[gmx-users] parallel simulation in dual core PC

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 21 19:38:06 CEST 2010

Arden Perkins wrote:
> Did you preprocess the .tpr file for 2 cores with grompp? Also, I 
> believe you have to have an additional -np 2 after the mdrun_mpi 
> command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr 
> -g 200ns.log
> -c 200ns.gro -np 2
> -- at least this is what I understand from what my prof told me. We just 
> started running parallel simulations for an undergraduate research 
> project and I believe that is how we input commands. I'm sure the 
> gromacs experts will correct me if I'm wrong.

Since this is Gromacs 4.0.5, there is no differentiation when running grompp 
regarding the number of processors, so there is no -np flag for grompp.

There is also no need for mdrun_mpi -np; the number of nodes is taken from 
mpirun -np.

In addition, if all the output files are named 200ns.*, then you can save 
yourself some typing:

mpirun -np 2 mdrun_mpi -deffnm 200ns


> Good luck!
> Arden
> On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin <jiangsl at phys.sinica.edu.tw 
> <mailto:jiangsl at phys.sinica.edu.tw>> 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.
>     How can I do for that?
>     Any and all assistance is greatly appreciated.
>     Hsin-Lin
>     --
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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