On 21/04/2010 11:29 PM, Hsin-Lin wrote:
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?
GROMACS will run very slowly, because it needs low latency
communication. Gigabit ethernet is too slow here. See papers by Carsten
Kutzner, for example.
Mark
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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
