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[Bug 1038586] [NEW] VM crashes when safepoint and synchronizing

To: openjdk@xxxxxxxxxxxxxxxxxxx
From: Karida <karidashell@xxxxxxxxx>
Date: Sun, 19 Aug 2012 07:26:31 -0000
Reply-to: Bug 1038586 <1038586@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
Public bug reported:

 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

** Affects: openjdk-6 (Ubuntu)
     Importance: Undecided
         Status: New

-- 
You received this bug notification because you are a member of OpenJDK,
which is subscribed to openjdk-6 in Ubuntu.
https://bugs.launchpad.net/bugs/1038586

Title:
  VM crashes when safepoint and synchronizing

Status in “openjdk-6” package in Ubuntu:
  New

Bug description:
   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

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Follow ups

[Bug 1038586] [NEW] VM crashes when safepoint and synchronizing
From: Karida, 2012-08-19
References

[Bug 1038586] [NEW] VM crashes when safepoint and synchronizing
From: Karida, 2012-08-19