[gmx-users] IRIX PROBLEMS

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 9 10:58:00 CET 2003

On Tue, 2003-12-09 at 10:44, Raj Badhan wrote:
> Dear Users,
> Firstly thank you too all who have passed on suggestions for my 
> EM runs with ATP, I'm half way there now, but I'm sure I will be 
> bugging you all again for more assistance.
> Secondly, we are having troubles running our simulations on the 
> Universities high performance computer system.
> They have installed Gromacs in double precision for us, and I can 
> quite happily run my simulations using a single processor (-np 1) 
> by issuing the MPIRUN command. But when we try to run in 
> parallel on 4 processors, we get an error message back stating 
> that the run input files were designed 256 nodes and were 
> expecting to be for 4 nodes.

please start your tests with a simple system, e.g. the water box from
the tutorial

grompp -np 4
mpirun -c 4 mdrun

should work (for LAM, for SGI mpirun you may need different command

Energy minimization in parallel does not work IIRC.

> This occurs when initiating the MDRUN command for the first set of 
> energy minimisations on out protein.
> We are not allowed interactive access to the server, and must 
> submit batch jobs of each commands. Now, these commands 
> seem to be fine as we can run the sims. on a single processor, but 
> there is always a problem when running in parallel.
> Could this be a conflict with some of the libraries, something like 
> FFTW and LAM-MPI??
The error message you showed suggests otherwise.

David van der Spoel, PhD, Assist. 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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