[gmx-users] mdrun_mpi performance

[Justin Lemkul]

On 10/25/16 12:34 PM, Steve Seibold wrote:
> HelloI finally got my mpi gromacs 5.0.4 installed and running (thank you Justin!).
>
> The problem is that the mdrun_mpi is running at 0.55ns/day on my quad-core 2.8 GHz computer while on my quad-core 2.0 GHz computer it is running 6.0ns/day. On both computers I am using all threads. The only difference between the two computers is that the 2.0 GHz computer is running Gromacs 5.1 without the mpi version and the 2.8 GHz computer is running 5.0.4 and the mpi version...
> Both computers are not running GPU and both are intel Xeon cpu processors...
> I have looked up "load imbalance" etc and nothing seems to help...
> What is my problem???

Probably an inherent overhead from using MPI, which is unnecessary for 
multi-core workstations or nodes.

If you want to know how a run spent its time, the entire detailed performance 
breakdown is at the end of the .log file.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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