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
-Justin
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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