[gmx-users] intel compiler + amd64: help needed.

David Mathog mathog at caltech.edu
Wed May 31 21:13:56 CEST 2006

> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
> (gdb) where
> #0  0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
> #1  0x00002aaaab140e6f in vfprintf () from /lib64/tls/libc.so.6
> #2  0x00002aaaab15e2a9 in vsprintf () from /lib64/tls/libc.so.6
> #3  0x00002aaaab149568 in sprintf () from /lib64/tls/libc.so.6
> #4  0x000000000040248b in mknb_code (format=0x40cd2e "s") at
> mknb_metacode.c:282

This says that there's a call to sprintf() at mknb_metacode.c line
282.  Just before that call check all the parameters that will
be passed to sprintf.  You can do that in the debugger, but you
might find it easier to just put a bunch of printf's in at that point. 
Looks like there's a a bad pointer in there somewhere.  Once you
figure out which variable is bogus trace back up through the following
code with the debugger (or more printf's)

> #5  0x0000000000401aaf in mknb_declare_real (name=0x7fffffffd0d0
> "ix1,iy1,iz1,fix1,fiy1,fiz1") at mknb_metacode.c:104
> #6  0x0000000000403e62 in mknb_declare_variables () at
> mknb_declarations.c:258
> #7  0x0000000000400fef in mknb_write_function () at mknb.c:154
> #8  0x00000000004017cf in main (argc=1, argv=0x7fffffffd628) at mknb.c:348

until you find out where things have gone wrong.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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