[gmx-users] Parallel running problem
David van der Spoel
spoel at xray.bmc.uu.se
Wed Sep 7 14:26:38 CEST 2005
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.
> 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
> -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
> -[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
> Fatal error: run input file short.tpr was made for 4
> while mdrun expected it to be for 1
> Alan Dodd (University of Bristol)
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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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