| Author |
 Topic  |
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JohnRichey
Starting Member
6 Posts |
 Posted - Sep 30 2009 : 3:59:31 PM
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I think this is a matlab error, moreso than a freesurfer error. Basically when I attempt to run the analysis/contrast gui using:
mkanalysis-sess -gui
Matlab seems to return a fault indicating a segmentation violation in the signal handler instead of opening up the gui. Any ideas?
The full output is pasted below:
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.0.4.352 (R14) Service Pack 2
January 29, 2005
This is a Classroom License for instructional use only.
Research and commercial use is prohibited.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> >> >>
------------------------------------------------------------------------
Segmentation violation detected at Wed Sep 30 15:48:22 2009
------------------------------------------------------------------------
Configuration:
MATLAB Version: 7.0.4.352 (R14) Service Pack 2
MATLAB License: 108608
Operating System: Linux 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 12 17:58:20 EDT 2007 x86_64
Window System: The X.Org Foundation (60801000), display :0.0
Current Visual: 0x21 (class 4, depth 16)
Processor ID: x86 Family 6 Model 15 Stepping 6, GenuineIntel
Virtual Machine: Java 1.5.0 with Sun Microsystems Inc. Java HotSpot(TM) Client VM
(mixed mode)
Default Charset: UTF-8
Register State:
eax = dd000000 ebx = f7ccda04
ecx = 00000055 edx = f574efb0
esi = f574efb0 edi = f57675d0
ebp = fffeea68 esp = fffee9b8
eip = f7a52d68 flg = 00010286
Stack Trace:
[0] libmwm_interpreter.so:FunctionHandleWorkspaceCI::customLoad(mcos::COSInterfacePtr, mcos::COSValue, mcos::COSDataTypePtr)(0xf60dde0c ", 0xfffeea90, 0xfffeeaa0, 0xfffeeab0) + 600 bytes
[1] libmwmcos.so:mcos::COSClassI::customLoad(mcos::COSInterfacePtr, mcos::COSValue, mcos::COSDataTypePtr)(0xf57675d0, 0xfffeebc0, 0xfffeebb0, 0xfffeeba0) + 92 bytes
[2] libmwmcos.so:mcos::InterfaceHeader::getInterface()(0xfffeec60, 0xf612d7b0, 2, 0xf746701e) + 1363 bytes
[3] libmwmcos.so:mcos::File::getInterface(unsigned) const(0xfffeec60, 0xf576e950 ", 1, 0xf74677ba) + 43 bytes
[4] libmwmcos.so:mcos::File::convertCOSInterfaceFromMatrix(mxArray_tag const*)(0xf576e950 ", 0xe37d0c30, 0xfffeecc8, 0xf7469bce) + 163 bytes
[5] libmwmcos.so:mcosConvertFromMATFileArray(mxArray_tag const*, mxArray_tag const**)(0xe37d0c30, 0xfffeeddc ", 0xe37d0cb0, 0xf747652e) + 194 bytes
[6] libmwmcos.so:omLoadOpaque(0xe37d0bf0, 0xe37d0c30, 0xfffeeddc ", 0) + 43 bytes
[7] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xfffefef0, 0, 0) + 4595 bytes
 libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff07f0, 0, 0) + 4100 bytes
[9] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff10f0, 0, 0) + 4100 bytes
[10] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff19f0, 0, 0) + 5858 bytes
[11] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff22f0, 0, 0) + 4100 bytes
[12] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff2bf0, 0, 0) + 4100 bytes
[13] libmx.so:_HandleArrayForStream(miStreamRec_tag*, miItem_tag*, int, int)(0xe3ac31b0 "IM", 0xffff2c80, 0, 0) + 4100 bytes
[14] libmx.so:miGetItemData(0xe3ac31b0 "IM", 0xffff2c80, 0xffffffff, 0) + 181 bytes
[15] libmx.so:miGetItem(0xe3ac31b0 "IM", 0xffff2cd0, 128, 0) + 372 bytes
[16] libmat.so:matGetVariable5(MATFile_tag*, char const*)(0xf582c430, 0xe3767ef4 "hgS_070000", 0, 0xf7ccda04) + 102 bytes
[17] libmat.so:matGetVariable(0xf582c430, 0xe3767ef4 "hgS_070000", 0, 0x00a49d79) + 25 bytes
[18] libmwm_interpreter.so:inLoadFcnPrivate(char const*, int, char**, bool, int, int, LoadDestination*)(0xffff2f40 "/usr/local/packages/freesurfer_v..", 0, 0xffff4050, 0) + 1259 bytes
[19] libmwm_interpreter.so:inLoadFcnWithLHS(0xffff2f40 "/usr/local/packages/freesurfer_v..", 0, 0xffff4050, 1) + 150 bytes
[20] libmwm_interpreter.so:inFullLoadFcn(1, 0xffff4440, 2, 0xffff44a0 ") + 498 bytes
[21] libmwm_dispatcher.so:Mfh_builtin<mxArray_tag>::dispatch_mf(int, mxArray_tag**, int, mxArray_tag**)(0xf57b4930, 1, 0xffff4440, 2) + 53 bytes
[22] libmwm_dispatcher.so:Mfh_MATLAB_fn::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xf57b4930, 1, 0xffff4440, 2) + 188 bytes
[23] libmwm_interpreter.so:inDispatchFromStack(306, 0x0889dc50 "load", 1, 2) + 1240 bytes
[24] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0x0889dc50 "load", 306, 1, 2) + 112 bytes
[25] libmwm_interpreter.so:.L914(1, 1728, 44, 0) + 137 bytes
[26] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 1728, 40, 0) + 315 bytes
[27] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xe372efb0, 0, 0xe372efb0, 0xfffffffe) + 484 bytes
[28] libmwm_interpreter.so:inWordsj(2, 0xffff4e70, 2, 0xffff4ed0 ") + 348 bytes
[29] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xe372efb0, 0, 2, 0xffff4e70) + 368 bytes
[30] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xe372efb0, 2, 0xffff4e70, 2) + 29 bytes
[31] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xe372efb0, 2, 0xffff4e70, 2) + 262 bytes
[32] libmwm_interpreter.so:inDispatchFromStack(501, 0xe392802c "hgload", 2, 2) + 1240 bytes
[33] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0xe392802c "hgload", 501, 2, 2) + 112 bytes
[34] libmwm_interpreter.so:.L914(1, 1333, 89, 0) + 137 bytes
[35] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 1333, 34, 0) + 315 bytes
[36] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xe37297f0, 0, 0xe37297f0, 3) + 484 bytes
[37] libmwm_interpreter.so:inWordsj(1, 0xffff5ed0, 3, 0xffff5f60) + 348 bytes
[38] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 0, 1, 0xffff5ed0) + 368 bytes
[39] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 1, 0xffff5ed0, 3) + 29 bytes
[40] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 1, 0xffff5ed0, 3) + 262 bytes
[41] libmwm_interpreter.so:ResolverFunctionDesc::CallFunction(int, mxArray_tag**, int, mxArray_tag**)(0xffff6274, 1, 0xffff5ed0, 3) + 373 bytes
[42] libmwm_interpreter.so:Resolver::CallMFunction(int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*)(0xffff6050, 1, 1, 0xe37d6230) + 994 bytes
[43] libmwm_interpreter.so:inResolveMFunctionCall(_m_function_desc*, int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*, inMarshalType*, unsigned, int, unsigned const*, int)(0x089208e0, 1, 1, 0xe37d6230) + 263 bytes
[44] libmwm_interpreter.so:accelMFunctionCall(_accelOp*, _accelOp**, _accelBytecode*, int*, inMarshalType*)(0xf576f710, 0xffff6978, 0xf6166938, 0xffff6904) + 123 bytes
[45] libmwm_interpreter.so:.L1443(0xf6166938, 0xffff6b8c, 0xffff6bf8, 0xf7a62c9b) + 95 bytes
[46] libmwm_interpreter.so:inExecuteHotSegment(_inJitAccelInfo*, opcodes*, int*)(0xffff6d08, 0xffff6d6c, 0xffff6d04, 0) + 1165 bytes
[47] libmwm_interpreter.so:.L1059(1, 157, 216, 0) + 508 bytes
[48] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 157, 211, 0) + 315 bytes
[49] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xe3729990, 0, 0xe3729990, 2) + 484 bytes
[50] libmwm_interpreter.so:inWordsj(1, 0xffff7b20, 2, 0xffff7bb0 ") + 348 bytes
[51] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 0, 1, 0xffff7b20) + 368 bytes
[52] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 1, 0xffff7b20, 2) + 29 bytes
[53] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 1, 0xffff7b20, 2) + 262 bytes
[54] libmwm_interpreter.so:ResolverFunctionDesc::CallFunction(int, mxArray_tag**, int, mxArray_tag**)(0xffff7ec4, 1, 0xffff7b20, 2) + 373 bytes
[55] libmwm_interpreter.so:Resolver::CallMFunction(int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*)(0xffff7ca0, 1, 1, 0xe37d8cb0) + 994 bytes
[56] libmwm_interpreter.so:inResolveMFunctionCall(_m_function_desc*, int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*, inMarshalType*, unsigned, int, unsigned const*, int)(0x08920a98, 1, 1, 0xe37d8cb0) + 263 bytes
[57] libmwm_interpreter.so:accelMFunctionCall(_accelOp*, _accelOp**, _accelBytecode*, int*, inMarshalType*)(0x0891ae60, 0xffff85c8, 0xf6166928, 0xffff8554) + 123 bytes
[58] libmwm_interpreter.so:.L1443(0xf6166928, 0xffff87dc, 0xffff8848, 0xf7a62c9b) + 95 bytes
[59] libmwm_interpreter.so:inExecuteHotSegment(_inJitAccelInfo*, opcodes*, int*)(0xffff8958, 0xffff89bc, 0xffff8954, 0) + 1165 bytes
[60] libmwm_interpreter.so:.L1059(1, 2259, 77, 0) + 508 bytes
[61] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 2259, 31, 0) + 315 bytes
[62] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xf569a5d0, 0, 0xf569a5d0, 0xfffffffe) + 484 bytes
[63] libmwm_interpreter.so:inWordsj(1, 0xffff9140, 1, 0xffff91a0 ") + 348 bytes
[64] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 0, 1, 0xffff9140) + 368 bytes
[65] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 1, 0xffff9140, 1) + 29 bytes
[66] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 1, 0xffff9140, 1) + 262 bytes
[67] libmwm_interpreter.so:inDispatchFromStack(471, 0x08919788 "gui_mainfcn", 1, 1) + 1240 bytes
[68] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0x08919788 "gui_mainfcn", 471, 1, 0xffffffff) + 112 bytes
[69] libmwm_interpreter.so:.L914(1, 251, 39, 0) + 137 bytes
[70] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 251, 27, 0) + 315 bytes
[71] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xf5698f10, 0, 0xf5698f10, 0xffffffff) + 484 bytes
[72] libmwm_interpreter.so:inWordsj(1, 0xffff9b70, 0, 0xffff9bd0) + 348 bytes
[73] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 0, 1, 0xffff9b70) + 368 bytes
[74] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 1, 0xffff9b70, 0) + 29 bytes
[75] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 1, 0xffff9b70, 0) + 262 bytes
[76] libmwm_interpreter.so:inDispatchFromStack(470, 0xf588f504 "mkanalysis_gui", 1, 0) + 1240 bytes
[77] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0xf588f504 "mkanalysis_gui", 470, 1, 0) + 112 bytes
[78] libmwm_interpreter.so:.L914(2, 0, 0, 0) + 137 bytes
[79] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(2, 0, 0, 0) + 315 bytes
[80] libmwm_interpreter.so:inInterPcode(2, 0, 0xffffa178 ", 0xf7a43913) + 93 bytes
[81] libmwm_interpreter.so:in_local_call_eval_function(int*, _pcodeheader*, int*, mxArray_tag**, inDebugCheck)(0, 0xffffab70, 0xffffabfc, 0xffffac28) + 163 bytes
[82] libmwm_interpreter.so:inEvalStringWithIsVarFcn(_memory_context*, char const*, EvalType, int, mxArray_tag**, inDebugCheck, _pcodeheader*, int*, bool (*)(void*, char const*), void*)(0xf7fea828, 0x088ec4d0 "h = mkanalysis_gui;\n", 0, 0) + 2358 bytes
[83] libmwm_interpreter.so:inEvalCmdNoEnd(0x088ec4d0 "h = mkanalysis_gui;\n", 0x088ec4d0 "h = mkanalysis_gui;\n", 0xffffadc8, 0xf7dbf053) + 85 bytes
[84] libmwbridge.so:mnParser(0xf7da78ea "@@@", 0xf7da79da "mnParser", 1, 0xf7dabb30 ") + 471 bytes
[85] libmwmcr.so:mcrInstance::mnParser()(0x0809e0a0, 0, 0xffffd118, 0x0804a902) + 96 bytes
[86] MATLAB:mcrMain(int, char**)(1, 0xffffd1c4 ", 0, 0xffffd138) + 308 bytes
[87] MATLAB:main(1, 0xffffd1c4 ", 0xffffd1cc, 0x00a14b46) + 23 bytes
[88] libc.so.6:__libc_start_main~(0x0804a7c4, 1, 0xffffd1c4 ", 0x0804a3d8) + 227 bytes
Please follow these steps in reporting this problem to The MathWorks so
that we have the best chance of correcting it:
1. Send this crash report to segv@mathworks.com for automated analysis.
For your convenience, this information has been recorded in:
/home/jar62/matlab_crash_dump.714
2. Also, if the problem is reproducible, send the crash report to
support@mathworks.com along with:
- A specific list of steps that will reproduce the problem
- Any M, MEX, MDL or other files required to reproduce the problem
- Any error messages displayed to the command window
A technical support engineer will contact you with further information.
Thank you for your assistance. Please save your workspace and restart
MATLAB before continuing your work.
------------------------------------------------------------------------
Segmentation violation detected at Wed Sep 30 15:48:22 2009
------------------------------------------------------------------------
Configuration:
MATLAB Version: 7.0.4.352 (R14) Service Pack 2
MATLAB License: 108608
Operating System: Linux 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 12 17:58:20 EDT 2007 x86_64
Window System: The X.Org Foundation (60801000), display :0.0
Current Visual: 0x21 (class 4, depth 16)
Processor ID: x86 Family 6 Model 15 Stepping 6, GenuineIntel
Virtual Machine: Java 1.5.0 with Sun Microsystems Inc. Java HotSpot(TM) Client VM
(mixed mode)
Default Charset: UTF-8
Register State:
eax = 00000059 ebx = f7ccda04
ecx = f7d72088 edx = 087240c0
esi = 00000000 edi = ffff4bb0
ebp = ffff53d8 esp = ffff53b4
eip = f7a8705b flg = 00010296
Stack Trace:
[0] libmwm_interpreter.so:(anonymous namespace)::inPrtlineErrMsg(int)(89, 0xf7ccda04, 0xffff5418 ", 0xf7a888e3) + 71 bytes
[1] libmwm_interpreter.so:(anonymous namespace)::Mfun_call_context::~Mfun_call_context()(0xffff5440, 0, 0xe37297f0, 0xf7a87d20) + 909 bytes
[2] libmwm_interpreter.so:inWordsj(1, 0xffff5ed0, 3, 0xffff5f60) + 683 bytes
[3] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 0, 1, 0xffff5ed0) + 368 bytes
[4] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 1, 0xffff5ed0, 3) + 29 bytes
[5] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xe37297f0, 1, 0xffff5ed0, 3) + 262 bytes
[6] libmwm_interpreter.so:ResolverFunctionDesc::CallFunction(int, mxArray_tag**, int, mxArray_tag**)(0xffff6274, 1, 0xffff5ed0, 3) + 373 bytes
[7] libmwm_interpreter.so:Resolver::CallMFunction(int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*)(0xffff6050, 1, 1, 0xe37d6230) + 994 bytes
libmwm_interpreter.so:inResolveMFunctionCall(_m_function_desc*, int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*, inMarshalType*, unsigned, int, unsigned const*, int)(0x089208e0, 1, 1, 0xe37d6230) + 263 bytes
[9] libmwm_interpreter.so:accelMFunctionCall(_accelOp*, _accelOp**, _accelBytecode*, int*, inMarshalType*)(0xf576f710, 0xffff6978, 0xf6166938, 0xffff6904) + 123 bytes
[10] libmwm_interpreter.so:.L1443(0xf6166938, 0xffff6b8c, 0xffff6bf8, 0xf7a62c9b) + 95 bytes
[11] libmwm_interpreter.so:inExecuteHotSegment(_inJitAccelInfo*, opcodes*, int*)(0xffff6d08, 0xffff6d6c, 0xffff6d04, 0) + 1165 bytes
[12] libmwm_interpreter.so:.L1059(1, 157, 216, 0) + 508 bytes
[13] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 157, 211, 0) + 315 bytes
[14] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xe3729990, 0, 0xe3729990, 2) + 484 bytes
[15] libmwm_interpreter.so:inWordsj(1, 0xffff7b20, 2, 0xffff7bb0 ") + 348 bytes
[16] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 0, 1, 0xffff7b20) + 368 bytes
[17] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 1, 0xffff7b20, 2) + 29 bytes
[18] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xe3729990, 1, 0xffff7b20, 2) + 262 bytes
[19] libmwm_interpreter.so:ResolverFunctionDesc::CallFunction(int, mxArray_tag**, int, mxArray_tag**)(0xffff7ec4, 1, 0xffff7b20, 2) + 373 bytes
[20] libmwm_interpreter.so:Resolver::CallMFunction(int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*)(0xffff7ca0, 1, 1, 0xe37d8cb0) + 994 bytes
[21] libmwm_interpreter.so:inResolveMFunctionCall(_m_function_desc*, int, int, _m_operand*, m_operand_storage*, int, _m_operand*, m_operand_storage*, int*, inMarshalType*, unsigned, int, unsigned const*, int)(0x08920a98, 1, 1, 0xe37d8cb0) + 263 bytes
[22] libmwm_interpreter.so:accelMFunctionCall(_accelOp*, _accelOp**, _accelBytecode*, int*, inMarshalType*)(0x0891ae60, 0xffff85c8, 0xf6166928, 0xffff8554) + 123 bytes
[23] libmwm_interpreter.so:.L1443(0xf6166928, 0xffff87dc, 0xffff8848, 0xf7a62c9b) + 95 bytes
[24] libmwm_interpreter.so:inExecuteHotSegment(_inJitAccelInfo*, opcodes*, int*)(0xffff8958, 0xffff89bc, 0xffff8954, 0) + 1165 bytes
[25] libmwm_interpreter.so:.L1059(1, 2259, 77, 0) + 508 bytes
[26] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 2259, 31, 0) + 315 bytes
[27] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xf569a5d0, 0, 0xf569a5d0, 0xfffffffe) + 484 bytes
[28] libmwm_interpreter.so:inWordsj(1, 0xffff9140, 1, 0xffff91a0 ") + 348 bytes
[29] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 0, 1, 0xffff9140) + 368 bytes
[30] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 1, 0xffff9140, 1) + 29 bytes
[31] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xf569a5d0, 1, 0xffff9140, 1) + 262 bytes
[32] libmwm_interpreter.so:inDispatchFromStack(471, 0x08919788 "gui_mainfcn", 1, 1) + 1240 bytes
[33] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0x08919788 "gui_mainfcn", 471, 1, 0xffffffff) + 112 bytes
[34] libmwm_interpreter.so:.L914(1, 251, 39, 0) + 137 bytes
[35] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(1, 251, 27, 0) + 315 bytes
[36] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*, bool)(0xf5698f10, 0, 0xf5698f10, 0xffffffff) + 484 bytes
[37] libmwm_interpreter.so:inWordsj(1, 0xffff9b70, 0, 0xffff9bd0) + 348 bytes
[38] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*, int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 0, 1, 0xffff9b70) + 368 bytes
[39] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 1, 0xffff9b70, 0) + 29 bytes
[40] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)(0xf5698f10, 1, 0xffff9b70, 0) + 262 bytes
[41] libmwm_interpreter.so:inDispatchFromStack(470, 0xf588f504 "mkanalysis_gui", 1, 0) + 1240 bytes
[42] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int, int*, int*)(0xf588f504 "mkanalysis_gui", 470, 1, 0) + 112 bytes
[43] libmwm_interpreter.so:.L914(2, 0, 0, 0) + 137 bytes
[44] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int, opcodes, inPcodeNest_tag*)(2, 0, 0, 0) + 315 bytes
[45] libmwm_interpreter.so:inInterPcode(2, 0, 0xffffa178 ", 0xf7a43913) + 93 bytes
[46] libmwm_interpreter.so:in_local_call_eval_function(int*, _pcodeheader*, int*, mxArray_tag**, inDebugCheck)(0, 0xffffab70, 0xffffabfc, 0xffffac28) + 163 bytes
[47] libmwm_interpreter.so:inEvalStringWithIsVarFcn(_memory_context*, char const*, EvalType, int, mxArray_tag**, inDebugCheck, _pcodeheader*, int*, bool (*)(void*, char const*), void*)(0xf7fea828, 0x088ec4d0 "h = mkanalysis_gui;\n", 0, 0) + 2358 bytes
[48] libmwm_interpreter.so:inEvalCmdNoEnd(0x088ec4d0 "h = mkanalysis_gui;\n", 0x088ec4d0 "h = mkanalysis_gui;\n", 0xffffadc8, 0xf7dbf053) + 85 bytes
[49] libmwbridge.so:mnParser(0xf7da78ea "@@@", 0xf7da79da "mnParser", 1, 0xf7dabb30 ") + 471 bytes
[50] libmwmcr.so:mcrInstance::mnParser()(0x0809e0a0, 0, 0xffffd118, 0x0804a902) + 96 bytes
[51] MATLAB:mcrMain(int, char**)(1, 0xffffd1c4 ", 0, 0xffffd138) + 308 bytes
[52] MATLAB:main(1, 0xffffd1c4 ", 0xffffd1cc, 0x00a14b46) + 23 bytes
[53] libc.so.6:__libc_start_main~(0x0804a7c4, 1, 0xffffd1c4 ", 0x0804a3d8) + 227 bytes
Segmentation violation occurred within signal handler.
Unable to complete stack trace (stack was probably corrupted)
Segmentation fault
[jar62@meehl fb1-preproc-study]$ |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 30 2009 : 4:06:22 PM
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| old version of matlab ... i'll install the new version |
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ark19
Junior Member
27 Posts |
Posted - Nov 16 2011 : 2:27:30 PM
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Hi Chris,
We are getting this same 'Segmentation Violation' error (excerpt pasted below) when trying to run VBM8 on the cluster. Is it still possible that it's a Matlab version issue? We're running our own instantiation of VBM8 (stored on Munin) to be able to maintain version consistency across cluster updates, but this works whenever we run the VBM8/spm8 on the cluster instead. Can you think of a way for us to resolve this and still be able to use our own instantiation, or if it might be caused by something else that I'm not thinking of?
Thanks!
Annchen
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'VBM8: Estimate & Write'
Initial Coarse Affine Registration..
Fine Affine Registration..
VBM8 Revision 369
Using 16 processors
------------------------------------------------------------------------
Segmentation violation detected at Mon Nov 14 11:45:55 2011
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding: UTF-8
GNU C Library : 2.12 stable
MATLAB License : 359028
MATLAB Root : /usr/local/matlab2011a
MATLAB Version : 7.12.0.635 (R2011a)
Operating System: Linux 2.6.32-131.12.1.el6.x86_64 #1 SMP Tue Aug 23 11:13:45 CDT 2011 x86_64
Processor ID : x86 Family 6 Model 10 Stepping 5, GenuineIntel
Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 0000000000000500 RBX = 0000000000000005
RCX = 0000000000000006 RDX = 0000000000000006
RSP = 00002baaafff5ce0 RBP = 0000000000000100
RSI = 00000000000001fa RDI = 0000000000000000
R8 = 000000000000000b R9 = 0000000000000000
R10 = 0000000000000000 R11 = 00000000000001ff
R12 = 00002bac0ceb5010 R13 = 0000000000000000
R14 = 0000000000000100 R15 = 0000000000000000
RIP = 00002bac0a204a5b EFL = 0000000000010202
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00002baa91e98f49 /usr/local/matlab2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00474953 fl::sysdep::linux::unwind_stack(void const**, unsigned long, unsigned long, fl::diag::thread_context const&)+000009
[ 1] 0x00002baa91e4edc1 /usr/local/matlab2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00171457 fl::diag::stacktrace_base::capture(fl::diag::thread_context const&, unsigned long)+000161
[ 2] 0x00002baa91e580dd /usr/local/matlab2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209117
[ 3] 0x00002baa91e58364 /usr/local/matlab2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209764 fl::diag::terminate_log(char const*, fl::diag::thread_context const&, bool)+000100
...
[114] 0x00002baa92e3ed6f /usr/local/matlab2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00200047
[115] 0x0000003dee4077e1 /lib64/libpthread.so.0+00030689
[116] 0x0000003dedce18ed /lib64/libc.so.6+00923885 clone+000109
This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Nov 16 2011 : 2:37:18 PM
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looks like the same matlab crash dumps that i've seen when matlab can't access enough RAM.
Are you requesting more than the default? |
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Freesurfer/Matlab wraparound error in Mkanalysis
