Matlab crashes when manipulating an array generated by a mex function

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Anon 2013-1-22

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Dear all,

I have written a Mex-function that generates an array. Actually, it is a topological sort algorithm. Now let's say I call this function

A = tsort(B); % contains a call to the mex function
A = otherfunction(A); % other function that modifies A contains only matlab code

then it happens quite often that Matlab crashes when calling otherfunction, even after minutes between my call to tsort and otherfunction. Did anyone experience such problems with his or her code. By the way, I am using Windows 7 64bit, Matlab 2012a and Microsoft Software Development Kit (SDK) 7.1 as compiler.

Thanks for your help, Anon

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Anon 2013-1-22

在 MATLAB Online 中打开

Thanks for your reply, Walter. Here is the c-code. I have included a minimal example in the help text that hopefully outlines, what the algorithm does.

// file: tsort_mex.c
// steepest gradient
// inp 1: SE (steepest downward neighbor grid, uint32)
//        matrix with, e.g.
//        [4 0 4 7;
//         4 4 4 7;
//         5 5 8 8]; 
//        indicates that cell 1 drains to 4, cell 2 drains 
//        to 4 and cell 9 to 8 etc... Cells with SE == 0 don't 
//        drain anywhere
// inp 2: seed pixels (linear index, uint32)
//        above example 4
// inp 3: nr of missing values (scalar, double)
//        above example 0
//
// outp 1: topological order list of linear indices (uint32)
//         above example: 12 9 6 3 11 8 5 2 10 7 1
// outp 2: linear indices of the childs of outp 1 (uint32)
//         above example: 8  8 5 5 7 7 4 4 4 4 4
#include "mex.h"
#include "matrix.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
  mwSize nrc, nrow, ncol; 
  mwIndex IX, IXN, neigh, row, col, r, c, nrLM, pix1, pix2, pLM;
  int coln[8] = {0, 1, 1, 1, 0, -1, -1, -1};
  int rown[8] = {-1, -1, 0, 1, 1, 1, 0, -1};
  int *SN, *ix, *ixc, *LOCALMINIMA, *MV;
      if( nrhs > 3 || nlhs > 2 ) {
          mexErrMsgTxt("Need 3 inputs and no more than 2 output");
      }
  // input data
    SN    = mxGetData(prhs[0]);
  nrow  = mxGetM(prhs[0]);
  ncol  = mxGetN(prhs[0]);
  nrc   = nrow*ncol;
  LOCALMINIMA  = mxGetData(prhs[1]);
  nrLM  = mxGetNumberOfElements(prhs[1]);
  
  MV = mxGetData(prhs[2]);
  
  // output 
  plhs[0] = mxCreateNumericMatrix((mwSize) nrow*ncol - nrLM,(mwSize) 1, mxUINT32_CLASS, mxREAL);
  plhs[1] = mxCreateNumericMatrix((mwSize) nrow*ncol - nrLM,(mwSize) 1, mxUINT32_CLASS, mxREAL);
  
  ix      = mxGetData(plhs[0]);
  ixc     = mxGetData(plhs[1]);
  
  // set initial pointer locations
  pix1 = (nrc-nrLM-MV[0]-1);
  pix2 = (nrc-nrLM-MV[0]-1);
  pLM  = 0;
  
  // IX = LOCALMINIMA(pLM)
  IX = LOCALMINIMA[pLM] - 1;
  
  while (pix1 >= 0) {
    row = IX%nrow;
    col = (IX-row)/nrow;
    
    for ( neigh = 0; neigh < 8; neigh++ ) {
      // row index of neighbor
      r = row + rown[neigh];
      // column index of neighbor
      c = col + coln[neigh];
      // potential neigbhor outside grid boundaries?
      // if yes, go back to beginning of the for loop
            if (r<0 || r >= nrow || c < 0 || c >=ncol) {
               continue;
            }
      
      IXN = c*nrow + r;
      
      if (SN[IXN] == (IX+1)) {
        ixc[pix1] = (int) IX+1;
        ix[pix1]  = (int) IXN+1;
        pix1 = pix1-1;
        
      }
    }
    
    // no upslope neighbor
    if (ix[pix2] == 0) {
      pLM = pLM +1;
      if (pLM > nrLM) {
      return;
      }
      IX = LOCALMINIMA[pLM] -1;
    } else {
      IX = ix[pix2] - 1;
      pix2 = pix2-1;
    }
  }
  return;
}

Anon 2013-1-24

Hi Colin,

I intend to work with uint32 in Matlab, since some of matrices I work with require large amounts of memory.

Thanks, Anon

James Tursa 2013-1-24

@anon: The mex function is likely corrupting memory but that corruption isn't detected until later on after the mex routine has returned control back to MATLAB. E.g., the mex routine might have corrupted another variable in the workspace that has nothing to do with the mex routine, and it isn't until you get back to MATLAB and do downstream stuff that the error has an effect and crashes MATLAB. If you are unfamiliar with debugging then I suggest you follow my advice and put in lots of checks all over your code to detect when you are out-of-bounds or dereferencing a NULL pointer etc.

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Answer 1

Jan 2013-1-24

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编辑：Jan 2013-1-24

It is a bad idea to use int * pointers on a 64 bit system. mwSize and mwIndex is smarter and avoids the typical crashes.

When ix is a pointer to a UINT32 array, use a uint32_T * to access its elements instead of an int.

You check c to be smaller than 0, but are you sure than mwIndex is signed at all? If your algorithm required a signed type, use mwSignedIndex explicitly.

It is easy to write a C-Mex file, which corrupts the memory. Frequently the crash does not occur inside the C-Mex, because C is very tolerant to brute memory access, in opposite to Matlab.

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Anon 2013-1-28

Thank you everyone for your replies. I have changed the pointer class and used mwSignedIndex as suggested by Jan. So far, I haven't experienced any crashes anymore.

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