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

[Rajiv]

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Yes i noticed them. Since i am not using MPI-enabled threats ( I use single PC contains 24 threads with 1 GPU and OpenMP installed), the -multi command doesn't work. 


I wonder is there any other way without using MPI-enabled or should i have reconfigure with MPI? 

> 
> 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. 
There is an example command line in the PDF file I pointed to. 
The idea is to start all three simulations with one command line, 
either using -multi 3 or -multidir dir1 dir2 dir3 

Carsten 

> 
> 
>> 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 
> http://arxiv.org/src/1507.00898v1/anc/supporting.pdf 
> 
> Carsten