[gmx-users] more than 100% CPU

Warren Gallin wgallin at ualberta.ca
Fri Aug 19 01:26:04 CEST 2011

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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