[gmx-users] more than 100% CPU

[Warren Gallin]

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.
>> 
>> Best,
>> Jae H. Park
>> 
>> =======================
>> Jae Hyun Park, Ph. D.
>> Physics Division
>> Oak Ridge National Laboratory
>> PO. Box 2008, MS-6372
>> Oak Ridge, TN 37831
>> Phone (865) 241-1482
>> E-mail parkj at ornl.gov
>> 
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