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

Thu, 01 Jun 2006 00:37:40 -0700

Hi Jones,

There are two things I can think of immediately:

1. Make sure to set optimization and architecture options for portable code. By default, the intel compiler might generate binaries that use SSE3-specific stuff, although it is unlikely in this part of the code.

2. Try setting "CC_FOR_BUILD=gcc" before running configure, or as an argument when calling make. This will use a different compiler for code that is executed during the build process (important for cross-compiling, and on systems where you cannot execute mpicc-compiled programs outside the queue).

Cheers,

Erik


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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]    [EMAIL PROTECTED]   http://folding.bmc.uu.se
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