[gmx-users] Best step to run simulation over GPU?

라지브간디 rajiv at kaist.ac.kr
Mon Jul 27 04:53:23 CEST 2015


Thanks for the info.

Can i put the command as below if i wanna run 3 simulation which has 24 processor with 1 GPU

mdrun -deffnm first -multi 1

mdrun -deffnm second -multi 2

mdrun -deffnm third -multi 3

or i have to specify -multi 3 to all cases ? I am bit confused with this. thanks.

> On 24 Jul 2015, at 08:48, RJ <rajiv at kaist.ac.kr> wrote: 
> Dear gmx, 
> I have a single PC contains 24 threads with GTX 980Ti. 
> I would like to know how do i run the 3 or 2 simulation in same time with above mentioned PC would have similar speed. 
Simply try it out :) 

It could be beneficial to use the -multi options of gmx mdrun 
to start the multiple simulations. This way GROMACS would automatically 
take care of proper process placement and pinning. 

You could make a quick check with, e.g., mdrun -nsteps 5000 -resethway -multi ? 
to get a performance estimate for 2 and for 3 simulations. 

There is more information about this on page 7 of 


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