[gmx-users] GPU Not Being Utilized during mdrun

[Smith, Micholas D.]

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!
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.