[gmx-users] GPU Not Being Utilized during mdrun

[Vito Spadavecchio]

I'm currently running a simple 1ns calculation with 500,000 steps with dt =
2fs and structures being stored every 10ps.

On Thu, Jul 14, 2016 at 11:31 AM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> Quick question, what is your integration stepsize?
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Vito
> Spadavecchio <spadavecchio at gmail.com>
> Sent: Thursday, July 14, 2016 2:28 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] GPU Not Being Utilized during mdrun
>
> Hello
>
> After building GROMACS with GPU support and running some simple MD, I am
> only getting ~20ns/day (which is what I would expect to get out of my
> i7-6700k cpu only. My machine currently has a 1080 GTX in it, which should
> even on moderately large systems, be getting ~100ns/day)
>
>  I've tried launching a mdrun with with the following command:
>
>   gmx mdrun -deffnm md_0_1 -gpu_id 0 -nb gpu
>
>
>
> With the following in my md.mdp file:
>
> ; Neighborsearching
>
> cutoff-scheme   = Verlet
>
>
>
> The top of the log file for the mdrun notes:
>
> Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
> > Hardware detected:
> >   CPU info:
> >     Vendor: GenuineIntel
> >     Brand:  Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
> >     SIMD instructions most likely to fit this hardware: AVX2_256
> >     SIMD instructions selected at GROMACS compile time: AVX2_256
> >   GPU info:
> >     Number of GPUs detected: 1
> >     #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
> > compatible
> > Reading file md_0_1.tpr, VERSION 5.1.2 (single precision)
> > Changing nstlist from 10 to 40, rlist from 1 to 1.099
> > Using 1 MPI thread
> > Using 8 OpenMP threads
> > 1 GPU user-selected for this run.
> > Mapping of GPU ID to the 1 PP rank in this node: 0
> >
>
> The output of *nvidia-smi *on my machine is:
>
> hu Jul 14 11:25:04 2016
> >
> >
> +-----------------------------------------------------------------------------+
> > | NVIDIA-SMI 367.27                 Driver Version: 367.27
> >    |
> >
> >
> |-------------------------------+----------------------+----------------------+
> > | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr.
> > ECC |
> > | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util
> Compute
> > M. |
> >
> >
> |===============================+======================+======================|
> > |   0  GeForce GTX 1080    Off  | 0000:01:00.0      On |
> >  N/A |
> > | 30%   41C    P8     7W / 180W |    730MiB /  8113MiB |      3%
> >  Default |
> >
> >
> +-------------------------------+----------------------+----------------------+
> >
> >
> >
> >
> +-----------------------------------------------------------------------------+
> > | Processes:                                                       GPU
> > Memory |
> > |  GPU       PID  Type  Process name                               Usage
> >    |
> >
> >
> |=============================================================================|
> > |    0      1035    G   /usr/lib/xorg/Xorg
> > 424MiB |
> > |    0      2132    G   compiz
> > 103MiB |
> > |    0      5296    G   ...s-passed-by-fd --v8-snapshot-passed-by-fd
> >  59MiB |
> > |    0     14079    G   ...s-passed-by-fd --v8-snapshot-passed-by-fd
> >  31MiB |
> > |    0     14234    G   ...ing<BrotliEncoding --disable-features=Doc
> > 108MiB |
> >
> >
> +-----------------------------------------------------------------------------+
>
>
> and output of *nvcc --version* is:
>
> nvcc: NVIDIA (R) Cuda compiler driver
> > Copyright (c) 2005-2015 NVIDIA Corporation
> > Built on Tue_Aug_11_14:27:32_CDT_2015
> > Cuda compilation tools, release 7.5, V7.5.17
>
>
> Does anyone have any ideas what the problem might be?
>
> Thanks!
> --
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