[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
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!
> 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:
> 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
> -c 200ns.gro.
> When the simulation starts, I use the commend, "top", to check the
> 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
> How can I do for that?
> Any and all assistance is greatly appreciated.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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