Error After Increasing Macro in C

Error After Increasing Macro in C

I am trying to calculate a correlation measure for 18456 genes but the
compiler (Dev C) exits after increasing macros GENE or INDEX to a value
between 4000 and 5000 or bigger. For example it works well with:
# define GENE 4000
# define INDEX 3000
but not with:
#define GENE 5000
#define INDEX 100
Input file is a space delimited text file with 18456 rows and 57 columns.
Here is the code:
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <time.h>
#include <limits.h>
#define GENE 5000
#define N 57
#define INDEX 1000
int main (void) {
clock_t start, stop;
double t = 0.0;
int i, j, p, q, wp, wq;
double x;
double *S_matrix = (double *)malloc(INDEX * GENE * sizeof(double));
double sum_S, S_max;
double S[11] = {0};
double r = 0.0, xbar = 0.0, ybar = 0.0, sx = 0.0, sy = 0.0;
// read E matrix
FILE *fq;
double E[GENE][N] = {{0}};
if ((fq = fopen("E_disease.txt", "r")) == NULL )
{
printf("Error\n");
exit(EXIT_FAILURE);
}
fq = fopen("E_disease.txt","r");
printf("\n");
for (i=0;i<GENE;i++)
{
for(j=0;j<N;j++)
{
fscanf(fq,"%lf",&x);
E[i][j] = x;
}
}
printf("\n");
fclose(fq);
// calculate correlation
assert((start = clock())!=-1);
for(p=0; p < INDEX; p++)
{
for(q=0; q < GENE; q++)
{
for(i=0; i<11; i++)
{
/*compute xbar */
for(j = i; j < N; j++)
{
xbar += E[p][j];
}
xbar /= N;
/*compute ybar*/
for(j = i; j < N; j++)
{
ybar += E[q][j];
}
ybar /= N;
/* compute standard deviation of x*/
for(j = i; j < N; j++)
{
sx += (E[p][j] - xbar) * (E[p][j] - xbar);
}
sx = sqrt(sx);
/* compute standard deviation of y */
for(j = i; j < N; j++)
{
sy += (E[q][j] - ybar) * (E[q][j] - ybar);
}
sy = sqrt(sy);
/*compute r, the correlation coefficient between the two
arrays */
for( j = i; j < N; j++ )
{
r += (((E[p][j] - xbar)/sx) * ((E[q][j] - ybar)/sy));
}
r /= (N);
if(r>0)
{
S[i] = r;
}
else if(r<=0)
{
S[i] = 0;
}
}
for(j=0, sum_S=0; j<11; j++)
{
sum_S += S[j];
}
for(j=0, S_max = 0; j<11; j++)
{
if(S[j] > S_max)
{
S_max = S[j];
}
}
S_matrix[p*GENE + q] = sum_S/(11*S_max);
}
}
FILE * fs;
fs = fopen ("s_matrix.txt", "w+");
for(wp=0; wp<INDEX; ++wp)
{
for(wq=0; wq<GENE; ++wq)
{
fprintf(fs, "%lf", S_matrix[wp*GENE + wq]);
fprintf(fs, "\t");
}
fprintf(fs, "\n");
printf("\n");
}
fclose(fs);
stop = clock();
t = (double) (stop-start)/CLOCKS_PER_SEC;
printf("Run time: %f\n", t);
//print results
//return (0);
getchar();
}