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

[Jones de Andrade]

Hi all.

Sorry for answering twice, but I tried a bit more with the debuggers and,
despite not finding how to fix what I'm doing wrong, I could get some extra
information:

Using "idb":

Intel(R) Debugger for Intel(R) EM64T -based Applications, Version 9.0-16,
Build 20051121
(idb) load ./mknb
Reading symbolic information from /home/johannes/src/gromacs/gromacs-3.3
/src/gmxlib/nonbonded/nb_kernel/mknb...done
(idb) run
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.
Thread received signal SEGV
stopped at [<opaque> __find_specmb(...) 0x00002aaaab15a88c]

Information:  An <opaque> type was presented during execution of the
previous command.  For complete type information on this symbol,
recompilation of the program will be necessary.  Consult the compiler man
pages for details on producing full symbol table information.

And using "idb -gdb":

Intel(R) Debugger for Intel(R) EM64T -based Applications, Version 9.0-16,
Build 20051121
(idb) file ./mknb
Reading symbols from /home/johannes/src/gromacs/gromacs-3.3
/src/gmxlib/nonbonded/nb_kernel/mknb...done.
(idb) run
Starting program: /home/johannes/src/gromacs/gromacs-3.3
/src/gmxlib/nonbonded/nb_kernel/mknb
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.
Program received signal SIGSEGV
__find_specmb () in /lib64/tls/libc.so.6

Now, using "gdb, file, run, where", as suggested, I get:

GNU gdb 6.3
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
(gdb) file ./mknb
Reading symbols from /home/johannes/src/gromacs/gromacs-3.3
/src/gmxlib/nonbonded/nb_kernel/mknb...done.
Using host libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) run
Starting program: /home/johannes/src/gromacs/gromacs-3.3
/src/gmxlib/nonbonded/nb_kernel/mknb
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.

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
#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

Well, what does this kind of stuff means? It worries about the libc 4 times,
but also about the other files. :( What shall I look at?

David Mathog: thanks also. But, how could I fix that?

Thanks a lot for everything.

Jones

On 5/31/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> gdb> where
> it will tell you the line in the mknb this was called from.
> if you call a library function with garbage data it may crash there...
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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