[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.
> 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)
> ______________________________________________________
> Click here to donate to the Hurricane Katrina relief effort.
> http://store.yahoo.com/redcross-donate3/
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list