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Bug 31 - consistent segfault on starting the 3D viewer
consistent segfault on starting the 3D viewer
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P2 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2009-02-26 12:58 CST by Mark Longair
Modified: 2009-04-20 18:44 CDT
2 users (show)

See Also:
Description Mark Longair 2009-02-26 12:58:31 CST 
I've just set up a new computer with Ubuntu Intrepid Ibex, and
the JVM crashes every time on starting up the 3D viewer, indicating
that the problematic frame is in libGL.so.1.2 - this is different
from the other 3D viewer crash bug report, so I've reported this as
a new one.  I hope that's OK.  I've included the hs_error*.log
below.

#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0xa629ac42, pid=6622, tid=2789604240
#
# Java VM: Java HotSpot(TM) Client VM (11.0-b15 mixed mode linux-x86)
# Problematic frame:
# C  [libGL.so.1+0x39c42]
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

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

Current thread (0x0923d800):  JavaThread "J3D-Renderer-1" [_thread_in_native, id=6831, stack(0xa640f000,0xa6460000)]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x00000010

Registers:
EAX=0x00000000, EBX=0xa62bbff4, ECX=0xa66926a0, EDX=0xa619c128
ESP=0xa645ec10, EBP=0xa645ec28, ESI=0x00000000, EDI=0x092b3180
EIP=0xa629ac42, CR2=0x00000010, EFLAGS=0x00010282

Top of Stack: (sp=0xa645ec10)
0xa645ec10:   092b3180 097b5088 00000000 a62bbff4
0xa645ec20:   00000000 092b3180 a645ec98 a6278e6c
0xa645ec30:   a619c128 00000000 00000000 00000000
0xa645ec40:   00008014 a617f000 9d70cf18 a617f0e8
0xa645ec50:   a617f000 00000000 0045ec68 0927cba8
0xa645ec60:   092db3e8 9d81d558 0003fff4 0923dd14
0xa645ec70:   00000025 00000000 0000000b 00000100
0xa645ec80:   00000000 a181d562 a6278d9b a617f000 

Instructions: (pc=0xa629ac42)
0xa629ac32:   e5 83 ec 18 8b 55 08 8b 42 14 8b 48 0c 8b 45 10
0xa629ac42:   8b 40 10 89 44 24 08 8b 45 0c 8b 40 10 89 44 24 

Stack: [0xa640f000,0xa6460000],  sp=0xa645ec10,  free space=319k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libGL.so.1+0x39c42]
C  [libGL.so.1+0x17e6c]  glXMakeCurrentReadSGI+0xdc
C  [libGL.so.1+0x1814b]  glXMakeCurrent+0x2b
C  [libj3dcore-ogl.so+0xdb5f]  Java_javax_media_j3d_NativePipeline_createNewContext+0x150
j  javax.media.j3d.NativePipeline.createNewContext(Ljavax/media/j3d/Canvas3D;JJJJZZZZ)J+0
j  javax.media.j3d.NativePipeline.createNewContext(Ljavax/media/j3d/Canvas3D;JLjavax/media/j3d/Drawable;JLjavax/media/j3d/Context;ZZZZ)Ljavax/media/j3d/Context;+25
j  javax.media.j3d.Canvas3D.createNewContext(JLjavax/media/j3d/Drawable;JLjavax/media/j3d/Context;ZZZZ)Ljavax/media/j3d/Context;+18
j  javax.media.j3d.Canvas3D.createNewContext(Ljavax/media/j3d/Context;Z)Ljavax/media/j3d/Context;+36
j  javax.media.j3d.Renderer.doWork(J)V+3721
j  javax.media.j3d.J3dThread.run()V+19
v  ~StubRoutines::call_stub
V  [libjvm.so+0x21b03d]
V  [libjvm.so+0x30f778]
V  [libjvm.so+0x21a950]
V  [libjvm.so+0x21a9dd]
V  [libjvm.so+0x28b045]
V  [libjvm.so+0x3a01bd]
V  [libjvm.so+0x3108a9]
C  [libpthread.so.0+0x650f]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  javax.media.j3d.NativePipeline.createNewContext(Ljavax/media/j3d/Canvas3D;JJJJZZZZ)J+0
j  javax.media.j3d.NativePipeline.createNewContext(Ljavax/media/j3d/Canvas3D;JLjavax/media/j3d/Drawable;JLjavax/media/j3d/Context;ZZZZ)Ljavax/media/j3d/Context;+25
j  javax.media.j3d.Canvas3D.createNewContext(JLjavax/media/j3d/Drawable;JLjavax/media/j3d/Context;ZZZZ)Ljavax/media/j3d/Context;+18
j  javax.media.j3d.Canvas3D.createNewContext(Ljavax/media/j3d/Context;Z)Ljavax/media/j3d/Context;+36
j  javax.media.j3d.Renderer.doWork(J)V+3721
j  javax.media.j3d.J3dThread.run()V+19
v  ~StubRoutines::call_stub

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

Java Threads: ( => current thread )
  0x09292800 JavaThread "J3D-InputDeviceScheduler-1" [_thread_blocked, id=6843, stack(0xa99b8000,0xa9a09000)]
  0x09336400 JavaThread "J3D-SoundSchedulerUpdateThread-1" [_thread_blocked, id=6842, stack(0xa9967000,0xa99b8000)]
  0x092bbc00 JavaThread "J3D-RenderStructureUpdateThread-1" [_thread_blocked, id=6841, stack(0xa9916000,0xa9967000)]
  0x092e1800 JavaThread "J3D-BehaviorScheduler-1" [_thread_blocked, id=6840, stack(0xa6200000,0xa6251000)]
  0x09288800 JavaThread "Thread-2" [_thread_blocked, id=6839, stack(0xa98c5000,0xa9916000)]
  0x09328c00 JavaThread "J3D-TransformStructureUpdateThread-1" [_thread_blocked, id=6838, stack(0xa9874000,0xa98c5000)]
  0x09327800 JavaThread "J3D-RenderingEnvironmentStructureUpdateThread-1" [_thread_blocked, id=6837, stack(0xa9823000,0xa9874000)]
  0x092c0400 JavaThread "J3D-SoundStructureUpdateThread-1" [_thread_blocked, id=6836, stack(0xa97d2000,0xa9823000)]
  0x09289000 JavaThread "J3D-GeometryStructureUpdateThread-1" [_thread_blocked, id=6835, stack(0xa9726000,0xa9777000)]
  0x09737800 JavaThread "J3D-BehaviorStructureUpdateThread-1" [_thread_blocked, id=6834, stack(0xa96d5000,0xa9726000)]
  0x09285c00 JavaThread "pool-1-thread-1" [_thread_blocked, id=6833, stack(0xaa2f3000,0xaa344000)]
  0xa614fc00 JavaThread "3D-V-IMP-updater" daemon [_thread_blocked, id=6832, stack(0xaa2a2000,0xaa2f3000)]
=>0x0923d800 JavaThread "J3D-Renderer-1" [_thread_in_native, id=6831, stack(0xa640f000,0xa6460000)]
  0x0923d400 JavaThread "J3D-MasterControl-1" [_thread_blocked, id=6830, stack(0xa63be000,0xa640f000)]
  0x096eb800 JavaThread "J3D-NotificationThread" [_thread_blocked, id=6829, stack(0xa636d000,0xa63be000)]
  0x093f1000 JavaThread "J3D-TimerThread" [_thread_blocked, id=6828, stack(0xa631c000,0xa636d000)]
  0x093ed400 JavaThread "J3D-RenderingAttributesStructureUpdateThread" [_thread_blocked, id=6827, stack(0xa62cb000,0xa631c000)]
  0x092d1800 JavaThread "TimerQueue" daemon [_thread_blocked, id=6825, stack(0xa5ee1000,0xa5f32000)]
  0xa5a9e400 JavaThread "SliceSelector" [_thread_blocked, id=6823, stack(0xa60a8000,0xa60f9000)]
  0xa5ab6400 JavaThread "DestroyJavaVM" [_thread_blocked, id=6622, stack(0xbf9e0000,0xbfa30000)]
  0xa5a7b800 JavaThread "SocketListener" [_thread_in_native, id=6638, stack(0xa5fd4000,0xa6025000)]
  0x096fcc00 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=6636, stack(0xa5f83000,0xa5fd4000)]
  0x096fa000 JavaThread "AWT-Shutdown" [_thread_blocked, id=6635, stack(0xa5f32000,0xa5f83000)]
  0x09555c00 JavaThread "AWT-XAWT" daemon [_thread_in_native, id=6633, stack(0xa5e90000,0xa5ee1000)]
  0x0952cc00 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=6632, stack(0xa5e17000,0xa5e68000)]
  0x09283800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=6630, stack(0xa5700000,0xa5751000)]
  0x09281c00 JavaThread "CompilerThread0" daemon [_thread_blocked, id=6629, stack(0xa5556000,0xa55d7000)]
  0x09280000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=6628, stack(0xa5505000,0xa5556000)]
  0x0926f000 JavaThread "Finalizer" daemon [_thread_blocked, id=6627, stack(0xa5475000,0xa54c6000)]
  0x0926a800 JavaThread "Reference Handler" daemon [_thread_blocked, id=6626, stack(0xa5424000,0xa5475000)]

Other Threads:
  0x09267000 VMThread [stack: 0xa53a3000,0xa5424000] [id=6625]
  0x0928d800 WatcherThread [stack: 0xa5751000,0xa57d2000] [id=6631]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
 def new generation   total 1536K, used 1019K [0x423f0000, 0x42590000, 0x49830000)
  eden space 1408K,  66% used [0x423f0000, 0x424daf50, 0x42550000)
  from space 128K,  62% used [0x42550000, 0x42563ea8, 0x42570000)
  to   space 128K,   0% used [0x42570000, 0x42570000, 0x42590000)
 tenured generation   total 18984K, used 13449K [0x49830000, 0x4aaba000, 0xa0bf0000)
   the space 18984K,  70% used [0x49830000, 0x4a552600, 0x4a552600, 0x4aaba000)
 compacting perm gen  total 15616K, used 15400K [0xa0bf0000, 0xa1b30000, 0xa4bf0000)
   the space 15616K,  98% used [0xa0bf0000, 0xa1afa360, 0xa1afa400, 0xa1b30000)
No shared spaces configured.

Dynamic libraries:
06000000-0642a000 r-xp 00000000 08:05 3483089    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/client/libjvm.so
0642a000-06444000 rw-p 0042a000 08:05 3483089    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/client/libjvm.so
06444000-06864000 rw-p 06444000 00:00 0 
08048000-08056000 r-xp 00000000 08:05 3137790    /home/mark/fiji/fiji
08056000-08057000 r--p 0000d000 08:05 3137790    /home/mark/fiji/fiji
08057000-08058000 rw-p 0000e000 08:05 3137790    /home/mark/fiji/fiji
08058000-0805a000 rw-p 08058000 00:00 0 
09203000-09ac1000 rw-p 09203000 00:00 0          [heap]
40000000-4001a000 r-xp 00000000 08:05 4702220    /lib/ld-2.8.90.so
4001a000-4001b000 r-xp 4001a000 00:00 0          [vdso]
4001b000-4001c000 r--p 0001a000 08:05 4702220    /lib/ld-2.8.90.so
4001c000-4001d000 rw-p 0001b000 08:05 4702220    /lib/ld-2.8.90.so
4001d000-4001f000 rw-p 4001d000 00:00 0 
4001f000-40020000 r--p 4001f000 00:00 0 
40020000-40021000 rwxp 40020000 00:00 0 
40021000-40027000 r-xp 00000000 08:05 3483140    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/native_threads/libhpi.so
40027000-40028000 rw-p 00006000 08:05 3483140    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/native_threads/libhpi.so
40028000-4002f000 r--s 00000000 08:05 5194753    /usr/lib/gconv/gconv-modules.cache
4002f000-40031000 r-xp 00000000 08:05 4719427    /lib/tls/i686/cmov/libdl-2.8.90.so
40031000-40032000 r--p 00001000 08:05 4719427    /lib/tls/i686/cmov/libdl-2.8.90.so
40032000-40033000 rw-p 00002000 08:05 4719427    /lib/tls/i686/cmov/libdl-2.8.90.so
40033000-40116000 r-xp 00000000 08:05 5177686    /usr/lib/libstdc++.so.6.0.10
40116000-4011a000 r--p 000e3000 08:05 5177686    /usr/lib/libstdc++.so.6.0.10
4011a000-4011b000 rw-p 000e7000 08:05 5177686    /usr/lib/libstdc++.so.6.0.10
4011b000-40121000 rw-p 4011b000 00:00 0 
40121000-40145000 r-xp 00000000 08:05 4719428    /lib/tls/i686/cmov/libm-2.8.90.so
40145000-40146000 r--p 00023000 08:05 4719428    /lib/tls/i686/cmov/libm-2.8.90.so
40146000-40147000 rw-p 00024000 08:05 4719428    /lib/tls/i686/cmov/libm-2.8.90.so
40147000-40154000 r-xp 00000000 08:05 4702229    /lib/libgcc_s.so.1
40154000-40155000 r--p 0000c000 08:05 4702229    /lib/libgcc_s.so.1
40155000-40156000 rw-p 0000d000 08:05 4702229    /lib/libgcc_s.so.1
40156000-40157000 rw-p 40156000 00:00 0 
40157000-402af000 r-xp 00000000 08:05 4719424    /lib/tls/i686/cmov/libc-2.8.90.so
402af000-402b1000 r--p 00158000 08:05 4719424    /lib/tls/i686/cmov/libc-2.8.90.so
402b1000-402b2000 rw-p 0015a000 08:05 4719424    /lib/tls/i686/cmov/libc-2.8.90.so
402b2000-402b6000 rw-p 402b2000 00:00 0 
402b6000-402cb000 r-xp 00000000 08:05 4719438    /lib/tls/i686/cmov/libpthread-2.8.90.so
402cb000-402cc000 r--p 00014000 08:05 4719438    /lib/tls/i686/cmov/libpthread-2.8.90.so
402cc000-402cd000 rw-p 00015000 08:05 4719438    /lib/tls/i686/cmov/libpthread-2.8.90.so
402cd000-402cf000 rw-p 402cd000 00:00 0 
402cf000-402d6000 r-xp 00000000 08:05 4719440    /lib/tls/i686/cmov/librt-2.8.90.so
402d6000-402d7000 r--p 00007000 08:05 4719440    /lib/tls/i686/cmov/librt-2.8.90.so
402d7000-402d8000 rw-p 00008000 08:05 4719440    /lib/tls/i686/cmov/librt-2.8.90.so
402d8000-402e0000 rw-s 00000000 08:05 3047476    /tmp/hsperfdata_mark/6622
402e0000-402e2000 r--s 0004e000 08:05 3483056    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/ext/vecmath.jar
402e2000-402e3000 r--s 00002000 08:05 8323073    /home/mark/fiji/misc/Fiji.jar
402e3000-402e7000 r-xp 00000000 08:05 5178978    /usr/lib/libXtst.so.6.1.0
402e7000-402e8000 rw-p 00003000 08:05 5178978    /usr/lib/libXtst.so.6.1.0
402e8000-402fd000 r-xp 00000000 08:05 4719430    /lib/tls/i686/cmov/libnsl-2.8.90.so
402fd000-402fe000 r--p 00014000 08:05 4719430    /lib/tls/i686/cmov/libnsl-2.8.90.so
402fe000-402ff000 rw-p 00015000 08:05 4719430    /lib/tls/i686/cmov/libnsl-2.8.90.so
402ff000-40301000 rw-p 402ff000 00:00 0 
40301000-40308000 r-xp 00000000 08:05 4719431    /lib/tls/i686/cmov/libnss_compat-2.8.90.so
40308000-40309000 r--p 00006000 08:05 4719431    /lib/tls/i686/cmov/libnss_compat-2.8.90.so
40309000-4030a000 rw-p 00007000 08:05 4719431    /lib/tls/i686/cmov/libnss_compat-2.8.90.so
4030a000-40313000 r-xp 00000000 08:05 4719435    /lib/tls/i686/cmov/libnss_nis-2.8.90.so
40313000-40314000 r--p 00008000 08:05 4719435    /lib/tls/i686/cmov/libnss_nis-2.8.90.so
40314000-40315000 rw-p 00009000 08:05 4719435    /lib/tls/i686/cmov/libnss_nis-2.8.90.so
40315000-4031f000 r-xp 00000000 08:05 4719433    /lib/tls/i686/cmov/libnss_files-2.8.90.so
4031f000-40320000 r--p 00009000 08:05 4719433    /lib/tls/i686/cmov/libnss_files-2.8.90.so
40320000-40321000 rw-p 0000a000 08:05 4719433    /lib/tls/i686/cmov/libnss_files-2.8.90.so
40321000-4032c000 r-xp 00000000 08:05 3483135    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libverify.so
4032c000-4032d000 rw-p 0000b000 08:05 3483135    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libverify.so
4032d000-40350000 r-xp 00000000 08:05 3483112    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libjava.so
40350000-40352000 rw-p 00023000 08:05 3483112    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libjava.so
40352000-40361000 r-xp 00000000 08:05 3483136    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libzip.so
40361000-40363000 rw-p 0000e000 08:05 3483136    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libzip.so
40363000-404fb000 rwxp 40363000 00:00 0 
404fb000-42363000 rwxp 404fb000 00:00 0 
42363000-4236a000 rwxp 42363000 00:00 0 
4236a000-423e3000 rwxp 4236a000 00:00 0 
423e3000-423ef000 r--s 002c7000 08:05 3483050    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/ext/j3dcore.jar
423ef000-423f0000 r--s 00001000 08:05 8225       /home/mark/fiji/plugins/AnalyzeSkeleton_.jar
423f0000-42590000 rwxp 423f0000 00:00 0 
42590000-49830000 rwxp 42590000 00:00 0 
49830000-4aaba000 rwxp 49830000 00:00 0 
4aaba000-a0bf0000 rwxp 4aaba000 00:00 0 
a0bf0000-a1b30000 rwxp a0bf0000 00:00 0 
a1b30000-a4bf0000 rwxp a1b30000 00:00 0 
a4bf0000-a4bf1000 rwxp a4bf0000 00:00 0 
a4bf1000-a4c2a000 rwxp a4bf1000 00:00 0 
a4c2a000-a4c34000 rwxp a4c2a000 00:00 0 
a4c34000-a4ee4000 rwxp a4c34000 00:00 0 
a4ee4000-a4eec000 rwxp a4ee4000 00:00 0 
a4eec000-a4f04000 rwxp a4eec000 00:00 0 
a4f04000-a4f0f000 rwxp a4f04000 00:00 0 
a4f0f000-a51bf000 rwxp a4f0f000 00:00 0 
a51bf000-a51c7000 rwxp a51bf000 00:00 0 
a51c7000-a51e0000 rwxp a51c7000 00:00 0 
a51e0000-a5370000 r--s 02eed000 08:05 3483229    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/rt.jar
a5370000-a53a3000 rw-p a5370000 00:00 0 
a53a3000-a53a4000 ---p a53a3000 00:00 0 
a53a4000-a5424000 rwxp a53a4000 00:00 0 
a5424000-a5427000 ---p a5424000 00:00 0 
a5427000-a5475000 rwxp a5427000 00:00 0 
a5475000-a5478000 ---p a5475000 00:00 0 
a5478000-a54c6000 rwxp a5478000 00:00 0 
a54c6000-a5505000 r--p 00000000 08:05 5210982    /usr/lib/locale/en_GB.utf8/LC_CTYPE
a5505000-a5508000 ---p a5505000 00:00 0 
a5508000-a5556000 rwxp a5508000 00:00 0 
a5556000-a5559000 ---p a5556000 00:00 0 
a5559000-a55d7000 rwxp a5559000 00:00 0 
a55d7000-a55e5000 r--s 00192000 08:05 3483051    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/ext/j3dutils.jar
a55e5000-a55ec000 r--s 00116000 08:05 3137791    /home/mark/fiji/ij.jar
a55ec000-a55ee000 r--s 00015000 08:05 8224       /home/mark/fiji/plugins/Stitching_.jar
a55ee000-a55f2000 r--s 00049000 08:05 8193       /home/mark/fiji/plugins/LSM_Toolbox.jar
a55f2000-a55f4000 r--s 0000e000 08:05 8198       /home/mark/fiji/plugins/ij-ImageIO_.jar
a55f4000-a55f5000 r--s 00006000 08:05 8199       /home/mark/fiji/plugins/Jython_Interpreter.jar
a55f5000-a55f6000 r--s 00009000 08:05 8207       /home/mark/fiji/plugins/CLI_.jar
a55f6000-a55f7000 r--s 00011000 08:05 8214       /home/mark/fiji/plugins/Color_Inspector_3D.jar
a55f7000-a55f8000 r--s 00005000 08:05 8209       /home/mark/fiji/plugins/lens_correction.jar
a55f8000-a55f9000 r--s 00002000 08:05 8221       /home/mark/fiji/plugins/Fiji_Updater.jar
a55f9000-a55fa000 r--s 00001000 08:05 8226       /home/mark/fiji/plugins/Skeletonize3D_.jar
a55fa000-a55fb000 r--s 00005000 08:05 8205       /home/mark/fiji/plugins/registration_3d.jar
a55fb000-a55fc000 r--s 00006000 08:05 8202       /home/mark/fiji/plugins/BeanShell_Interpreter.jar
a55fc000-a55fe000 r-xp 00000000 08:05 5178935    /usr/lib/libXau.so.6.0.0
a55fe000-a55ff000 rw-p 00001000 08:05 5178935    /usr/lib/libXau.so.6.0.0
a55ff000-a5600000 r--s 00004000 08:05 8222       /home/mark/fiji/plugins/Multi_Thresholder.jar
a5600000-a56ff000 rw-p a5600000 00:00 0 
a56ff000-a5700000 ---p a56ff000 00:00 0 
a5700000-a5703000 ---p a5700000 00:00 0 
a5703000-a5751000 rwxp a5703000 00:00 0 
a5751000-a5752000 ---p a5751000 00:00 0 
a5752000-a57d2000 rwxp a5752000 00:00 0 
a57d2000-a584d000 r-xp 00000000 08:05 3483097    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libawt.so
a584d000-a5854000 rw-p 0007b000 08:05 3483097    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libawt.so
a5854000-a5878000 rw-p a5854000 00:00 0 
a5878000-a58bb000 r-xp 00000000 08:05 3483146    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/xawt/libmawt.so
a58bb000-a58bd000 rw-p 00042000 08:05 3483146    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/xawt/libmawt.so
a58bd000-a58be000 rw-p a58bd000 00:00 0 
a58be000-a58cb000 r-xp 00000000 08:05 5178950    /usr/lib/libXext.so.6.4.0
a58cb000-a58cd000 rw-p 0000c000 08:05 5178950    /usr/lib/libXext.so.6.4.0
a58cd000-a59b8000 r-xp 00000000 08:05 5178117    /usr/lib/libX11.so.6.2.0
a59b8000-a59b9000 r--p 000ea000 08:05 5178117    /usr/lib/libX11.so.6.2.0
a59b9000-a59bb000 rw-p 000eb000 08:05 5178117    /usr/lib/libX11.so.6.2.0
a59bb000-a59bc000 rw-p a59bb000 00:00 0 
a59bc000-a59c4000 r-xp 00000000 08:05 5178958    /usr/lib/libXi.so.6.0.0
a59c4000-a59c5000 r--p 00007000 08:05 5178958    /usr/lib/libXi.so.6.0.0
a59c5000-a59c6000 rw-p 00008000 08:05 5178958    /usr/lib/libXi.so.6.0.0
a59c6000-a59c7000 r-xp 00000000 08:05 5179877    /usr/lib/libxcb-xlib.so.0.0.0
a59c7000-a59c8000 r--p 00000000 08:05 5179877    /usr/lib/libxcb-xlib.so.0.0.0
a59c8000-a59c9000 rw-p 00001000 08:05 5179877    /usr/lib/libxcb-xlib.so.0.0.0
a59c9000-a59e0000 r-xp 00000000 08:05 5179879    /usr/lib/libxcb.so.1.0.0
a59e0000-a59e1000 r--p 00016000 08:05 5179879    /usr/lib/libxcb.so.1.0.0
a59e1000-a59e2000 rw-p 00017000 08:05 5179879    /usr/lib/libxcb.so.1.0.0
a59e2000-a59e6000 r-xp 00000000 08:05 5178946    /usr/lib/libXdmcp.so.6.0.0
a59e6000-a59e7000 rw-p 00003000 08:05 5178946    /usr/lib/libXdmcp.so.6.0.0
a59e7000-a59f6000 r--s 0013a000 08:05 8194       /home/mark/fiji/plugins/VIB_.jar
a59f6000-a59f8000 r--s 00001000 08:05 8204       /home/mark/fiji/plugins/register_virtual_stack_slices.jar
a59f8000-a59f9000 r--s 00001000 08:05 8212       /home/mark/fiji/plugins/Analyze_Reader_Writer.jar
a59f9000-a59fa000 r--s 0001c000 08:05 8218       /home/mark/fiji/plugins/View5D_.jar
a59fa000-a59fc000 r--s 00007000 08:05 8210       /home/mark/fiji/plugins/SplineDeformationGenerator_.jar
a59fc000-a59fd000 r--s 00006000 08:05 8208       /home/mark/fiji/plugins/Javascript_.jar
a59fd000-a59fe000 r--s 00017000 08:05 8203       /home/mark/fiji/plugins/bUnwarpJ_.jar
a59fe000-a59ff000 r--s 00000000 08:05 8220       /home/mark/fiji/plugins/IJ_Robot.jar
a59ff000-a5a00000 r--s 00001000 08:05 8213       /home/mark/fiji/plugins/Color_Histogram.jar
a5a00000-a5b00000 rw-p a5a00000 00:00 0 
a5b00000-a5b01000 r--s 00006000 08:05 8201       /home/mark/fiji/plugins/JRuby_Interpreter.jar
a5b01000-a5b09000 r--s 000d4000 08:05 8196       /home/mark/fiji/plugins/TrakEM2_.jar
a5b09000-a5b0b000 r--s 00017000 08:05 8215       /home/mark/fiji/plugins/Image_5D.jar
a5b0b000-a5b0c000 r--s 00002000 08:05 8216       /home/mark/fiji/plugins/M_I_P.jar
a5b0c000-a5b0e000 r--s 0000f000 08:05 8195       /home/mark/fiji/plugins/mpicbg_.jar
a5b0e000-a5b0f000 r--s 00000000 08:05 8223       /home/mark/fiji/plugins/Daltonize_.jar
a5b0f000-a5b10000 r--s 00011000 08:05 8217       /home/mark/fiji/plugins/Interactive_3D_Surface_Plot.jar
a5b10000-a5b11000 r--s 00012000 08:05 8227       /home/mark/fiji/plugins/TurboReg_.jar
a5b11000-a5b13000 r--s 0000c000 08:05 8211       /home/mark/fiji/plugins/level_sets.jar
a5b13000-a5b15000 r--s 00018000 08:05 8206       /home/mark/fiji/plugins/IO_.jar
a5b15000-a5b16000 r--s 0000b000 08:05 8228       /home/mark/fiji/plugins/TransformJ_.jar
a5b16000-a5b78000 r--s 007f1000 08:05 8197       /home/mark/fiji/plugins/loci_tools.jar
a5b78000-a5b7a000 r--s 0000c000 08:05 8219       /home/mark/fiji/plugins/Volume_Viewer.jar
a5b7a000-a5b7b000 r--s 00007000 08:05 8200       /home/mark/fiji/plugins/Clojure_Interpreter.jar
a5b7b000-a5b8a000 r--s 00139000 08:05 3358933    /home/mark/fiji/jars/edu_mines_jtk.jar
a5b8a000-a5b91000 r--s 000b2000 08:05 3358942    /home/mark/fiji/jars/js.jar
a5b91000-a5b92000 r--s 0000b000 08:05 3358945    /home/mark/fiji/jars/jzlib-1.0.7.jar
a5b92000-a5b94000 r--s 0000f000 08:05 3358932    /home/mark/fiji/jars/clibwrapper_jiio.jar
a5b94000-a5b9f000 r--s 0015c000 08:05 3358940    /home/mark/fiji/jars/jpedalSTD.jar
a5b9f000-a5ba6000 r--s 00110000 08:05 3483228    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/resources.jar
a5ba6000-a5bb9000 r--s 0016d000 08:05 3358937    /home/mark/fiji/jars/jai_core.jar
a5bb9000-a5bba000 r--s 00005000 08:05 7823366    /home/mark/fiji/jars/fiji-scripting.jar
a5bba000-a5bc8000 r--s 00115000 08:05 3358935    /home/mark/fiji/jars/itext-1.3.jar
a5bc8000-a5bca000 r--s 00007000 08:05 3358927    /home/mark/fiji/jars/Jama-1.0.2.jar
a5bca000-a5bd1000 r--s 0006a000 08:05 7823362    /home/mark/fiji/jars/clojure.jar
a5bd1000-a5bd4000 r--s 00031000 08:05 3358936    /home/mark/fiji/jars/jai_codec.jar
a5bd4000-a5bf0000 r--s 001be000 08:05 3358944    /home/mark/fiji/jars/jython2.2.1/jython.jar
a5bf0000-a5bf5000 r--s 00040000 08:05 3358931    /home/mark/fiji/jars/bsh-2.0b4.jar
a5bf5000-a5c42000 r--s 003e1000 08:05 3358941    /home/mark/fiji/jars/jruby.jar
a5c42000-a5c47000 r--s 00070000 08:05 7823364    /home/mark/fiji/jars/jacl.jar
a5c47000-a5cd2000 r--s 006d0000 08:05 7823365    /home/mark/fiji/jars/batik.jar
a5cd2000-a5ce6000 r--s 00131000 08:05 3358930    /home/mark/fiji/jars/ant.jar
a5ce6000-a5ce9000 r--s 0002d000 08:05 3358934    /home/mark/fiji/jars/imagescience.jar
a5ce9000-a5cf8000 r--s 000ef000 08:05 7823361    /home/mark/fiji/jars/javac.jar
a5cf8000-a5d07000 r--s 0012d000 08:05 3358939    /home/mark/fiji/jars/jfreechart-1.0.9.jar
a5d07000-a5d0c000 r--s 00065000 08:05 3358946    /home/mark/fiji/jars/postgresql-8.2-506.jdbc3.jar
a5d0c000-a5d6e000 r--s 007f1000 08:05 7823363    /home/mark/fiji/jars/loci_tools.jar
a5d6e000-a5d74000 r--s 00046000 08:05 3358938    /home/mark/fiji/jars/jcommon-1.0.12.jar
a5d74000-a5d75000 r--s 00002000 08:05 3358928    /home/mark/fiji/jars/ant-launcher.jar
a5d75000-a5d88000 r-xp 00000000 08:05 3483127    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libnet.so
a5d88000-a5d89000 rw-p 00013000 08:05 3483127    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libnet.so
a5d89000-a5e08000 r-xp 00000000 08:05 3483102    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libfontmanager.so
a5e08000-a5e12000 rw-p 0007e000 08:05 3483102    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libfontmanager.so
a5e12000-a5e17000 rw-p a5e12000 00:00 0 
a5e17000-a5e1a000 ---p a5e17000 00:00 0 
a5e1a000-a5e68000 rwxp a5e1a000 00:00 0 
a5e68000-a5e6f000 r-xp 00000000 08:05 3483128    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libnio.so
a5e6f000-a5e70000 rw-p 00006000 08:05 3483128    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libnio.so
a5e70000-a5e71000 r-xp 00000000 08:05 3483117    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libjawt.so
a5e71000-a5e72000 rw-p 00000000 08:05 3483117    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libjawt.so
a5e72000-a5e76000 r-xp 00000000 08:05 5178986    /usr/lib/libXxf86vm.so.1.0.0
a5e76000-a5e77000 r--p 00003000 08:05 5178986    /usr/lib/libXxf86vm.so.1.0.0
a5e77000-a5e78000 rw-p 00004000 08:05 5178986    /usr/lib/libXxf86vm.so.1.0.0
a5e78000-a5e80000 r-xp 00000000 08:05 5178942    /usr/lib/libXcursor.so.1.0.2
a5e80000-a5e81000 rw-p 00007000 08:05 5178942    /usr/lib/libXcursor.so.1.0.2
a5e81000-a5e89000 r-xp 00000000 08:05 5178972    /usr/lib/libXrender.so.1.3.0
a5e89000-a5e8a000 r--p 00007000 08:05 5178972    /usr/lib/libXrender.so.1.3.0
a5e8a000-a5e8b000 rw-p 00008000 08:05 5178972    /usr/lib/libXrender.so.1.3.0
a5e8b000-a5e8f000 r-xp 00000000 08:05 5178952    /usr/lib/libXfixes.so.3.1.0
a5e8f000-a5e90000 rw-p 00003000 08:05 5178952    /usr/lib/libXfixes.so.3.1.0
a5e90000-a5e93000 ---p a5e90000 00:00 0 
a5e93000-a5ee1000 rwxp a5e93000 00:00 0 
a5ee1000-a5ee4000 ---p a5ee1000 00:00 0 
a5ee4000-a5f32000 rwxp a5ee4000 00:00 0 
a5f32000-a5f35000 ---p a5f32000 00:00 0 
a5f35000-a5f83000 rwxp a5f35000 00:00 0 
a5f83000-a5f86000 ---p a5f83000 00:00 0 
a5f86000-a5fd4000 rwxp a5f86000 00:00 0 
a5fd4000-a5fd7000 ---p a5fd4000 00:00 0 
a5fd7000-a6025000 rwxp a5fd7000 00:00 0 
a6025000-a607d000 rw-s 00000000 00:09 1212436    /SYSV00000000 (deleted)
a607d000-a609f000 r-xp 00000000 08:05 3483110    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libj3dcore-ogl.so
a609f000-a60a0000 rw-p 00021000 08:05 3483110    /home/mark/fiji/java/linux/jdk1.6.0_10/jre/lib/i386/libj3dcore-ogl.so
a60a0000-a60a2000 r-xp 00000000 08:05 5178944    /usr/lib/libXdamage.so.1.1.0
a60a2000-a60a3000 rw-p 00001000 08:05 5178944    /usr/lib/libXdamage.so.1.1.0
a60a3000-a60a5000 rw-s f891c000 00:0e 16234      /dev/dri/card0
a60a5000-a60a8000 r--s 00000000 08:05 7160597    /var/cache/fontconfig/de9486f0b47a4d768a594cb4198cb1c6-x86.cache-2
a60a8000-a60ab000 ---p a60a8000 00:00 0 
a60ab000-a60f9000 rwxp a60ab000 00:00 0 
a60f9000-a60ff000 r--s 00000000 08:05 7160549    /var/cache/fontconfig/089dead882dea3570ffc31a9898cfb69-x86.cache-2
a60ff000-a6100000 r--s 00000000 08:05 7160598    /var/cache/fontconfig/4794a0821666d79190d59a36cb4f44b5-x86.cache-2
a6100000-a61f7000 rw-p a6100000 00:00 0 
a61f7000-a6200000 ---p a61f7000 00:00 0 
a6200000-a6203000 ---p a6200000 00:00 0 
a6203000-a6251000 rwxp a6203000 00:00 0 
a6251000-a625f000 r--s 00000000 08:05 7160698    /var/cache/fontconfig/865f88548240fee46819705c6468c165-x86.cache-2
a625f000-a6261000 r--s 00000000 08:05 7160702    /var/cache/fontconfig/2c5ba8142dffc8bf0377700342b8ca1a-x86.cache-2
a6261000-a62b7000 r-xp 00000000 08:05 5178883    /usr/lib/libGL.so.1.2
a62b7000-a62bc000 r--p 00055000 08:05 5178883    /usr/lib/libGL.so.1.2
a62bc000-a62c1000 rwxp 0005a000 08:05 5178883    /usr/lib/libGL.so.1.2
a62c1000-a62c2000 rwxp a62c1000 00:00 0 
a62c2000-a62c9000 r-xp 00000000 08:05 5179146    /usr/lib/libdrm.so.2.3.1
a62c9000-a62ca000 r--p 00006000 08:05 5179146    /usr/lib/libdrm.so.2.3.1
a62ca000-a62cb000 rw-p 00007000 08:05 5179146    /usr/lib/libdrm.so.2.3.1
a62cb000-a62ce000 ---p a62cb000 00:00 0 
a62ce000-a631c000 rwxp a62ce000 00:00 0 
a631c000-a631f000 ---p a631c000 00:00 0 
a631f000-a636d000 rwxp a631f000 00:00 0 
a636d000-a6370000 ---p a636d000 00:00 0 
a6370000-a63be000 rwxp a6370000 00:00 0 
a63be000-a63c1000 ---p a63be000 00:00 0 
a63c1000-a640f000 rwxp a63c1000 00:00 0 
a640f000-a6412000 ---p a640f000 00:00 0 
a6412000-a6460000 rwxp a6412000 00:00 0 
a6460000-a668d000 r-xp 00000000 08:05 5195361    /usr/lib/dri/i915_dri.so
a668d000-a6694000 r--p 0022c000 08:05 5195361    /usr/lib/dri/i915_dri.so
a6694000-a66a3000 rw-p 00233000 08:05 5195361    /usr/lib/dri/i915_dri.so
a66a3000-a66ae000 rw-p a66a3000 00:00 0 
a66ae000-a66d2000 r-xp 00000000 08:05 5179188    /usr/lib/libexpat.so.1.5.2
a66d2000-a66d4000 r--p 00023000 08:05 5179188    /usr/lib/libexpat.so.1.5.2
a66d4000-a66d5000 rw-p 00025000 08:05 5179188    /usr/lib/libexpat.so.1.5.2
a66d5000-a6ad5000 rw-s d0800000 00:0e 16234      /dev/dri/card0
a6ad5000-a6ed5000 rw-s d0800000 00:0e 16234      /dev/dri/card0
a6ed5000-a72d5000 rw-s d1800000 00:0e 16234      /dev/dri/card0
a72d5000-a76d5000 rw-s d1c00000 00:0e 16234      /dev/dri/card0
a76d5000-a96d5000 rw-s d2000000 00:0e 16234      /dev/dri/card0
a96d5000-a96d8000 ---p a96d5000 00:00 0 
a96d8000-a9726000 rwxp a96d8000 00:00 0 
a9726000-a9729000 ---p a9726000 00:00 0 
a9729000-a9777000 rwxp a9729000 00:00 0 
a978e000-a979b000 r--s 00000000 08:05 7160826    /var/cache/fontconfig/e13b20fdb08344e0e664864cc2ede53d-x86.cache-2
a979b000-a97a2000 r--s 00000000 08:05 7160596    /var/cache/fontconfig/d52a8644073d54c13679302ca1180695-x86.cache-2
a97a2000-a97ad000 r--s 00000000 08:05 7160599    /var/cache/fontconfig/0f34bcd4b6ee430af32735b75db7f02b-x86.cache-2
a97ad000-a97b5000 r--s 00000000 08:05 7160600    /var/cache/fontconfig/e3de0de479f42330eadf588a55fb5bf4-x86.cache-2
a97b5000-a97b7000 r--s 00000000 08:05 7160601    /var/cache/fontconfig/da1bd5ca8443ffe22927a23ce431d198-x86.cache-2
a97b7000-a97ba000 r--s 00000000 08:05 7160602    /var/cache/fontconfig/de156ccd2eddbdc19d37a45b8b2aac9c-x86.cache-2
a97ba000-a97bd000 r--s 00000000 08:05 7160603    /var/cache/fontconfig/6d41288fd70b0be22e8c3a91e032eec0-x86.cache-2
a97bd000-a97c0000 r--s 00000000 08:05 7160604    /var/cache/fontconfig/a755afe4a08bf5b97852ceb7400b47bc-x86.cache-2
a97c0000-a97c2000 r--s 00000000 08:05 7160605    /var/cache/fontconfig/646addb8444faa74ee138aa00ab0b6a0-x86.cache-2
a97c2000-a97c3000 r--s 00000000 08:05 7160606    /var/cache/fontconfig/4c73fe0c47614734b17d736dbde7580a-x86.cache-2
a97c3000-a97c4000 r--s 00000000 08:05 7160608    /var/cache/fontconfig/a2ab74764b07279e7c36ddb1d302cf26-x86.cache-2
a97c4000-a97c5000 r--s 00000000 08:05 7160609    /var/cache/fontconfig/fd9505950c048a77dc4b710eb6a628ed-x86.cache-2
a97c5000-a97c8000 r--s 00000000 08:05 7160611    /var/cache/fontconfig/e383d7ea5fbe662a33d9b44caf393297-x86.cache-2
a97c8000-a97c9000 r--s 00000000 08:05 7160621    /var/cache/fontconfig/99e8ed0e538f840c565b6ed5dad60d56-x86.cache-2
a97c9000-a97cf000 r--s 00000000 08:05 7160627    /var/cache/fontconfig/945677eb7aeaf62f1d50efc3fb3ec7d8-x86.cache-2
a97cf000-a97d2000 r--s 00000000 08:05 7160927    /var/cache/fontconfig/603b2eb47209ddb3c5269b217a306167-x86.cache-2
a97d2000-a97d5000 ---p a97d2000 00:00 0 
a97d5000-a9823000 rwxp a97d5000 00:00 0 
a9823000-a9826000 ---p a9823000 00:00 0 
a9826000-a9874000 rwxp a9826000 00:00 0 
a9874000-a9877000 ---p a9874000 00:00 0 
a9877000-a98c5000 rwxp a9877000 00:00 0 
a98c5000-a98c8000 ---p a98c5000 00:00 0 
a98c8000-a9916000 rwxp a98c8000 00:00 0 
a9916000-a9919000 ---p a9916000 00:00 0 
a9919000-a9967000 rwxp a9919000 00:00 0 
a9967000-a996a000 ---p a9967000 00:00 0 
a996a000-a99b8000 rwxp a996a000 00:00 0 
a99b8000-a99bb000 ---p a99b8000 00:00 0 
a99bb000-a9a09000 rwxp a99bb000 00:00 0 
a9a09000-a9dff000 rw-p a9a09000 00:00 0 
a9e00000-a9ef9000 rw-p a9e00000 00:00 0 
a9ef9000-a9f00000 ---p a9ef9000 00:00 0 
aa000000-aa0f2000 rw-p aa000000 00:00 0 
aa245000-aa2a2000 rw-p aa245000 00:00 0 
aa2a2000-aa2a5000 ---p aa2a2000 00:00 0 
aa2a5000-aa2f3000 rwxp aa2a5000 00:00 0 
aa2f3000-aa2f6000 ---p aa2f3000 00:00 0 
aa2f6000-aa344000 rwxp aa2f6000 00:00 0 
aa400000-aa483000 rw-p aa400000 00:00 0 
aa483000-aa500000 ---p aa483000 00:00 0 
bf9e0000-bf9e3000 ---p bf9e0000 00:00 0 
bf9e3000-bfa30000 rwxp bffb2000 00:00 0          [stack]
bfa30000-bfa31000 rw-p bffff000 00:00 0 

VM Arguments:
jvm_args: -Dpython.cachedir.skip=false -Dplugins.dir=/home/mark/fiji -Xmx1511m 
java_command: <unknown>
Launcher Type: generic

Environment Variables:
JAVA_HOME=/home/mark/fiji/java/linux/jdk1.6.0_10/jre
PATH=/home/mark/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/var/lib/gems/1.8/bin/:/home/mark/android-sdk-linux_x86-1.0_r2/tools/
USERNAME=mark
SHELL=/bin/bash
DISPLAY=:0.0

Signal Handlers:
SIGSEGV: [libjvm.so+0x3ccf60], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x3ccf60], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x30e830], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x30e830], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x30e830], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x30e830], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x310d00], sa_mask[0]=0x00000004, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x310aa0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x310aa0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x310aa0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x310aa0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004


---------------  S Y S T E M  ---------------

OS:lenny/sid

uname:Linux 2.6.27-12-generic #1 SMP Thu Feb 5 09:26:35 UTC 2009 i686
libc:glibc 2.8.90 NPTL 2.8.90 
rlimit: STACK infinity, CORE 0k, NPROC 16310, NOFILE 1024, AS infinity
load average:0.42 0.42 0.32

CPU:total 2 (1 cores per cpu, 2 threads per core) family 6 model 12 stepping 2, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, ht

Memory: 4k page, physical 2063528k(1166376k free), swap 1951856k(1951856k free)

vm_info: Java HotSpot(TM) Client VM (11.0-b15) for linux-x86 JRE (1.6.0_10-b33), built on Sep 26 2008 01:18:27 by "java_re" with gcc 3.2.1-7a (J2SE release)

time: Wed Feb 25 17:18:40 2009
elapsed time: 259 seconds
Comment 1 Johannes Schindelin 2009-02-26 14:23:07 CST 
I _think_ it should be solved by detecting that an obsolete OpenGL is installed.  I have no idea how to detect that, though (maybe Canvas3D.queryProperties() shows something interesting?).
Comment 2 Mark Longair 2009-02-26 15:29:20 CST 
(In reply to comment #1)
> I _think_ it should be solved by detecting that an obsolete OpenGL is
> installed.  I have no idea how to detect that, though (maybe
> Canvas3D.queryProperties() shows something interesting?).

libGL.so.1 is in the package libgl1-mesa-glx, which is at version
7.2-1ubuntu2 on the system which segfaults.  However, I have other
systems where that package is at the older version 7.0.3-7 where it
runs fine.  There seems to be no later version available in Ubuntu,
and presumably this runs fine for most other people on Intrepid, so
I'm not sure if an obsolete version of OpenGL is likely to be the
problem.  But perhaps I misunderstood what you meant?

(This system has two cores, whereas my older one has one, so I suppose
it's possible this is a concurrency problem.)
Comment 3 Mark Longair 2009-02-27 20:10:17 CST 
A couple more details about this problem:

- I've tried using version 1.5.2 of Java3D but the same problem exists.

- I forgot to include the terminal output.  This is included below - the
  errors "***** polygon with only one vertex?! *****" and "failed to
  create drawable" may tell

 : mark@cava:~/fiji
 ./fiji 
/home/mark/.ImageJ_3D_Viewer.props (No such file or directory)
Java 3D WARNING : reported GLX version = 1.2
    GLX version 1.3 or higher is required
    The reported version number may be incorrect.  There is a known
    ATI driver bug in glXQueryVersion that incorrectly reports the GLX
    version as 1.2 when it really is 1.3, so Java 3D will attempt to
    run anyway.
***** polygon with only one vertex?! *****

failed to create drawable
#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x51b87c42, pid=17602, tid=1369811856
#
# Java VM: Java HotSpot(TM) Client VM (11.0-b15 mixed mode linux-x86)
# Problematic frame:
# C  [libGL.so.1+0x39c42]
#
# An error report file with more information is saved as:
# /home/mark/fiji/hs_err_pid17602.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted
Comment 4 Mark Longair 2009-02-28 10:32:10 CST 
After some more investigation, it seems that this is linked to the offscreen
rendering - as a workaround one can run Fiji with:

  ./fiji -Dj3d.noOffScreen=true --

I can reproduce a similar crash with the OffScreenTest example in j3d-examples
with Java3D versions 1.5.1, 1.5.2 and current daily snapshots, so I've
reported this upstream:

  https://java3d.dev.java.net/issues/﷒0﷓
Comment 5 Johannes Schindelin 2009-04-19 19:50:07 CDT 
As far as I remember, Bene put some detection into the 3D viewer, which should help this issue.  Could you try again, please?
Comment 6 Mark Longair 2009-04-20 18:44:36 CDT 
Great - it works now without the -Dj3d.noOffScreen=true parameter.  I'll close this bug as fixed, but of course leave open the Java3D one...