[gmx-users] GPU warnings

Tue Nov 6 00:03:27 CET 2012

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

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
> >>
> >>
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 

======================================================================

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/