[gmx-users] intel compiler + amd64: help needed.
lindahl at sbc.su.se
Thu Jun 1 09:34:12 CEST 2006
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
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).
> 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
> #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
> #7 0x0000000000400fef in mknb_write_function () at mknb.c:154
> #8 0x00000000004017cf in main (argc=1, argv=0x7fffffffd628) at
> 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.
> 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 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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