[gmx-developers] CVS Version - segmentation faults in double precision

[Marc Baaden]

>>> Berk Hess said:
 >> I did only --disable-float (plus some prefix stuff).
 >> Are you sure you used the right binary/compilation?
 >> At the top of the md.log file you can now see when the code was compiled.

Yes. Verified.
I also just recompiled with only the --disable-float option.
Same result: segmentation fault.
Something very fishy seems to be going on.
Any suggestions ?


The run ends like this:
[..]
Back Off! I just backed up ener.edr to ./#ener.edr.3#
Steepest Descents:
   Tolerance (Fmax)   =  5.00000e+02
   Number of steps    =          200
s.sh: line 2:   825 Segmentation fault      mdrun_d -v -s em_vide -o em_vide -c after_em_vide -g em_videlog


I have put the output of running with -debug here:
http://www.shaman.ibpc.fr/mdrun_d.log


What else could I do to find the origin for this segmentation fault ?

The weird thing as I said is that it runs fine in single precision.
What kind of stuff would depend on precision ??


Lastly I add the end of an strace output below:
[..]
brk(0)                                  = 0x82ae000
brk(0x82db000)                          = 0x82db000
write(3, "Adding 16384 J particles for SR "..., 52) = 52
write(3, "Adding 16384 J particles for SR "..., 42) = 42
write(3, "Adding 16384 J particles for SR "..., 47) = 47
brk(0)                                  = 0x82db000
brk(0x830b000)                          = 0x830b000
write(3, "Adding 16384 J particles for SR "..., 52) = 52
write(3, "Adding 16384 J particles for SR "..., 42) = 42
old_mmap(NULL, 135168, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x40317000
write(3, "Adding 16384 J particles for SR "..., 47) = 47
write(3, "nsearch = 1378\n", 15)        = 15
write(4, "Configuring nonbonded kernels..."..., 33) = 33
write(4, "Testing ia32 SSE2 support...", 28) = 28
rt_sigaction(SIGILL, {0x8146ba0, [ILL], SA_RESTORER|SA_RESTART, 0x401da6f8}, {SIG_DFL}, 8) = 0
write(4, " present.\n", 10)             = 10
write(4, "\n\n", 2)                     = 2
--- SIGSEGV (Segmentation fault) @ 0 (0) ---
+++ killed by SIGSEGV +++

Thanks,
Marc

-- 
 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217