[gmx-users] md using mpich

[David van der Spoel]

On Mon, 2004-10-18 at 14:21, gianluca santarossa wrote:
> Hi all,
>     I 'm in trouble when launching molecular dynamic simulations in 
> parallel with more then 4 procs.
> First of all, I can launch minimizations using any number of procs and 
> it ends correctly.
> Moreover, when I run the simulation with 4 or less procs, everything 
> works fine.
> But if I launch the same simulation using 5 procs or more it doesn't 
> work. The odd thing is that it doesn't exit with errors, but it waits 
> for data which never arrive.
> 
there is a problem in mpich that makes that jobs never end, it has to do
with interaction between MPI and grid software. There is a workaround in
the CVS code that will shortly be released in beta.
> I'm using gromacs 3.2 compiled from source on a cluster mounting Rocks 
> (Red-hat based).
> My command is just
> 
> /opt/mpich/gnu/bin/mpirun -np 6 -nolocal -machinefile machines 
> /usr/local/bin/mdrun_mpi -np 6 -v
> 
> and the output is something like
> 
> [cut]
> starting mdrun 'Generated by genbox'
> 100 steps,      0.2 ps.
> 
> 
> and, after some time, it writes out
> p4_1636:  p4_error: Timeout in establishing connection to remote process: 0
> Received disconnect from 192.168.1.250: Command terminated on signal 13.
> 
> 
> I repeat: other software run, and even the minimization with gromacs 
> works fine.
> I don't know what's happening. Any ideas?
> 
> Thanks
> Gianluca
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-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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