[MINC-users] dynamic memory allocation for hyperslabs

[Simon Eskildsen]

Hi Thomas,

If you want to dynamically allocate a 3D array, I would recommend
doing something like the code below to avoid multiple allocations in
for loops. Not sure if it solves your problem though.

Best,
Simon


dtemp = alloc_3d_double(CX, CY, CZ);

...given the function:

double ***alloc_3d_double(int n1, int n2, int n3)
{
    double ***iii, **ii, *i;
    int j;

    iii = (double ***) calloc(n1,sizeof(double **));
    alloc_error_check(iii);
    ii = (double **) calloc(n1 * n2,sizeof(double *));
    alloc_error_check(ii);
    iii[0] = ii;
    for (j = 1; j < n1; j++) {
        iii[j] = iii[j - 1] + n2;
    }
    i = (double *) calloc(n1 * n2 * n3,sizeof(double));
    alloc_error_check(i);
    ii[0] = i;
    for (j = 1; j < n1 * n2; j++) {
        ii[j] = ii[j - 1] + n3;
    }
    return iii;
}

...and the definition:


#define alloc_error_check(p) { \
    if ((p) == NULL) { \
        fprintf(stderr, "ERROR! Allocation failure. Probably out of
memory.\n"); \
        exit(1); \
    } \
}

On Wed, Apr 27, 2011 at 3:59 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> Hi,
>
> I'm trying to dynamically allocate memory for a hyperslab, but this always seems to lead to a seg fault.  I used hyper-test.c to try and figure out the problem. The normal hyper-test.c compiles and runs fine, so I changed "dtemp[CX][CY][CZ];" to "double ***dtemp;" and then allocate the necessary memory by doing:
>
>        dtemp=malloc(CX * sizeof(double**));
>        for(i=0; i< CX; i++)
>        {
>        dtemp[i]=malloc(CY * sizeof(double*));
>                for(j=0; j < CY; j++)
>                {
>                dtemp[i][j]=malloc(CZ * sizeof(double) );
>                }
>        }
>
> However this resulted in a seg fault on the line:
>
> if (fabs(r - dtemp[i][j][k]) > 1.0e-15)
>
> So even though "miget_real_value_hyperslab" returns 0 and says it gets the hyperslab correctly, there seems to be a problem dereferencing "dtemp" when the memory has been dynamically allocated.
>
> Is there something wrong with my C? Or does "miget_real_value_hyperslab" not work correctly for dynamically allocated memory?
>
> Many thanks for any help!
>
> Best,
>
> Thomas
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