[gmx-users] Parallel running problem

[Alan Dodd]

Thanks for all your help, I thought I had compiled
with MPI but from trying to reinstall, it appears not.
The system I'm trying to install on is using mpich,
rather than lammpi.  I wouldn't have thought this
would be a problem, but installing fftw locally
doesn't work - it can't find the mpi libraries.  Both
using the rpms and compiling from source seem to
produce similar errors.  I'm pretty sure others have
used mpich, so have any of you come across a similar
problem (and, ideally, a solution?)
Thanks,
Alan

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On Wed, 2005-09-07 at 05:18 -0700, Alan Dodd wrote:
> > Hello Gromacs users,
> > I gather this problem is similar to many previous,
> but
> > can't see an obvious solution in the replies to
> any of
> > them.  I've been trying to get GROMACS to run on
> this
> > sample dual-core, dual-socket opteron box that we
> have
> > on loan.  Despite my best efforts, I seem unable
> to
> > get mdrun to understand that it's supposed to run
> on
> > more than one node.  I'm telling it to do so, and
> it
> > even appreciates it's supposed to in the output
> (see
> > below), but then decides I've told it to run on
> just
> > the one and dies.  Has anyone any idea what's
> going
> > wrong?  Is it just some kind of incompatibility
> with
> > mpich/the hardware?
> Have you compiled with MPI?
> 
> you can check by typing
> ldd `which mdrun`
> It should show some MPI libraries.
> 
> Dual core opterons run fine by the way. We have a
> brand new cluster
> humming along at 85 decibel.
> > 
> > Input: 
> > mpirun -np 4 -machinefile machines mdrun -np 4 
> > 
> > mdrun output:
> > for all file options
> >          -np    int      4  Number of nodes, must
> be
> > the same as used for
> >                             grompp
> >          -nt    int      1  Number of threads to
> start
> > on each node
> >       -[no]v   bool     no  Be loud and noisy
> > -[no]compact   bool    yes  Write a compact log
> file
> >   -[no]multi   bool     no  Do multiple
> simulations in
> > parallel (only with
> >                             -np > 1)
> >    -[no]glas   bool     no  Do glass simulation
> with
> > special long range
> >                             corrections
> >  -[no]ionize   bool     no  Do a simulation
> including
> > the effect of an X-Ray
> >                             bombardment on your
> system
> > 
> > 
> > Back Off! I just backed up md.log to ./#md.log.5#
> > Reading file short.tpr, VERSION 3.2.1 (single
> > precision)
> > Fatal error: run input file short.tpr was made for
> 4
> > nodes,
> >              while mdrun expected it to be for 1
> > nodes.
> > 
> > 
> > Alan Dodd (University of Bristol)
> > 
> > 
> > 	
> > 		
> >
> _
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