[gmx-users] parallel simulation in dual core PC

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 21 01:02:22 CEST 2010

On 21/04/2010 12:55 AM, Hsin-Lin wrote:
> Hi,
> I want to use my dual core PC to do the simulation.
> The version of GROMACS installed is version 4.0.5.
> According the message post by others on mailing list before.
> I type "lamboot" first, and type the commend:
> mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
> -c 200ns.gro.
> When the simulation starts, I use the commend, "top", to check the utility
> of CPU.
> I found there is only one core which is used by GROMACS.
> And the utility of this core is separated to 52% and 48% for two mdrun_mpi
> jobs.

Depending what is being measured by what, this could be a correct 
result. We can't really tell because we don't know how you've set up 
LAM, or how your top works.

Do a short test calculation with one and two processors and compare the 
run times.


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