[gmx-users] parallel simulation in dual core PC

[Hsin-Lin]

Hi,

I compare the run times.
The calculation of two processors is faster than one.
And I saw the utility of the two cores large than 85% separately.
I can sure it's exactly parallel simulation in my PC now.

Another question is:
someone told me the interconnect, 1G Ethernet, of the machine in our lab. is
too slow to do parallel simulation.  
What the effect should be in this kind of slow Ethernet environment? 
Is it why the utility of CPU are always less than 35% when I submit the same
job to the machine in our lab.?
   
Hsin-Lin
> 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.

Depending what is being measured by what, this could be a correct 
result. We can't really tell because we don't know how you've set up 
LAM, or how your top works.

Do a short test calculation with one and two processors and compare the 
run times.

Mark