[gmx-users] md using mpich
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 20 09:27:42 CEST 2004
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
> 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?
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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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