Re: Segmentation fault

This is a discussion on Re: Segmentation fault within the C Programming forums, part of the General Programming Boards category; Hi all, I had recently met with segmentation fault in my program but i could not figure out why it ...

  1. #1
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    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...
    ================================================
    Code:
    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;
    .
    . 
    .
    .
    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);
                                  }
    
    .
    .
    .
    .
    ================================================
    and the error starts at "start = (AMINO*)pop1;" ...
    could anone kindly enlighten me why ?

    Thanks so much!!

  2. #2
    CSharpener vart's Avatar
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    start->seq

    start is just a pointer, where it is allocated?
    you cannot dereference pointer that points nowhere
    The first 90% of a project takes 90% of the time,
    the last 10% takes the other 90% of the time.

  3. #3
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    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.
    Callou collei we'll code the way
    Of prime numbers and pings!

  4. #4
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    Code:
    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; 
    }
    
    ============================

  5. #5
    CSharpener vart's Avatar
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    Code:
    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
    The first 90% of a project takes 90% of the time,
    the last 10% takes the other 90% of the time.

  6. #6
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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 ?
    Last edited by turkish_van; 01-18-2007 at 07:52 AM.

  7. #7
    CSharpener vart's Avatar
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    Quote 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 ?
    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)
    The first 90% of a project takes 90% of the time,
    the last 10% takes the other 90% of the time.

  8. #8
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    Oh my god vart ... you are so on the spot ... you actually pointed to something that i had neglected ...
    Thanks so much!!!!

  9. #9
    Frequently Quite Prolix dwks's Avatar
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    Code:
    #include<strings.h>
    I think you meant
    Code:
    #include<string.h>
    dwk

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