where the best place to increase the max heap would be, and I settled on line 13 (“HEAPMAX=4096M”) of the swift executable. I should mention that all of this is using swift-0.95-RC6.
>> That did get rid of the out of memory exception, but this time I got a Bus error:
>> 
>> /home/ozik/swift_dist/swift-0.95-RC6/bin/swift: line 188: 108521 Bus error               (core dumped) java -Xmx4096M -XX:+HeapDumpOnOutOfMemoryError -Djava.endorsed.dirs=/home/ozik/swift_dist/swift-0.95-RC6/lib/endorsed -DUID=5702 -DGLOBUS_HOSTNAME=blogin3 -DCOG_INSTALL_PATH=/home/ozik/swift_dist/swift-0.95-RC6 -Dswift.home=/home/ozik/swift_dist/swift-0.95-RC6 -Djava.security.egd=file:///dev/urandom -Dscript.dir=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/scripts -Drestart.log.name=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/restart.log -Ddebug.dir.prefix=run003/ -classpath /home/ozik/swift_dist/swift-0.95-RC6/etc:/home/ozik/swift_dist/swift-0.95-RC6/libexec:/home/ozik/swift_dist/swift-0.95-RC6/lib/ant.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/antlr-2.7.5.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/castor-0.9.6.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/coaster-bootstrap.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-abstraction-common-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-grapheditor-0.47.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-jglobus-1.7.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-karajan-0.36-dev.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-coaster-0.3.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-dcache-0.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-gt2-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-local-2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-localscheduler-0.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-ssh-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-webdav-2.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-resources-1.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-swift-svn.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-util-0.92.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-httpclient.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-logging-1.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix32.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix-asn1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-common-0.2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-core-0.2.2-patch-b.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-regexp-1.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-slide-webdavlib-2.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jaxrpc.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jce-jdk13-131.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jcommon-1.0.18.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jfreechart-1.0.15.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jgss.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jline-0.9.94.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jsr173_1.0_api.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jug-lgpl-2.0.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/junit.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/log4j-1.2.16.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/puretls.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/resolver.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/stringtemplate.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/vdldefinitions.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean_xpath.jar: org.griphyn.vdl.karajan.Loader -runid run003 -logfile /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/run003.log -sites.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/sites.xml -tc.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/apps -config /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/cf repast.swift -lines=823543 -inst=16807 -upf=unrolledParamFile.txt
>> 
>> Any ideas on this?
>> 
>> Jonathan
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> 
> 