[gmx-users] MPIRUN problem when switched to 8 np (searched the list)

[Florian Haberl]

Hi,

On Sunday, 30. September 2007 19:12, liu xin wrote:
> Thanks Mark
>
> But there's no standard error output at all for my problem, it seems mdrun
> stagnated at this point, I dont know if anybody had met this situation
> before...and now I'm compiling LAMMPI as you suggested, hope this works for
> me.

does your calculation run with PBS or any queuing system?
You can try to run mpirun or others like mpiexec with a verbose option.

In your previous mail you wrote something about running jobs with mpd, is it 
your queuing system 
(http://www-unix.mcs.anl.gov/mpi/mpich1/docs/mpichntman/node39.htm), i don`t 
know if its outdated (webpage seems so).


Here gromacs run without problems with different mpi implementations also with 
intel-mpi, mvapich.

>
> On 10/1/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > liu xin wrote:
> > > Dear GMXers
> > >
> > > my mdrun stops when I try to do it with 8 nodes, but there's no error
> > > message, here's the end of the md0.log:
> >
> > The log file won't be helpful if the problem is outside of GROMACS, and
> > the fact that it isn't helpful is strongly diagnostic of that. You need
> > the standard error to diagnose what your system problem is.
> >
> > > "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> > > LINCS: A Linear Constraint Solver for molecular simulations
> > > J. Comp. Chem. 18 (1997) pp. 1463-1472
> > > -------- -------- --- Thank You --- -------- --------
> > >
> > >
> > > Initializing LINear Constraint Solver
> > >   number of constraints is 3632
> > >   average number of constraints coupled to one constraint is 2.9"
> > >
> > >
> > > I also tried 6 nodes or 10 nodes, but mdrun always stops here, there's
> > > no problem if I ran it by -np 4.
> > > I searched the list, I found some people said that this probably
> > > because the MPI version, currently, we used the 1.2.7
> >
> > MPICH  for GROMACS is not supported at all. Try LAM if you suspect the
> > MPI install, and I would suspect it.
> >
> > Mark
> > _______________________________________________
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Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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