[gmx-users] Need help on a SEGV mdrun mpi failure

[David]

On Fri, 2003-10-24 at 18:20, Mostyn Lewis wrote:
> Hello,
> 
> Sent this last night but it seems to have been lost (Maybe because it
> had a 270K attachment of topol.top.bz2?). So here goes again.
> 
> I'm having a problem with a benchmark case which causes SEGV (signal 11)
> in most cases of a MPI run with more than 4 CPUs. The failure is always
> in bondfree.c (gromacs-3.1.4 + gromacs-3.1.5_pre1) in the angles routine
> at line 535
> 
>     ivec_sub(SHIFT_IVEC(g,ai),jt,dt_ij);
>     ivec_sub(SHIFT_IVEC(g,ak),jt,dt_kj);
>     t1=IVEC2IS(dt_ij);
>     t2=IVEC2IS(dt_kj);
> 
>       rvec_inc(fr->fshift[t1],f_i);
>       rvec_inc(fr->fshift[CENTRAL],f_j);
> ----->rvec_inc(fr->fshift[t2],f_k);
>     }                                           /* 168 TOTAL    */
> 
> This line has a BAD t2 value which causes an out of bounds reference
> (actually a little later in x=a[XX]+b[XX]; at line 235 in vec.h due to
> the expansion of rvec_inc)
> 
thanks for the bug report... Had I had this half a year ago, then it
would have saved me a lot of time. As it is, this has been fixed in the
CVS version of the code (unless I'm terribly wrong), as I assume that
this is a run with a protein in little water...


> I enclose a run below with the grompp and mdrun_mpi output followed by
> some dbx debugging output showing some values. This was on a 24 CPU
> SUN SMP box (Sunfire 6800) using 8 CPUs.
> I get the same failure on a cluster of Linux (2 CPU Xeon) boxes doing
> MPI across Gigabit ethernet. The failure occurs in Linux land using
> Intel/PGI and LAM/mpich combinations - so I think this is problem and/or
> Gromacs dependent.
> 
> I'm not a Molecular persona at all, just a humble benchmarker and seek
> help from the enlightened.
> 
> Any files you'd like (topol.top ...) or more debugging are available
> on request.
> 
> Sorry this is so long. Any help would be appreciated.
> 

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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