segmentation fault

**yazdan59** · 06-27-2007

I want to use fopen , fclose, fscanf , fgetc , etc. for about 5000 times in one program. But when it reaches to 4200, the “segmentation fault” is occurred. What should I do in order to leave this error and run my program completely?
(I do the program in Linux i386, Suse 8.2 with gcc compiler)

**MacGyver** · 06-27-2007

Originally Posted by yazdan59

What should I do in order to leave this error and run my program completely?

Find the error.
Fix the error.
Search for other errors. If you find an error, goto step 2.
Enjoy a nice pizza and a coke.

**Salem** · 06-27-2007

There should be no problem doing this in a correct program, there must obviously be some bugs in your code.

Without seeing the code, it's all just guess-work. There are many 1000's of ways of screwing up which result in seg faults.

**yazdan59** · 06-27-2007

here is the code. what change i should do in the code? please help me if you can.

Code:

#include"stdio.h"
#include"stdlib.h"
#define numloop 5000
#define helixsize 8
main()
{
char hyphen = '!';char atomname = 'H';char u,r,l,d;
int t=0;int i,j,jj,ii;int RESIDUES,CHAINS,natom;
int nuatom[2000];int nures[2000];
char line[200];char name1[2000];char aa[2000];char bb[2000];char dna[2000];char NAME[10];

FILE *out;
out=fopen("output.c","w");
FILE *out2;
out2=fopen("output2.c","w");
FILE *in1;
in1=fopen("outnames.c","r");

int no = 0;int fin = 0;int test,num;

for (j=0; j<numloop; j++)
{
char q1[43]="/home/Yazdan/dnabase/datadssp/1/";
char q2[43]="/home/Yazdan/dnabase/datadssp/2/";

fscanf(in1,"%9s\n", &NAME);

strcat(q1,NAME);
strcat(q2,NAME);

FILE *in;

if ( ( in=fopen(q1,"r") ) != NULL ) { printf("file is available here:%s\n",q1);  in=fopen(q1,"r"); no = no +1;}
else if ( ( in=fopen(q2,"r") ) != NULL ) { printf("file is available here:%s\n",q2);  in=fopen(q2,"r"); no = no +1;}
else	{
	printf("file is not available in sources\n");
	fin=fin+1;
	continue;
	}

for (i=1; i<30; i++)
{
if (i==7)	{fscanf(in,"%4d%4d", &RESIDUES,&CHAINS);}
else	{
	fgets(line,150,in);
	fprintf(out,"%s",line);
	}
	}

natom =RESIDUES+CHAINS-1;

int n=0;
for (i=1; i<natom+1; i++)
{
fscanf(in,"%4d%3d%2s%2s%3s", &nuatom[i],&nures[i],&name1[i],&aa[i],&dna[i]);
fgets(line,150,in);
if(dna[i]==atomname) { n=n+1;}
}

int length=0;
int k=0;
int kk=0;

for (i=1; i<natom+1; i++)
{
if( (dna[i]==atomname)|(dna[i+1]==atomname)|(dna[i+2]==atomname)|(dna[i-1]==atomname)|(dna[i-2]==atomname) )
{
length=length+1;
bb[k]=aa[i];
k=k+1;
if (length >= helixsize) {
	if (kk==0) {	for (ii=0; ii<k; ii++)							{
			if( (t != 0) & (t%75 == 0) ) { fprintf(out2,"\n"); }
			fprintf(out2," %c",bb[ii]);					                t=t+1;
			if(ii==k-1){kk=1;}
			}
		}
	else if (kk==1){
		if( (t != 0) & (t%75 == 0) ) { fprintf(out2,"\n"); }
		fprintf(out2," %c",bb[k-1]);
		t=t+1;
			}
	}
}
else {
if (length!=0) {printf("length=%d\n",length);}
length=0;k=0;kk=0;
}
}
	
fclose(in);
fprintf(out,"\nno = %d\n",no);
}/*for number of loops*/
fclose(in1);
fclose(out);
fclose(out2);
}/*for main*/

**MacGyver** · 06-27-2007

First of all, you're allocating 12,210 bytes on the stack, just in terms of the arrays.... You really shouldn't do that imo....

Anyway, your indenting is terrible and you're making it extremely hard on yourself and others to actually read your code and figure out what in the world you're trying to do and what you're actually doing.

Code:

if ( ( in=fopen(q1,"r") ) != NULL )
{ printf("file is available here:&#37;s\n",q1);  in=fopen(q1,"r"); no = no +1;}

You open a file, check if it's successful, and then open it again. Wastes of memory and resources.

Code:

else if ( ( in=fopen(q2,"r") ) != NULL )
{ printf("file is available here:%s\n",q2);  in=fopen(q2,"r"); no = no +1;}

Same thing as before.

Also, you're never closing in until the end, which means you only close the last file opened with in inside the loop. Fix the resource leak.

**yazdan59** · 06-27-2007

Originally Posted by MacGyver

You open a file, check if it's successful, and then open it again. Wastes of memory and resources.

Also, you're never closing in until the end, which means you only close the last file opened with in inside the loop. Fix the resource leak.

there are 5000 files which may locate in two different folders. Note that they may be located. it may not be available. So, first file should check if there is in source directories or not. Then do some work on it. we can not close that file at the end of if section because it is needed to read from that file. in this case, how can i run it successfully? if there is a better way, please let me know.

**megastar** · 06-27-2007

hi!

Code:

Originally Posted by MacGyver  
You open a file, check if it's successful, and then open it again. Wastes of memory and resources.

Also, you're never closing in until the end, which means you only close the last file opened with in inside the loop. Fix the resource leak.

Code:

there are 5000 files which may locate in two different folders. Note that they may be located. it may not be available. So, first file should check if there is in source directories or not. Then do some work on it. we can not close that file at the end of if section because it is needed to read from that file. in this case, how can i run it successfully? if there is a better way, please let me know.

1.Agreed that they may be located and not available .
The very act of fopen being succesful(i.e. no NULL value) implies the file has been LOCATED,OPENED AND THE CORRESPONDING FILE POINTER IS POINTING TO THE FILE STRUCTURE.
So no need to open it twice .
You are basically checking the availability of either of files else performing the
requisite operations.

**megastar** · 06-27-2007

2.

Code:

for (j=0; j<numloop; j++)
{
char q1[43]="/home/Yazdan/dnabase/datadssp/1/";
char q2[43]="/home/Yazdan/dnabase/datadssp/2/";

numloop =5000 if q1[43],q2[43]
need to be initialized with same string always they may be done outside
loop.

**megastar** · 06-27-2007

Code:

#define numloop 5000

Code:

char aa[2000];char bb[2000];char dna[2000];

Code:

for (j=0; j<numloop; j++)

Code:

{fscanf(in,"%4d%4d", &RESIDUES,&CHAINS);}

Code:

natom =RESIDUES+CHAINS-1;

Code:

for (i=1; i<natom+1; i++)

Code:

bb[k]=aa[i];

numloop is 5000 but size of arrays is 2000
the 'natom=residues+chains-1' loop is user input dependent.
Check if you are not exceeding the limits in any cases.
This may be a cause of segmentation fault

**Salem** · 06-27-2007

As mentioned - fix the indentation.

Or use an indent program to make a start, then keep it clean.

Code:

#include"stdio.h"
#include"stdlib.h" /*!! Use <> for system includes */
#include <string.h>
#define numloop 5000
#define helixsize 8
int main()
{
    char hyphen = '!';
    char atomname = 'H';
    char u, r, l, d;
    int t = 0;
    int i, j, jj, ii;
    int RESIDUES, CHAINS, natom;
    int nuatom[2000];/*!! Consider putting these 6 variables into a struct */
    int nures[2000];/*!! Also, make 2000 another #define constant */
    char line[200];
    char name1[2000];
    char aa[2000];
    char bb[2000];
    char dna[2000];
    char NAME[10];

    FILE *out;
    out = fopen("output.c", "w");
    FILE *out2;
    out2 = fopen("output2.c", "w");
    FILE *in1;
    in1 = fopen("outnames.c", "r");

    int no = 0;
    int fin = 0;
    int test, num;

    for (j = 0; j < numloop; j++) {
        char q1[43] = "/home/Yazdan/dnabase/datadssp/1/";
        char q2[43] = "/home/Yazdan/dnabase/datadssp/2/";

        fscanf(in1, "%9s\n", &NAME); /*!! No & required, NAME is an array of char already */

        strcat(q1, NAME);
        strcat(q2, NAME);

        FILE *in;

        if ((in = fopen(q1, "r")) != NULL) {
            printf("file is available here:%s\n", q1);
            in = fopen(q1, "r"); /*!! it's already open, trying again won't help */
            no = no + 1;
        } else if ((in = fopen(q2, "r")) != NULL) {
            printf("file is available here:%s\n", q2);
            in = fopen(q2, "r");
            no = no + 1;
        } else {
            printf("file is not available in sources\n");
            fin = fin + 1;
            continue;
        }

        for (i = 1; i < 30; i++) {
            if (i == 7) {
                fscanf(in, "%4d%4d", &RESIDUES, &CHAINS);
            } else {
                fgets(line, 150, in); /*!! in place of "150", use  "sizeof(line)"  */
                fprintf(out, "%s", line);
            }
        }

        natom = RESIDUES + CHAINS - 1;
        /*!! Add a diagnostic check to make sure it's less than 2000-1 */

        int n = 0;
        for (i = 1; i < natom + 1; i++) {
            /*!! I would suggest fgets() the whole line to begin with, then sscanf on that line */
            /*!! rather than fscanf + some random fgets() to remove trailing data. */
            fscanf(in, "%4d%3d%2s%2s%3s", &nuatom[i], &nures[i], &name1[i], &aa[i], &dna[i]);
            fgets(line, 150, in);
            if (dna[i] == atomname) {
                n = n + 1;
            }
        }

        int length = 0;
        int k = 0;
        int kk = 0;

        /*!! consider making this a separate function to stop main getting too long */
        for (i = 1; i < natom + 1; i++) {
            /*!! you probably want || here, not | */
            if ((dna[i] == atomname) | (dna[i + 1] == atomname) | (dna[i + 2] == atomname) |
                (dna[i - 1] == atomname) | (dna[i - 2] == atomname)) {
                length = length + 1;
                bb[k] = aa[i];
                k = k + 1;
                if (length >= helixsize) {
                    if (kk == 0) {
                        for (ii = 0; ii < k; ii++) {
                            if ((t != 0) & (t % 75 == 0)) {
                                fprintf(out2, "\n");
                            }
                            fprintf(out2, " %c", bb[ii]);
                            t = t + 1;
                            if (ii == k - 1) {
                                kk = 1;
                            }
                        }
                    } else if (kk == 1) {
                        if ((t != 0) & (t % 75 == 0)) {
                            fprintf(out2, "\n");
                        }
                        fprintf(out2, " %c", bb[k - 1]);
                        t = t + 1;
                    }
                }
            } else {
                if (length != 0) {
                    printf("length=%d\n", length);
                }
                length = 0;
                k = 0;
                kk = 0;
            }
        }

        fclose(in);
        fprintf(out, "\nno = %d\n", no);
    }                           /*for number of loops */
    fclose(in1);
    fclose(out);
    fclose(out2);
    return 0;
}                               /*for main */


Then fix these warnings
$ gcc -std=c99 -Wall foo.c
foo.c:6: warning: return type defaults to `int'
foo.c: In function `main':
foo.c:37: warning: char format, different type arg (arg 3)
foo.c:39: warning: implicit declaration of function `strcat'
foo.c:7: warning: unused variable `hyphen'
foo.c:9: warning: unused variable `u'
foo.c:9: warning: unused variable `r'
foo.c:9: warning: unused variable `l'
foo.c:9: warning: unused variable `d'
foo.c:11: warning: unused variable `jj'
foo.c:31: warning: unused variable `test'
foo.c:31: warning: unused variable `num'

**yazdan59** · 06-27-2007

Originally Posted by Salem

Code:

if ((in = fopen(q1, "r")) != NULL) {
            printf("file is available here:%s\n", q1);
            in = fopen(q1, "r"); /*!! it's already open, trying again won't help */
            no = no + 1;
        } else if ((in = fopen(q2, "r")) != NULL) {
            printf("file is available here:%s\n", q2);
            in = fopen(q2, "r");            no = no + 1;
        } else {
            printf("file is not available in sources\n");
            fin = fin + 1;
            continue;
        }

Thanks for all of your suggestions particularly Salem. I only deleted these two section(with color above) and every thing works properly.
Your comments were very useful.

**vart** · 06-27-2007

fscanf(in1,"%9s\n", &NAME);

NAME is already a pointer (array name is a pointer to the first element)
no need to use &

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