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Immortalin / peptide-shaker

Automatically exported from code.google.com/p/peptide-shaker
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PeptideShaker does not start #9

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
Double-click on PeptideShaker.jar

> What is the expected output? What do you see instead?
Start PeptideShaker

> What version of the product are you using? On what operating system?
14.5 or 14.6 - both do not work

> Please provide any additional information below.
That's what I get in the error log file:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x6d0ae53d, pid=3264, tid=2112
#
# JRE version: 6.0_31-b05
# Java VM: Java HotSpot(TM) Client VM (20.6-b01 mixed mode windows-x86 )
# Problematic frame:
# C  [awt.dll+0xae53d]
#
# 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 (0x66d23400):  JavaThread "AWT-Windows" daemon 
[_thread_in_native, id=2112, stack(0x66f40000,0x66f90000)]

siginfo: ExceptionCode=0xc0000005, writing address 0xe23bf4ac

Registers:
EAX=0xe23bf4ac, EBX=0x0000001b, ECX=0x00000020, EDX=0x66e10ce0
ESP=0x66f8f784, EBP=0x00000080, ESI=0x66e10ce0, EDI=0xe23bf4ac
EIP=0x6d0ae53d, EFLAGS=0x00010202

Top of Stack: (sp=0x66f8f784)
0x66f8f784:   66dd8718 00000001 00000020 000c55c0
0x66f8f794:   00148cc0 00000400 e23bf4ac 00000000
0x66f8f7a4:   00000000 00000020 0000001b 6d0b07d3
0x66f8f7b4:   00000000 66e10ce0 00000000 00000000
0x66f8f7c4:   00000000 00000080 00000020 0000001b
0x66f8f7d4:   00000080 00000004 00000000 00000000
0x66f8f7e4:   66e10ce0 0000001b 00000003 66f8f95c
0x66f8f7f4:   698199e8 437f8000 6d0b24f2 6d0b3d2f 

Instructions: (pc=0x6d0ae53d)
0x6d0ae51d:   18 8d 0c ad 00 00 00 00 89 4c 24 44 8d a4 24 00
0x6d0ae52d:   00 00 00 8b 4c 24 44 8b e9 c1 e9 02 8b f2 8b f8
0x6d0ae53d:   f3 a5 8b cd 8b 6c 24 50 83 e1 03 f3 a4 8b 7c 24
0x6d0ae54d:   14 03 d5 03 c7 4b 85 db 7f d9 8b 44 24 58 85 c0 

Register to memory mapping:

EAX=0xe23bf4ac is an unknown value
EBX=0x0000001b is an unknown value
ECX=0x00000020 is an unknown value
EDX=0x66e10ce0 is an unknown value
ESP=0x66f8f784 is pointing into the stack for thread: 0x66d23400
EBP=0x00000080 is an unknown value
ESI=0x66e10ce0 is an unknown value
EDI=0xe23bf4ac is an unknown value

Stack: [0x66f40000,0x66f90000],  sp=0x66f8f784,  free space=317k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [awt.dll+0xae53d]  D3DContext::UploadTileToTexture+0x42d

[error occurred during error reporting (printing native stack), id 0xc0000005]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  sun.awt.windows.WToolkit.eventLoop()V+0
j  sun.awt.windows.WToolkit.run()V+52
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

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

Java Threads: ( => current thread )
  0x69814800 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3988, stack(0x67510000,0x67560000)]
  0x66e30400 JavaThread "AWT-EventQueue-0" [_thread_in_native, id=816, stack(0x67420000,0x67470000)]
=>0x66d23400 JavaThread "AWT-Windows" daemon [_thread_in_native, id=2112, 
stack(0x66f40000,0x66f90000)]
  0x66db4400 JavaThread "AWT-Shutdown" [_thread_blocked, id=1716, stack(0x66ef0000,0x66f40000)]
  0x66dc4400 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=1972, stack(0x66ea0000,0x66ef0000)]
  0x66971000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=1940, stack(0x66bc0000,0x66c10000)]
  0x6696e800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=2516, stack(0x66b70000,0x66bc0000)]
  0x66969c00 JavaThread "Attach Listener" daemon [_thread_blocked, id=2220, stack(0x66b20000,0x66b70000)]
  0x66968400 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=2140, stack(0x66ad0000,0x66b20000)]
  0x6695a800 JavaThread "Finalizer" daemon [_thread_blocked, id=2692, stack(0x66a80000,0x66ad0000)]
  0x66955c00 JavaThread "Reference Handler" daemon [_thread_blocked, id=1856, stack(0x66a30000,0x66a80000)]
  0x002b6c00 JavaThread "main" [_thread_blocked, id=1132, stack(0x008c0000,0x00910000)]

Other Threads:
  0x66952000 VMThread [stack: 0x669e0000,0x66a30000] [id=2488]
  0x6697c000 WatcherThread [stack: 0x66c10000,0x66c60000] [id=1684]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
 def new generation   total 39296K, used 9362K [0x02990000, 0x05430000, 0x21d90000)
  eden space 34944K,  26% used [0x02990000, 0x032b4a90, 0x04bb0000)
  from space 4352K,   0% used [0x04bb0000, 0x04bb0000, 0x04ff0000)
  to   space 4352K,   0% used [0x04ff0000, 0x04ff0000, 0x05430000)
 tenured generation   total 87424K, used 0K [0x21d90000, 0x272f0000, 0x60590000)
   the space 87424K,   0% used [0x21d90000, 0x21d90000, 0x21d90200, 0x272f0000)
 compacting perm gen  total 12288K, used 9889K [0x60590000, 0x61190000, 0x64590000)
   the space 12288K,  80% used [0x60590000, 0x60f38790, 0x60f38800, 0x61190000)
No shared spaces configured.

Code Cache  [0x00910000, 0x009c8000, 0x02910000)
 total_blobs=389 nmethods=155 adapters=170 free_code_cache=32810880 largest_free_block=0

Dynamic libraries:
0x00400000 - 0x00425000     C:\Program Files\Java\jre6\bin\java.exe
0x7c900000 - 0x7c9b2000     C:\WINDOWS\system32\ntdll.dll
0x7c800000 - 0x7c8f6000     C:\WINDOWS\system32\kernel32.dll
0x77dd0000 - 0x77e6b000     C:\WINDOWS\system32\ADVAPI32.dll
0x77e70000 - 0x77f03000     C:\WINDOWS\system32\RPCRT4.dll
0x77fe0000 - 0x77ff1000     C:\WINDOWS\system32\Secur32.dll
0x7c340000 - 0x7c396000     C:\Program Files\Java\jre6\bin\msvcr71.dll
0x6d7f0000 - 0x6da9f000     C:\Program Files\Java\jre6\bin\client\jvm.dll
0x7e410000 - 0x7e4a1000     C:\WINDOWS\system32\USER32.dll
0x77f10000 - 0x77f59000     C:\WINDOWS\system32\GDI32.dll
0x76b40000 - 0x76b6d000     C:\WINDOWS\system32\WINMM.dll
0x76390000 - 0x763ad000     C:\WINDOWS\system32\IMM32.DLL
0x6d7a0000 - 0x6d7ac000     C:\Program Files\Java\jre6\bin\verify.dll
0x6d320000 - 0x6d33f000     C:\Program Files\Java\jre6\bin\java.dll
0x6d7e0000 - 0x6d7ef000     C:\Program Files\Java\jre6\bin\zip.dll
0x6d000000 - 0x6d14c000     C:\Program Files\Java\jre6\bin\awt.dll
0x73000000 - 0x73026000     C:\WINDOWS\system32\WINSPOOL.DRV
0x77c10000 - 0x77c68000     C:\WINDOWS\system32\msvcrt.dll
0x774e0000 - 0x7761e000     C:\WINDOWS\system32\ole32.dll
0x773d0000 - 0x774d3000 
    C:\WINDOWS\WinSxS\x86_Microsoft.Windows.Common-Controls_6595b64144ccf1df_6.0.26
00.6028_x-ww_61e65202\COMCTL32.dll
0x77f60000 - 0x77fd6000     C:\WINDOWS\system32\SHLWAPI.dll
0x74720000 - 0x7476c000     C:\WINDOWS\system32\MSCTF.dll
0x755c0000 - 0x755ee000     C:\WINDOWS\system32\msctfime.ime
0x7c9c0000 - 0x7d1d7000     C:\WINDOWS\system32\shell32.dll
0x6d230000 - 0x6d27f000     C:\Program Files\Java\jre6\bin\fontmanager.dll
0x66fd0000 - 0x67176000     C:\WINDOWS\system32\d3d9.dll
0x67180000 - 0x67186000     C:\WINDOWS\system32\d3d8thk.dll
0x77c00000 - 0x77c08000     C:\WINDOWS\system32\VERSION.dll
0x6d600000 - 0x6d613000     C:\Program Files\Java\jre6\bin\net.dll
0x71ab0000 - 0x71ac7000     C:\WINDOWS\system32\WS2_32.dll
0x71aa0000 - 0x71aa8000     C:\WINDOWS\system32\WS2HELP.dll
0x71a50000 - 0x71a8f000     C:\WINDOWS\System32\mswsock.dll
0x76f20000 - 0x76f47000     C:\WINDOWS\system32\DNSAPI.dll
0x76d60000 - 0x76d79000     C:\WINDOWS\system32\iphlpapi.dll
0x76fb0000 - 0x76fb8000     C:\WINDOWS\System32\winrnr.dll
0x76f60000 - 0x76f8c000     C:\WINDOWS\system32\WLDAP32.dll
0x67240000 - 0x67249000     C:\WINDOWS\system32\netware\NWWS2NDS.DLL
0x67250000 - 0x67298000     C:\WINDOWS\system32\NETWIN32.DLL
0x672a0000 - 0x672b5000     C:\WINDOWS\system32\CLNWIN32.DLL
0x672c0000 - 0x672e0000     C:\WINDOWS\system32\LOCWIN32.DLL
0x672e0000 - 0x6730b000     C:\WINDOWS\system32\NCPWIN32.dll
0x71ad0000 - 0x71ad9000     C:\WINDOWS\system32\WSOCK32.dll
0x67350000 - 0x6735c000     C:\WINDOWS\system32\netware\NWWS2SLP.DLL
0x67360000 - 0x67367000     C:\WINDOWS\system32\NWSRVLOC.dll
0x76fc0000 - 0x76fc6000     C:\WINDOWS\system32\rasadhlp.dll
0x673c0000 - 0x67418000     C:\WINDOWS\system32\hnetcfg.dll
0x71a90000 - 0x71a98000     C:\WINDOWS\System32\wshtcpip.dll
0x6d620000 - 0x6d629000     C:\Program Files\Java\jre6\bin\nio.dll
0x77120000 - 0x771ab000     C:\WINDOWS\system32\OLEAUT32.DLL
0x6d1a0000 - 0x6d1c3000     C:\Program Files\Java\jre6\bin\dcpr.dll
0x76bf0000 - 0x76bfb000     C:\WINDOWS\system32\PSAPI.DLL
0x67560000 - 0x67601000     C:\WINDOWS\system32\dbghelp.dll

VM Arguments:
jvm_args: -Xms128M -Xmx1500M 
java_command: eu.isas.peptideshaker.gui.PeptideShakerGUI
Launcher Type: SUN_STANDARD

Environment Variables:
CLASSPATH=C:\Program Files\HostExplorer.nt\hcljrcsv.jar;C:\Program 
Files\HostExplorer.nt\;
PATH=C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Program 
Files\Agilent\MassHunter\Workstation\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Quant\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Qual\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Acq\Bin\release\;C:\Perl\bin\;C:\oracle\ora
92\bin;C:\Program Files\Oracle\jre\1.3.1\bin;C:\Program 
Files\Oracle\jre\1.1.8\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wb
em;C:\Program Files\Common Files\Adaptec 
Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program
 Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Bruker 
Daltonik\NTDS\Bin;C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;Y:.;Z:.
USERNAME=poliakov
OS=Windows_NT
PROCESSOR_IDENTIFIER=x86 Family 15 Model 4 Stepping 10, GenuineIntel

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

OS: Windows XP Build 2600 Service Pack 3

CPU:total 2 (1 cores per cpu, 2 threads per core) family 15 model 4 stepping 
10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ht

Memory: 4k page, physical 3668036k(2921304k free), swap 5552508k(4845412k free)

vm_info: Java HotSpot(TM) Client VM (20.6-b01) for windows-x86 JRE 
(1.6.0_31-b05), built on Feb  3 2012 18:44:09 by "java_re" with MS VC++ 7.1 
(VS2003)

time: Wed Feb 29 11:31:56 2012
elapsed time: 1 seconds

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\conf folder).

Original issue reported on code.google.com by inosmire...@gmail.com on 29 Feb 2012 at 4:37

Attachments:

GoogleCodeExporter commented 9 years ago 
This is usually caused by a hardware error, usually memory related. It may also 
be caused by a bug in the Java Virtual Machine.

I would recommend that you try to re-install/update your Java version.

Do the following - remove old java first:
http://java.com/en/download/uninstall.jsp

Install latest version:
http://java.com/en/download/installed.jsp

Also please make sure that you are fully up to date on Windows updates and 
service packs.

I'd also recommend upgrading your PeptideShaker version to 0.14.7.

If you have another computer available you could also try running PeptideShaker 
there, just to make sure that the error is limited to the single machine/setup. 
As we've never seen this particular issue before.

Please let us know if any of this helps.

Original comment by harald.b...@gmail.com on 29 Feb 2012 at 7:01

GoogleCodeExporter commented 9 years ago 
(As this seemed to be a Java or hardware error I am now closing this issue.)

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 12:10