[gmx-users] GPU warnings

[Szilárd Páll]

Hi,

On Tue, Nov 6, 2012 at 12:03 AM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> Hi,
>
> I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
> benchmark with the following command line:
>
> mdrun_intel_cuda5 -v -s topol.tpr -testverlet
>
> "WARNING: Oversubscribing the available 0 logical CPU cores with 1
> thread-MPI threads."
>
> 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
>

That is bizzarre. Could you run with "-debug 1" and have a look at the
mdrun.debug output which should contain a message like:
"Detected N processors, will use this as the number of supported hardware
threads."

I'm wondering, is N=0 in your case!?


> (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
> ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4
> cores (8 threads) without the GPU. Yet, I don't see any performance gain
> with more that 4 -nt threads.
>
> mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
> mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
> mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
> mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
> mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
>

I guess there is not much point in not using all cores, is it? Note that
the performance drops after 4 threads because Hyper-Threading with OpenMP
doesn't always help.


>
> I have also attached my log file (from "mdrun_intel_cuda5 -v -s topol.tpr
> -testverlet") in case you find it helpful.
>

I don't see it attached.

--
Szilárd


>
> Thanks,
> Thomas
>
>
>
> On 5 November 2012 18:54, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
>
> > The first warning indicates that you are starting more threads than the
> > hardware supports which would explain the poor performance.
> >
> > Could share a log file of the suspiciously slow run as well as the
> command
> > line you used to start mdrun?
> >
> > Cheers,
> >
> > --
> > Szilárd
> >
> >
> > On Sun, Nov 4, 2012 at 5:32 PM, Albert <mailmd2011 at gmail.com> wrote:
> >
> > > well, IC.
> > > the performance is rather poor than GTX590..... 32ns/day vs 4 ns/day
> > > probably that's also something related to the warnings?
> > >
> > > THX
> > >
> > >
> > >
> > > On 11/04/2012 01:59 PM, Justin Lemkul wrote:
> > >
> > >>
> > >>
> > >> On 11/4/12 4:55 AM, Albert wrote:
> > >>
> > >>> hello:
> > >>>
> > >>>   I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti
> (2
> > x
> > >>> 1344
> > >>> CUDA cores), and I got the following warnings:
> > >>>
> > >>> thank you very much.
> > >>>
> > >>> ---------------------------**messages----------------------**
> > >>> -------------
> > >>>
> > >>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> > >>> per node
> > >>> with 2 MPI processes.
> > >>>           This will cause considerable performance loss!
> > >>>
> > >>> 2 GPUs detected on host boreas:
> > >>>    #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >>> compatible
> > >>>    #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC:  no, stat:
> > >>> compatible
> > >>>
> > >>> 2 GPUs auto-selected to be used for this run: #0, #1
> > >>>
> > >>> Using CUDA 8x8x8 non-bonded kernels
> > >>> Making 1D domain decomposition 1 x 2 x 1
> > >>>
> > >>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> > >>> We have just committed the new CPU detection code in this branch,
> > >>> and will commit new SSE/AVX kernels in a few days. However, this
> > >>> means that currently only the NxN kernels are accelerated!
> > >>> In the mean time, you might want to avoid production runs in 4.6.
> > >>>
> > >>>
> > >> I can't address the first warning, but the second is fairly obvious.
> > >>  You're not using an official release, you're using the development
> > version
> > >> - let the user beware.  The code is not yet production-ready.
> > >>
> > >> -Justin
> > >>
> > >>
> > > --
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>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang at pharm.uoa.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
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