Re: malloc patch for 2.2.4

[Jakub Jelinek <jakub at redhat dot com>]

On Wed, Aug 29, 2001 at 11:28:36AM +0200, Christian Iseli wrote:
> #0  0x400d2740 in chunk_alloc () from /lib/libc.so.6
> (gdb) where
> #0  0x400d2740 in chunk_alloc () from /lib/libc.so.6
> #1  0x400d3f79 in calloc () from /lib/libc.so.6
> #2  0x08198c2b in s_MemAllocator (ptr=0x0, size=16, flags=4, allocator=eA_Calloc) at ncbimem.c:261
> #3  0x08198e94 in Nlm_MemNew (size=16) at ncbimem.c:339
> #4  0x08199901 in ValNodeNew (vnp=0x0) at ncbimisc.c:466
> #5  0x080d291d in SeqEntryNew () at objsset.c:829
> #6  0x080e66b5 in FastaToSeqEntryInternalExEx (input=0x82ca418, type=2, next_char=0x0, is_na=1 '\001', errormsg=0x0, parseSeqId=0 '\000',
>     special_symbol=0x0, prefix=0xbffff520 "", ctrptr=0xbffff536, mask_ptr=0xbffff514, trustID=1 '\001') at tofasta.c:1932
> #7  0x080e5c9c in FastaToSeqEntryForDb (fp=0x82ca418, is_na=1, errormsg=0x0, parseSeqId=0, prefix=0xbffff520 "", ctrptr=0xbffff536,
>     mask_ptr=0xbffff514) at tofasta.c:1403
> #8  0x0804b7aa in Nlm_Main () at megablast.c:1007
> #9  0x081970ed in main (argc=15, argv=0xbffff5d4) at ncbimain.c:100
> #10 0x40072733 in __libc_start_main () from /lib/libc.so.6
> 
> but sometimes the process dies while accessing an invalid pointer in one of 
> the program's functions.
> 
> I have tried to compile with -fno-strict-aliasing.  I have tried to apply your 
> malloc volatile patch.  Still, I get the same behaviour.
> 
> What can I do to help track this down ?

I'd suggest using ElectricFence, MALLOC_CHECK_ or some similar memory
allocation checker.

	Jakub