[gmx-users] Parallel running problem

[Peter C. Lai]

On Fri, Sep 16, 2005 at 03:23:07AM -0700, Alan Dodd wrote:
> 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
> 

I dunno, I recently (a few months ago, really) compiled 3.2.1 against
mpich1.2.5.2 initially and then against mpich1.2.6 on a dual-socket p3 
with gcc3.4.2 and ran all the test suites with no problems (I was actually 
running gromacs-mpich to debug the new FreeBSD kernel scheduler while getting 
some side work out of the otherwise idle cpus), so I really don't know what 
your problem is either [i.e. WORKSFORME albeit on a different platform] :(

Note that I also linked FFTW against MPICH - I think this is a critical step
(and everything was built as single precision, but I vaguely remember running
double over mpich without any problems either).

> --- 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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> 
> 
> 
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-- 
Peter C. Lai
Cesium Hyperfine Enterprises
http://cowbert.2y.net/