Hi,
use dynamic memory alloction instead, it will eat up a lot of
memory :) so if you'll have problems you will have to split
your processing to several blocks and read from the file always
only part of data.
char *g;
g = (char *)malloc(SIZE*sizeof(char));
...
/* your algorithm */
...
free(g);
but I would not recomend this, istead I would really partition
data to several smaller blocks as I wrote earlier.
Cheers
Ziza
On Sun, Jan 30, 2005 at 04:32:45PM -0200, Daniel Silvestre wrote:
> Greetings GCC people,
>
> Thank you all for the helpfull tips. The problem really was the system
> size limit of the stack. I've just used the ulimit and the problem was
> gone.
> By the way, I don't know how to use memory allocation to create very
> large arrays (> 10^6 positions). My programs are very simple. But I've
> to load a entire genome/chromosome in a array. And the genome is just
> a very long string (at most 250000000 of chars).
> Some weeks ago, I wrote some perl scripts to do the same task but
> they're much more slow then the C versions. There's a code example.
> It's really a silly code so any comments will be very helpfull.
>
> Best regards,
> --
> Daniel Marques
> GFT - Grupo de Física Teórica
> IFSC - Instituto de Física de S?o Carlos
> sala 16 - Edifício central
> tel: +55(16)33759769 ramal 25
> #include <stdio.h>
> #include <string.h>
> #include <stdlib.h>
> #define SIZE 250000000
> #define N 10000000
>
> int main(int argc, char *argv[]){
>
> FILE *gen, *arq1, *fdp;
>
> char *p, str[2], strng[80], g[SIZE], w[SIZE], c;
> int key, i, j, count, cnt, counter[N+1], sum;
> int counts[N];
> int p0, p1, p2, index, cmp;
>
> p0 = 1; p1 = 4; p2 = 16;
> count = 0;
>
>
> gen = fopen("ltrnsgn.txt", "r");
> while(!feof(gen)) {
> if((p = fgets(str,2, gen)) != NULL){
> g[count] = *p;
> count++;
> }
> }
> fclose(gen);
>
> for(i = 0; i < count; i++){
>
> if(g[i] == 'A') g[i] = 0;
> else if(g[i] == 'T') g[i] = 1;
> else if(g[i] == 'G') g[i] = 2;
> else if(g[i] == 'C') g[i] = 3;
>
> }
>
> for(index = 0; index < 64; index++){
>
> i = j = cnt = sum = 0;
> for(i = 0; i < N; i++){counts[i] = 0; counter[i] = 0;}
> for(i = 0; i < count-2; i++) w[i] = 0;
>
> for(i = 0; i < count-2; i++){
> cmp = g[0+i]*p0+g[1+i]*p1+g[2+i]*p2;
> if(index == cmp) w[i] = 1;
> else w[i] = 0;
>
> }
>
> for(i = 0; i < count-2; i++){
> if(w[i] == 1){
> cnt = cnt++;
> j++;
> }
> else if(w[i] == 0){
> counts[j] = counts[j]++;
> }
> }
> for(i = 0; i < count-2; i++){
> counts[i] = counts[i] - 2;
> if(counts[i] < 0) counts[i] = 0;
> }
>
> for(i = 0; i < N; i++){
> key = 1;
> j = 1;
> while(key == 1){
> if(counts[i] < j){counter[j] = counter[j]++; key = 0;
> }else{j++; key = 1;}
> }
> }
>
> for(i = 0; i < N; i++) sum += counter[i];
>
> sprintf(strng, "all3times%d.dat", index);
>
> arq1 = fopen(strng, "w");
>
> for(i = 0; i < N; i++){
> if(counter[i]){
> fprintf(arq1, "%d %10.9f\n", i, (float)counter[i]/(float)(sum));
> }
> }
>
> fclose(arq1);
> }
>
> return (0);
> }
Attachment:
signature.asc
Description: Digital signature
