Question

I have this code segment in which I am opening/closing a file a number of times (in a loop):

for(i=1;i<max;i++)
     {
       /* other code */
       plot_file=fopen("all_fitness.out","w");
       for (j=0;j<pop_size;j++)
         fprintf(plot_file, "%lf %lf\n",oldpop[i].xreal[0],oldpop[i].obj);
       fclose(plot_file);
      /*other code*/
     }

I get a SIGABRT here, with the following backtrace:

#0  0x001fc422 in __kernel_vsyscall ()
#1  0x002274d1 in *__GI_raise (sig=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#2  0x0022a932 in *__GI_abort () at abort.c:92
#3  0x0025dee5 in __libc_message (do_abort=2, fmt=0x321578 "*** glibc detected *** %s: %s: 0x%s ***\n")
    at ../sysdeps/unix/sysv/linux/libc_fatal.c:189
#4  0x00267ff1 in malloc_printerr (action=<value optimized out>, str=0x6 <Address 0x6 out of bounds>, ptr=0x8055a60) at malloc.c:6217
#5  0x002696f2 in _int_free (av=<value optimized out>, p=<value optimized out>) at malloc.c:4750
#6  0x0026c7cd in *__GI___libc_free (mem=0x8055a60) at malloc.c:3716
#7  0x0025850a in _IO_new_fclose (fp=0x8055a60) at iofclose.c:88
#8  0x0804b9c0 in main () at ga.c:1100

The line number 1100, is the line where I am doing the fclose() in the above code segment. What is the reason for the above behavior? Any pointers is appreciated.

(I am on Linux and using gcc)

Answer 1

When you call fclose(), glibc releases some dynamically allocated structures; internally there is a free() call. malloc() and free() rely on rather complex, dynamically built structures. Apparently, glibc found that the structures were in an incoherent state, to the point that safe memory release cannot be done. glibc decided that the problem was serious enough to warrant an immediate abort.

This means that you have a bug somewhere in your code, possibly quite far from the snippet you show, a buffer overflow or a similar out-of-place memory write which damages the memory allocation structures.

You may want to try Valgrind or Electric Fence to sort such problems out.