VM crashes when safepoint and synchronizing

[Karida]

 A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (safepoint.cpp:300), pid=23231, tid=140562312316672
# guarantee(PageArmed == 0) failed: invariant

I am running weka in my code. About 50% of the time it crashes the JVM, at the same function: calcMargins(). Here is the function description: http://fiji.sc/javadoc/weka/classifiers/bayes/net/MarginCalculator.html

What I do in my code is I set up few iterations of inference in the bayes network:

while(iteration < 10){
  -mc.calcMargins(network); //to clear up the evidences in the bayes network
  -mc.setEvidence(node, 0); //to set the new evidences
  -mc.getMargins(node); // to get the marginal prob. of a node
}

Usually the JVM crashes at the beginning of second iteration: the calcMargins() function with the above error message.

Detailed error log:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (safepoint.cpp:300), pid=23231, tid=140562312316672
# guarantee(PageArmed == 0) failed: invariant
#
# JRE version: 6.0_24-b24
# Java VM: OpenJDK 64-Bit Server VM (20.0-b12 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea6 1.11.3
# Distribution: Ubuntu 10.04.1 LTS, package 6b24-1.11.3-1ubuntu0.10.04.1
# If you would like to submit a bug report, please include
# instructions how to reproduce the bug and visit:
# https://bugs.launchpad.net/ubuntu/+source/openjdk-6/
#

--------------- T H R E A D ---------------

Current thread (0x000000000175b000): VMThread [stack: 0x00007fd736a1c000,0x00007fd736b1d000] [id=23246]

Stack: [0x00007fd736a1c000,0x00007fd736b1d000], sp=0x00007fd736b1ba00, free space=1022k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0x7cf214] VMError::report(outputStream*)+0x12b4
V [libjvm.so+0x7cf4cb] VMError::report_and_die()+0x16b
V [libjvm.so+0x3d1946] report_vm_error(char const*, int, char const*, char const*)+0x56
V [libjvm.so+0x705fef] SafepointSynchronize::begin()+0x40f
V [libjvm.so+0x7d5a08] VMThread::loop()+0x358
V [libjvm.so+0x7d5b12] VMThread::run()+0x72
V [libjvm.so+0x690992] java_start(Thread*)+0x112

--------------- P R O C E S S ---------------

Java Threads: ( => current thread )
  0x00007fd730006800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=23252, stack(0x00007fd736416000,0x00007fd736517000)]
  0x00007fd730004000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=23251, stack(0x00007fd736517000,0x00007fd736618000)]
  0x00007fd730001000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=23250, stack(0x00007fd736618000,0x00007fd736719000)]
  0x0000000001788800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=23249, stack(0x00007fd736719000,0x00007fd73681a000)]
  0x0000000001769000 JavaThread "Finalizer" daemon [_thread_blocked, id=23248, stack(0x00007fd73681a000,0x00007fd73691b000)]
  0x0000000001762000 JavaThread "Reference Handler" daemon [_thread_blocked, id=23247, stack(0x00007fd73691b000,0x00007fd736a1c000)]
  0x00000000016e1800 JavaThread "main" [_thread_in_Java, id=23232, stack(0x00007fd743051000,0x00007fd743152000)]

Other Threads:
=>0x000000000175b000 VMThread [stack: 0x00007fd736a1c000,0x00007fd736b1d000] [id=23246]
  0x00007fd730011800 WatcherThread [stack: 0x00007fd736315000,0x00007fd736416000] [id=23253]

VM state:synchronizing (normal execution)

VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[0x00000000016e0690] Safepoint_lock - owner thread: 0x000000000175b000
[0x00000000016e0710] Threads_lock - owner thread: 0x000000000175b000

Heap
 PSYoungGen total 7792640K, used 6437727K [0x0000000615560000, 0x00000007fffe0000, 0x0000000800000000)
  eden space 7789440K, 82% used [0x0000000615560000,0x000000079e117f28,0x00000007f0c40000)
  from space 3200K, 100% used [0x00000007ffcc0000,0x00000007fffe0000,0x00000007fffe0000)
  to space 3328K, 0% used [0x00000007ff960000,0x00000007ff960000,0x00000007ffca0000)
 PSOldGen total 13981056K, used 3581867K [0x0000000240000000, 0x0000000595560000, 0x0000000615560000)
  object space 13981056K, 25% used [0x0000000240000000,0x000000031a9eac98,0x0000000595560000)
 PSPermGen total 21248K, used 7715K [0x0000000235a00000, 0x0000000236ec0000, 0x0000000240000000)
  object space 21248K, 36% used [0x0000000235a00000,0x0000000236188e38,0x0000000236ec0000)

Code Cache [0x00007fd73d575000, 0x00007fd73d7e5000, 0x00007fd740575000)
 total_blobs=728 nmethods=508 adapters=174 free_code_cache=48323392 largest_free_block=30464

Dynamic libraries:
00400000-00409000 r-xp 00000000 08:21 192559 /usr/lib/jvm/java-6-openjdk/jre/bin/java
00608000-00609000 r--p 00008000 08:21 192559 /usr/lib/jvm/java-6-openjdk/jre/bin/java
00609000-0060a000 rw-p 00009000 08:21 192559 /usr/lib/jvm/java-6-openjdk/jre/bin/java
016da000-02e77000 rw-p 00000000 00:00 0 [heap]
VM Arguments:
jvm_args: -Xms20g -Xmx23g
java_command: ChowLiu/InferenceOnBN ChowLiu/updateConfiguration ../../MST/MI_D90_TREE 1000 1
Launcher Type: SUN_STANDARD

Environment Variables:
CLASSPATH=:/local/yjiang/HadoopLearn/:/local/yjiang/HadoopLearn/lib/jgrapht-jdk1.6.jar:/local/yjiang/HadoopLearn/lib/jgraphtSource.jar:/local/yjiang/HadoopLearn/lib/weka.jar:/local/yjiang/HadoopLearn/lib/jo$
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/yjiang/bin
LD_LIBRARY_PATH=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64
SHELL=/bin/bash

Signal Handlers:
SIGSEGV: [libjvm.so+0x7cff30], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x7cff30], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x68d2c0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x68d2c0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x68d2c0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x68d2c0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x68ca70], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x68f0d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x68f0d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x68f0d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x68f0d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004

vm_info: OpenJDK 64-Bit Server VM (20.0-b12) for linux-amd64 JRE (1.6.0_24-b24), built on Jun 28 2012 04:42:16 by "buildd" with gcc 4.4.3