[gmx-users] more than 100% CPU

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Aug 19 02:52:39 CEST 2011

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%


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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