MATLAB Central Newsreader - Segmentation violation due to MEX code

Segmentation violation due to MEX code

Jose Antonio — Mon, 06 Jul 2009 12:43:24 -0400

Hi again

I am trying to implement a very simple subroutine embeding a CMEX code in Matlab.

Does anybody know if it is possible that I get a "Segmentation violation" error even if I don't go beyond the iput arrays' limits?

I have checked the code with small inputs, and works fine. But when I send a rather huge array, it crashes.

This is the code:
#include "mex.h"

/*
* Calculate_I_Values.c
* Used to speed up the I mapping calculations
*
* This is a MEX-file for MATLAB.
*/

/* The gateway function */
void mexFunction( int nlhs, mxArray *plhs[],
                  int nrhs, const mxArray *prhs[])
{
    /* variable declarations here */
    double *e, *x, *y, *I;
    int eRows, eCols, xRows, xCols, yRows, yCols, index, ySize;
    int m, i, j;
    double num, den;

    e = mxGetPr(prhs[0]);
    eRows = mxGetN(prhs[0]);
    eCols = mxGetM(prhs[0]);

    x = mxGetPr(prhs[1]);
    xRows = mxGetN(prhs[1]);
    xCols = mxGetM(prhs[1]);

    y = mxGetPr(prhs[2]);
    yRows = mxGetN(prhs[2]);
    yCols = mxGetM(prhs[2]);
    ySize = mxGetNumberOfElements(prhs[2]);

    /* Allocate output memory */
    plhs[0] = mxCreateDoubleMatrix(1, 256, mxREAL);
    I = mxGetPr(plhs[0]);

    /* code here */
    printf("The xNumRow is: %d\n", (int)xRows);
    printf("The xNumCol is: %d\n\n", (int)xCols);
    printf("The yNumRow is: %d\n", (int)yRows);
    printf("The yNumCol is: %d\n\n", (int)yCols);
    printf("The ySize is: %d\n\n", (int)ySize);
    printf("The eNumRow is: %d\n", (int)eRows);
    printf("The eNumCol is: %d\n\n", (int)eCols);

    for (m = 0; m <= 255; m++)
    {
        printf("m = %d -> ", (int)m);
        num = 0;
        den = 0;
        for (i = 0; i < yRows; i++)
            for (j = 0; j < yCols; j++)
            {
                index = i * yCols + j;
                if (index >= ySize)
                    printf("Wrong\n");
                else if (m == y[index])
                {
                    num += e[j] * x[i];
                    den++;
                 }
            }
        if (den == 0) I[m] = num;
        else I[m] = num / den;
    }

}

It is actually pretty simple, but...

I call the function by:
Calculate_I_Values(exposures.', x.', y.');

Obviously after compiling.

The first printf lines give me:
The xNumRow is: 361862
The xNumCol is: 1

The yNumRow is: 361862
The yNumCol is: 16

The ySize is: 5789792

The eNumRow is: 1
The eNumCol is: 16

So everyting is as it should be. But then I get the segmentation violation error.

I have commented different parts of the program, and concluded that the error is when I do y[index]. So I guess I am trying to access a memory address which is shouldn't...

But I have already controlled that the index does not exceed the size of the input array! (ySize)

Any clue would be appreciated :)

Thanks in advance
Jose

Re: Segmentation violation due to MEX code

Jose Antonio — Mon, 06 Jul 2009 13:34:17 -0400

I am pretty sure the problem has to do with memory allocation when calling the function.

I think so because I have tried to make it work with arrays with up to 4000 values and it performs correctly...

Any idea if what I say makes sense?

If so, how can I increase the memory assigned to the MEX function?

Thanks!

Re: Segmentation violation due to MEX code

James Tursa — Mon, 06 Jul 2009 19:52:02 -0400

Jose Antonio <juriguen@gmail.com> wrote in message <28112995.79623.1246887287751.JavaMail.jakarta@nitrogen.mathforum.org>...
> I am pretty sure the problem has to do with memory allocation when calling the function.
>
> I think so because I have tried to make it work with arrays with up to 4000 values and it performs correctly...
>
> Any idea if what I say makes sense?
>
> If so, how can I increase the memory assigned to the MEX function?
>
> Thanks!

Compiled and ran without seg fault a dozen times with random data using your specified sizes. So I can't reproduce your error. Are all of your inputs double class?

James Tursa

Re: Segmentation violation due to MEX code

Jose Antonio — Mon, 06 Jul 2009 20:17:02 -0400

Woah

It was that! Thanks so much.

I actually was using y being a matrix of integer values, since it is stored like that when reading an image (uint8)

What would be best to simply pass double(y) to the function or try to read them as integers?

In fact, I have modified the C code, and right now I use the y[index] values as indices for performing operations, rather than looping once and again for (m ...) and scanning all the data for (x...) for (y...)

Jose