memory errors while reading a large file in C - c

Question

I am very novice in working with malloc/realloc in C and so need some help. The following is short snippet of a big program where I intend to read a big (fasta) file almost 80000 line numbers and store the first line marked with > (name) and following line (sequence) in two separate arrays- fasta_name and fasta_seq. I have used a standard library which gives the output as a structure but I need to change it into arrays since later on the program I need to check input provided by the user with each of the fasta entries in the file..
The inputfile format is:
P21306\n
MSAWRKAGISYAAYLNVAAQAIRSSLKTELQTASVLNRSQTDAFYTQYKNGTAASEPTPITK\n
P38077\n
MLSRIVSNNATRSVMCHQAQVGILYKTNPVRTYATLKEVEMRLKSIKNIEKITKTMKIVASTRLSKAEKA\n
=======================
The code is:
KSEQ_INIT(gzFile, gzread) ///EXTERNAL LIBRARY FOR BIOLOGISTS READING FASTA FORMAT FILE///
int main(int argc,char *argv[])
{
char **fasta_name=(char **)malloc(sizeof(char *)*80000);
for(i=0;i<size;i++)
{
fasta_name[i]=(char*)malloc(sizeof(char)*50);
}
char **fasta_seq=(char**)malloc(sizeof(char *)*80000);
for(i=0;i<size;i++)
{
fasta_seq[i]=(char*)malloc(sizeof(char)*5000);
}
fpf = gzopen("fasta_seq_nr_uniprot.txt", "r");
seq = kseq_init(fpf);
while((l = kseq_read(seq)) >= 0)
{
strcpy(fasta_name[index1],seq->name.s);
strcpy(fasta_seq[index1],seq->seq.s);
index1++;
}
kseq_destroy(seq);
gzclose(fpf);
for(i=0;i<size;i++)
{
free(fasta_name[i]);
}
for(i=0;i<size;i++)
{
free(fasta_seq[i]);
}
free(fasta_name);
free(fasta_seq);
The program shows no compilation errors but the following memory errors and segmentation fault using Valgrind.
$ valgrind --track-origins=yes --leak-check=full ./Gwidd_uniprot_map2 xaa==3511== Memcheck, a memory error detector
==3511== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==3511== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright info
==3511== Command: ./map2 xaa
==3511==
--3511-- ./map2:
--3511-- dSYM directory has wrong UUID; consider using --dsymutil=yes
Opening file xaa
==3511== Use of uninitialised value of size 8
==3511== at 0x100012C43: __strcpy_chk (mc_replace_strmem.c:893)
==3511== by 0x100001A78: __inline_strcpy_chk (in ./map2)
==3511== by 0x10000183E: main (in ./map2)
==3511== Uninitialised value was created by a heap allocation
==3511== at 0x100011345: malloc (vg_replace_malloc.c:236)
==3511== by 0x10000170C: main (in ./map2)
==3511==
==3511== Invalid write of size 1
==3511== at 0x100012C43: __strcpy_chk (mc_replace_strmem.c:893)
==3511== by 0x100001A78: __inline_strcpy_chk (in ./map2)
==3511== by 0x10000183E: main (in ./map2)
==3511== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==3511==
==3511==
==3511== Process terminating with default action of signal 11 (SIGSEGV)
==3511== Access not within mapped region at address 0x0
==3511== at 0x100012C43: __strcpy_chk (mc_replace_strmem.c:893)
==3511== by 0x100001A78: __inline_strcpy_chk (in ./map2)
==3511== by 0x10000183E: main (in ./map2)
==3511== If you believe this happened as a result of a stack
==3511== overflow in your program's main thread (unlikely but
==3511== possible), you can try to increase the size of the
==3511== main thread stack using the --main-stacksize= flag.
==3511== The main thread stack size used in this run was 8388608.
==3511==
==3511== HEAP SUMMARY:
==3511== in use at exit: 6,674,813 bytes in 3,664 blocks
==3511== total heap usage: 3,807 allocs, 143 frees, 6,698,108 bytes allocated
==3511==
==3511== LEAK SUMMARY:
==3511== definitely lost: 0 bytes in 0 blocks
==3511== indirectly lost: 0 bytes in 0 blocks
==3511== possibly lost: 0 bytes in 0 blocks
==3511== still reachable: 6,674,813 bytes in 3,664 blocks
==3511== suppressed: 0 bytes in 0 blocks
==3511== Reachable blocks (those to which a pointer was found) are not shown.
==3511== To see them, rerun with: --leak-check=full --show-reachable=yes
==3511==
==3511== For counts of detected and suppressed errors, rerun with: -v
==3511== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)
Segmentation fault
CODE EDITED AS:
char **fasta_name=(char **)malloc(sizeof(char *)*80000);
if(fasta_name == NULL)
{
printf("Unable to allocate memory.\n");
exit(EXIT_FAILURE);
}
for(i=0;i<size;i++)
{
fasta_name[i]=(char*)malloc(sizeof(char)*50);
if(fasta_name[i] == NULL)
{
printf("Unable to allocate memory.\n");
exit(EXIT_FAILURE);
}
}
char **fasta_seq=(char**)malloc(sizeof(char *)*80000);
if(fasta_seq == NULL)
{
printf("Unable to allocate memory.\n");
exit(EXIT_FAILURE);
}
for(i=0;i<size;i++)
{
fasta_seq[i]=(char*)malloc(sizeof(char)*5000);
if(fasta_seq[i] == NULL)
{
printf("Unable to allocate memory.\n");
exit(EXIT_FAILURE);
}
}
fpf = gzopen("fasta_seq_nr_uniprot.txt", "r");
seq = kseq_init(fpf);
while((l = kseq_read(seq)) >= 0)
{
strcpy(fasta_name[index1],seq->name.s);
strcpy(fasta_seq[index1],seq->seq.s);
index1++;
}
kseq_destroy(seq);
gzclose(fpf);

Answer 1

Based on the error Access not within mapped region at address, I would say that you are accessing memory that's out of bounds, causing your segmentation fault. Check that malloc() doesn't return NULL to you after calling it, otherwise you risk accessing memory you don't actually own.
Do this after every single malloc() call. For example:
int *i = (int *) malloc(sizeof(int));
if(!i){
fprintf(stderr, "Something went wrong with malloc(), exiting...\n");
exit(1);
}
Another thing to check is to see if index1 is out of bounds of your allocations. I don't see where it's declared or initialized. Is it possible that your allocation for fasta_name and others is too small, given that you read information using a while loop that keeps incrementing the index?