[gmx-users] GPU low performance

Justin Lemkul jalemkul at vt.edu
Wed Feb 18 17:28:41 CET 2015

On 2/18/15 11:20 AM, Carmen Di Giovanni wrote:
> Justin,
> the problem is evident for all calculations.
> This is the log file  of a recent run:

Again, this is *part* of a .log file, but at least we're starting to get 
somewhere.  Please realize that I'm not insisting on this for no reason; there 
is critical information in the last part of the .log file!  We know what we're 
looking for - please give it to us so we can help!

A few things:

> GROMACS:    gmx mdrun, VERSION 5.0

Upgrade to 5.0.4 to avoid some GPU-specific bugs.  See the release notes.


> Using 1 MPI process
> Using 32 OpenMP threads

As was pointed out earlier, there is a lot of fine-tuning that can try to 
improve performance.  mdrun tries to guess what will be best for your hardware, 
but it's not always right.  See the linked page that was posted before, as well 
as the numerous discussions about improving GPU performance.


> System total charge: -0.012

Check your topology; something might be wrong here.


> There are: 434658 Atoms

Pretty big system, so you *might* be getting as good of performance as you can 
expect from the hardware.


> ............

There's important stuff you're leaving out here :)



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


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