On 22/04/2010 3:12 AM, Arden Perkins wrote:
Did you preprocess the .tpr file for 2 cores with grompp?
This was only necessary for GROMACS 3.
Also, I
believe you have to have an additional -np 2 after the mdrun_mpi
This was only necessary with early versions of MPI libraries.
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.
:-)
Mark
Good luck!
Arden
On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin <jian...@phys.sinica.edu.tw
<mailto:jian...@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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