Slightly off-topic, but for all but the smallest systems, I get a
further 10% efficiency by running a 16-process mpi job on an 8-core
machine. I suspect that the story is the same with threads. Thus, on a
16-core node, you could try starting 32 threads. Note that this will
report a 2x larger "efficiency" as you were discussing before, but by
checking the ns.day you will see that the benefit is between 5% and 16%
Chris.
It means you are running a lot of parallel processes, but that does
not translate into a linear increase in speed. So faster, but not 16X.
Warren Gallin
On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote:
Thank you, Warren.
Does that mean 16 times faster ?
Jae H. Park
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at
gromacs.org] On Behalf Of Warren Gallin
Sent: Thursday, August 18, 2011 7:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] more than 100% CPU
I believe that the current version of GROMACS supports threading,
which does not require mpi.
So mdrun is running threads at 100% of the activity of each of your
16 nodes, hence 1600%.
Warren Gallin
On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote:
Hi GMX users,
I installed GMX 4.5.3 recently.
But, when I just execute mdrun (without mpi, I did not installed
mpi-version of mdrun), the use of CPU appears more than 100% ("top"
command in LINUX). How is it possible?
For example, I am using 16-node machine. And if I simply run
"mdrun", then use of CPU is 1600%!!.
The simulation runs well and the results looks reasonable.
Is there anybody who can teach me what is happening? I would deeply
appreciate.
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