Re: Segmentation fault

Hi all,

I had recently met with segmentation fault in my program but i could not figure out why it had occured. Segmentation fault occurs when i am referencing to data that is not there ... So although my program could be compiled, it could not be ran due to segmentation fault ...

Part of my program is as shown below...
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Code:

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typedef struct amino{
char seq;
struct amino *before;
struct amino *after;       
}AMINO;

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int main (void)
{FILE *data, *output, *output1;
 data = fopen ("Sample.txt", "r");
 output = fopen ("output_sample1.txt","w");
 output1 = fopen ("output_sample2.txt","w");
 char input[100] = {};
 AMINO *ptr;
 AMINO *start;
 AMINO *start1;
 AMINO *next;
 AMINO *pop;
 AMINO *pop1;
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if (start->seq == ' ' || start->seq == '\n')
                              {  fprintf(output,"_");
                                  (AMINO*)pop = (AMINO*)start;
                                  (AMINO*)pop1 = (AMINO*)start->before;
                                  start = (AMINO*)pop1;
                                  start->after = NULL;
                                  free(pop);
                              }

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and the error starts at "start = (AMINO*)pop1;" ...
could anone kindly enlighten me why ?

Thanks so much!!

start->seq

start is just a pointer, where it is allocated?
you cannot dereference pointer that points nowhere

Well, since the problem is that you are not correctly malloc'ing memory somewhere, we need to see those mallocs.

Incidentally, what system are you running this on? This kind of bug is really where using a debugger offers more help than the forums could.

Code:

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thanks vart and QuestionC... below is my complete prog ... thanks so much
===========================
#include<stdio.h>
#include<stdlib.h>
#include<math.h>
#include<strings.h>

typedef struct amino{
char seq;
struct amino *before;
struct amino *after;       
}AMINO;

int main (void)
{FILE *data, *output, *output1;
 data = fopen ("Sample.txt", "r");
 output = fopen ("output_sample1.txt","w");
 output1 = fopen ("output_sample2.txt","w");
 char input[100] = {};
 AMINO *ptr;
 AMINO *start;
 AMINO *start1;
 AMINO *next;
 AMINO *pop;
 AMINO *pop1;
 
 while (fgets(input,100,data)!= NULL)
      { if (strstr(input, "SQ  SEQUENCE  " ) != NULL)
            { fprintf (output, "=================================\n");
              start = malloc (sizeof (AMINO));
              start1 = start;
              start->before = NULL;
              start->after = NULL;
                  while ( (start->seq = fgetc (data)) != '/')
                      { fprintf (output, "%c", start->seq);
                          if (start->seq == ' ' || start->seq == '\n')
                              {  fprintf(output,"_");
                                  (AMINO*)pop = (AMINO*)start;
                                  (AMINO*)pop1 = (AMINO*)start->before;
                                  start = (AMINO*)pop1;
                                  start->after = NULL;
                                  free(pop);
                              }
                        next = malloc (sizeof(AMINO));
                        start->after = next;                     
                        next->before = start;
                        start = next;
                        start->after = NULL;
                      }
              ptr = start1;
              while(ptr->after != NULL)
                  {fprintf (output1, "%c", ptr->seq);
                    ptr = ptr->after;
                    }
            fprintf(output1, "\n==============================\n");
            free (start1);
          }
      }
fclose (data);
fclose (output);
fclose (output1);
return EXIT_SUCCESS;
}

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Code:

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start->before = NULL;
//some stuff
pop1 = start->before; //so it is also NULL
start = pop1;//and start also set to NULL
start->after = NULL; //GPF

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Sorry vart ... is the code supposed to point out the error or was it to correct the error ?
I am so sorry ... just a C beginner ?
And what is GPF?
I think the struct AMINO has two pointers to itself so its before and after ...
but in start->before there contains an address and i want to assign it to pop1 ... but by putting it to null, isn't it like removing the address it had ?

Quote:

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Originally Posted by turkish_van

Sorry vart ... is the code supposed to point out the error or was it to correct the error ?
I am so sorry ... just a C beginner ?
And what is GPF?
I think the struct AMINO has two pointers to itself so its before and after ...
but in start->before there contains an address and i want to assign it to pop1 ... but by putting it to null, isn't it like removing the address it had ?

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I just illustrated the error, showed what acctually your code did. I havn't put anything in the vars, just add comments to show what acctually was placed by you in each variable

GPF - is General Protection Fault (segfault)

Oh my god vart ... you are so on the spot ... you actually pointed to something that i had neglected ...
Thanks so much!!!!

Code:

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#include<strings.h>

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I think you meant

Code:

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#include<string.h>

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