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The MEX code below segfaults on OS X Yosemite with Matlab 2015a, when building the Preconditioner:

#include <Eigen/Sparse>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[],int nrhs, const mxArray *prhs[])
{
    const mxArray *mx = prhs[0];
    if ( !mxIsSparse(prhs[0]) ) mexErrMsgTxt("Not a sparse matrix");
    mwSize M = mxGetM(prhs[0]);
    mwSize N = mxGetN(prhs[0]);
    double *pr = mxGetPr(prhs[0]);
    mwIndex *ir = mxGetIr(prhs[0]);
    mwIndex *jc = mxGetJc(prhs[0]);
    mwIndex NNZ = jc[N];

    Eigen::SparseMatrix<double> A(M, N);
    A.reserve( (int) NNZ );
    for (int i=0; i<NNZ; i++) {
        A.valuePtr()[i] = pr[i];
        A.innerIndexPtr()[i] = (int) ir[i];
    }
    for (int i=0; i<=N; i++) {
        A.outerIndexPtr()[i] = (int) jc[i];
    }

    mexPrintf("building precond:\n");
    Eigen::IncompleteLUT<double > prec(A);
    mexPrintf("building precond done.\n");

}

This is the MEX command I'm using:

mex -g eigenFail.cpp -I/usr/local/include/eigen3 -largeArrayDims

In my stand alone code this works just fine.

Here is the stack trace:

Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 000000010f71ff90  RBX = 0000000000000001
  RCX = 000000010f71fde0  RDX = 00007fff9183fdd2
  RSP = 00007fac64f954f5  RBP = 0000000000001000
  RSI = 0000000000000005  RDI = 000000010900da00

   R8 = 0000000000000003   R9 = 000000000000002c
  R10 = 000000000f71fed0  R11 = 00000001017a5000
  R12 = ff80000000001004  R13 = 000000010f71ffe8
  R14 = 000000010f71fe90  R15 = 000000012624fb04

  RIP = 000000010f71fe30  RFL = 000000012624a4a0

   CS = 000000010f720d58   FS = 000000010f720410   GS = 000000010f71fe60

Stack Trace (from fault):
[  0] 0x0000000102268964 /Applications/MATLAB_R2015a.app/bin/maci64/libmwfl.dylib+00031076 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[  1] 0x000000010226c02b /Applications/MATLAB_R2015a.app/bin/maci64/libmwfl.dylib+00045099 _ZN2fl4test17terminate_handledEv+00000763
[  2] 0x000000010226bac7 /Applications/MATLAB_R2015a.app/bin/maci64/libmwfl.dylib+00043719 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119
[  3] 0x0000000101d90f9b /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00380827 _Z32mnRunPathDependentInitializationv+00002875
[  4] 0x0000000101d91217 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00381463 _Z32mnRunPathDependentInitializationv+00003511
[  5] 0x0000000101d8f3a6 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00373670 mnFatalSignalHandler+00000262
[  6] 0x00007fff958b2f1a           /usr/lib/system/libsystem_platform.dylib+00020250 _sigtramp+00000026
[  7] 0x00000001101c3c10 /Applications/MATLAB_R2015a.app/sys/java/jre/maci64/jre/lib/./server/libjvm.dylib+07785488 _ZTV23JNI_ArgumentPusherVaArg+00000016
[  8] 0x000000012624fb04 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00064260 _ZN5Eigen8internal46sparse_cwise_binary_op_inner_iterator_selectorINS0_13scalar_sum_opIdEEKNS_12SparseMatrixIdLi0EiEES6_NS_17CwiseBinaryOpImplIS3_S6_S6_NS_6SparseEE13InnerIteratorES8_S8_EppEv+00000100
[  9] 0x0000000126250cc2 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00068802 _ZN5Eigen8internal46sparse_cwise_binary_op_inner_iterator_selectorINS0_13scalar_sum_opIdEEKNS_12SparseMatrixIdLi0EiEES6_NS_17CwiseBinaryOpImplIS3_S6_S6_NS_6SparseEE13InnerIteratorES8_S8_EC2ERKNS_13CwiseBinaryOpIS3_S6_S6_EEi+00000114
[ 10] 0x0000000126250c43 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00068675 _ZN5Eigen17CwiseBinaryOpImplINS_8internal13scalar_sum_opIdEEKNS_12SparseMatrixIdLi0EiEES6_NS_6SparseEE13InnerIteratorC2ERKS8_i+00000051
[ 11] 0x000000012624f863 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00063587 _ZN5Eigen17CwiseBinaryOpImplINS_8internal13scalar_sum_opIdEEKNS_12SparseMatrixIdLi0EiEES6_NS_6SparseEE13InnerIteratorC1ERKS8_i+00000035
[ 12] 0x000000012624ffa0 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00065440 _ZN5Eigen16SparseMatrixBaseINS_12SparseMatrixIdLi0EiEEE13assignGenericINS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS2_S9_EEEEvRKT_+00000400
[ 13] 0x000000012624f62e /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00063022 _ZN5Eigen16SparseMatrixBaseINS_12SparseMatrixIdLi0EiEEE6assignINS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS2_S9_EEEERS2_RKT_+00000622
[ 14] 0x000000012624f3b0 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00062384 _ZN5Eigen16SparseMatrixBaseINS_12SparseMatrixIdLi0EiEEEaSINS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS2_S9_EEEERS2_RKNS0_IT_EE+00000048
[ 15] 0x000000012624f2c4 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00062148 _ZN5Eigen12SparseMatrixIdLi0EiEaSINS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS1_S7_EEEERS1_RKNS_16SparseMatrixBaseIT_EE+00000100
[ 16] 0x000000012624f232 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00062002 _ZN5Eigen12SparseMatrixIdLi0EiEC2INS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS1_S7_EEEERKNS_16SparseMatrixBaseIT_EE+00000114
[ 17] 0x000000012624bfcd /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00049101 _ZN5Eigen12SparseMatrixIdLi0EiEC1INS_13CwiseBinaryOpINS_8internal13scalar_sum_opIdEEKS1_S7_EEEERKNS_16SparseMatrixBaseIT_EE+00000029
[ 18] 0x0000000126241ae6 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00006886 _ZN5Eigen13IncompleteLUTIdE14analyzePatternINS_12SparseMatrixIdLi0EiEEEEvRKT_+00000166
[ 19] 0x000000012624176f /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00005999 _ZN5Eigen13IncompleteLUTIdE7computeINS_12SparseMatrixIdLi0EiEEEERS1_RKT_+00000047
[ 20] 0x00000001262416b2 /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00005810 _ZN5Eigen13IncompleteLUTIdEC2INS_12SparseMatrixIdLi0EiEEEERKT_RKdi+00000290
[ 21] 0x000000012624153b /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00005435 _ZN5Eigen13IncompleteLUTIdEC1INS_12SparseMatrixIdLi0EiEEEERKT_RKdi+00000043
[ 22] 0x000000012624118d /Users/weissman/GIT_WORKING/PRIMME_CPP/PRIMME_EIGEN3/eigenFail.mexmaci64+00004493 mexFunction+00000653
[ 23] 0x0000000106ec31db /Applications/MATLAB_R2015a.app/bin/maci64/libmex.dylib+00070107 mexRunMexFile+00000091
[ 24] 0x0000000106ebf9f1 /Applications/MATLAB_R2015a.app/bin/maci64/libmex.dylib+00055793 _ZN7Mfh_mex30runMexFileWithSignalProtectionEiPP11mxArray_tagiS2_+00000113
[ 25] 0x0000000106ebfbcd /Applications/MATLAB_R2015a.app/bin/maci64/libmex.dylib+00056269 _ZN7Mfh_mex13dispatch_fileEiPP11mxArray_tagiS2_+00000285
[ 26] 0x0000000106f4a4bd /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_dispatcher.dylib+00386237 _ZN8Mfh_file16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000621
[ 27] 0x0000000106f4a5f3 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_dispatcher.dylib+00386547 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000035
[ 28] 0x000000010734203d /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01552445 _Z19inDispatchFromStackiPKcii+00001581
[ 29] 0x00000001072a5a88 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+00912008 inCallFcnFromReference+00000776
[ 30] 0x00000001072ea6c7 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01193671 inPcodeWalker+00006807
[ 31] 0x00000001072e676b /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01177451 inInterPcode+00000875
[ 32] 0x00000001072e7886 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01181830 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886
[ 33] 0x000000010737d819 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01796121 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00003401
[ 34] 0x0000000106f4a4f2 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_dispatcher.dylib+00386290 _ZN8Mfh_file16dispatch_fh_implEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000674
[ 35] 0x0000000106f4a5f3 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_dispatcher.dylib+00386547 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000035
[ 36] 0x0000000107324ebd /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01433277 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+00000141
[ 37] 0x00000001072dfadb /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01149659 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+00000171
[ 38] 0x00000001072dadc0 /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01129920 _Z12inEvalStringP15_memory_contextRKNSt3__112basic_stringIDsNS1_11char_traitsIDsEENS1_9allocatorIDsEEEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002608
[ 39] 0x00000001072db3dd /Applications/MATLAB_R2015a.app/bin/maci64/libmwm_interpreter.dylib+01131485 _ZN12InterpBridge22EvalCmdWithLocalReturnERKNSt3__112basic_stringIDsNS0_11char_traitsIDsEENS0_9allocatorIDsEEEEPibb+00000141
[ 40] 0x0000000106e5db0d /Applications/MATLAB_R2015a.app/bin/maci64/libmwbridge.dylib+00068365 _Z28evalCommandWithLongjmpSafetyRKNSt3__112basic_stringIDsNS_11char_traitsIDsEENS_9allocatorIDsEEEE+00000093
[ 41] 0x0000000106e5e06c /Applications/MATLAB_R2015a.app/bin/maci64/libmwbridge.dylib+00069740 _Z8mnParserv+00000700
[ 42] 0x0000000101d7b132 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00291122 _ZN11mcrInstance30mnParser_on_interpreter_threadEv+00000034
[ 43] 0x0000000101d55021 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00135201 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIvE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFvvEEE+00000033
[ 44] 0x0000000101d55ae9 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00137961 _ZN5boost6detail11task_objectIvNS_3_bi6bind_tIvPFvRKNS_8functionIFvvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025
[ 45] 0x0000000101d55476 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00136310 _ZN5boost6detail9task_baseIvE3runEv+00000182
[ 46] 0x0000000101d55217 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00135703 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIvE3runEv+00000023
[ 47] 0x0000000101d514e3 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00120035 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000035
[ 48] 0x00000001017d688d /Applications/MATLAB_R2015a.app/bin/maci64/libmwservices.dylib+00182413 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001053
[ 49] 0x0000000107cdb5f5 /Applications/MATLAB_R2015a.app/bin/maci64/libmwuix.dylib+00038389 _Z25isHandleUserEventCallbackPFvPvE+00000469
[ 50] 0x000000010189ef8d /Applications/MATLAB_R2015a.app/bin/maci64/libmwservices.dylib+01003405 _Z40svWS_ProcessPendingEventsWithLimitedRateb+00017149
[ 51] 0x000000010189a372 /Applications/MATLAB_R2015a.app/bin/maci64/libmwservices.dylib+00983922 _Z25svWS_ProcessPendingEventsiib+00000866
[ 52] 0x000000010189a06b /Applications/MATLAB_R2015a.app/bin/maci64/libmwservices.dylib+00983147 _Z25svWS_ProcessPendingEventsiib+00000091
[ 53] 0x0000000101d51737 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00120631 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000135
[ 54] 0x0000000101d51a6a /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00121450 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000346
[ 55] 0x0000000101d3a156 /Applications/MATLAB_R2015a.app/bin/maci64/libmwmcr.dylib+00024918 _Z26run_init_and_handle_eventsPv+00000054
[ 56] 0x00007fff91662268            /usr/lib/system/libsystem_pthread.dylib+00012904 _pthread_body+00000131
[ 57] 0x00007fff916621e5            /usr/lib/system/libsystem_pthread.dylib+00012773 _pthread_body+00000000
[ 58] 0x00007fff9166041d            /usr/lib/system/libsystem_pthread.dylib+00005149 thread_start+00000013
Steffen Weissmann
  • 1
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  • Where does it seg fault? Did you step through it using a debugger? Use Xcode and attach MATLAB as a process and debug your MEX code... then tell us where the seg fault is happening: http://stackoverflow.com/questions/23714141/preventing-a-mex-file-from-crashing-in-matlab/23714301?s=1|0.6282#23714301 – rayryeng Aug 02 '15 at 16:14
  • Thanks for the message. I think one can see from the Stack trace where it happens (trying to attach it...) – Steffen Weissmann Aug 02 '15 at 17:04
  • Edit your post to put the Stack trace in. Putting it in a comment looks a bit odd! – rayryeng Aug 02 '15 at 17:08
  • Okay, got it. There is no way to attach a file, right? – Steffen Weissmann Aug 02 '15 at 17:34
  • Yeah unfortunately you can't here... but one suggestion I have if you want is to upload the stack trace on a public sharing website or repository (Dropbox, Github gists, file sharing free sites, etc.)... that's if the stack trace is too large. However, if that isn't an option, you could copy and paste what MATLAB spits out and put it into your post.... but you did that already! Let me go through the trace and get back to you. – rayryeng Aug 02 '15 at 17:41
  • Did you also try debugging your code with XCode? I'd also like to see which exact line it seg faults at. It's not that clear in the stack trace. – rayryeng Aug 02 '15 at 17:58
  • 1
    That helped :) The problem is the line `A.reserve(NNZ)`, it has to be `A.resizeNonZeros(NNZ)` instead. Thank you @rayryeng! – Steffen Weissmann Aug 05 '15 at 08:47

0 Answers0