[gmx-users] Gromacs 2018 and GPU
jalemkul at vt.edu
Fri May 4 19:56:20 CEST 2018
On 5/4/18 1:48 PM, paul buscemi wrote:
> thank you for the prompt response. I will check out the link. Regarding 2) One can immediately determine if the GPU is/is running since Gromacs tells you at the beginning - in my case - that the CPU’s being used and linux system monitor tells you that all CPU’s are running, - not to mention the fan speed, and nvidia-smi registers no GPU running
> What I was asking was for the proper format for invoking the GPU . I used
> gmx mdrun -deffnm md_0_1 -nb gpu ## this is from the lysozyme tutorial MD page
> but this starts Gromacs using the CPU’s and was asking if this is a proper format for a single GPU.
With version 2018, you don't even need to use "-nb gpu," mdrun will
automatically run on the GPU if it is detected properly. As Mark said,
check your .log file for a full breakdown of how mdrun configured the
simulation using the available hardware.
>> On 4,May 2018, at 11:57 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> On Fri, May 4, 2018 at 6:43 PM paul buscemi <pbuscemi at q.com <mailto:pbuscemi at q.com>> wrote:
>>> I’ve been struggling for a for several days to get Gromacs-2018 to use my
>>> GPU. I followed the INSTALL instructions ( several times ! ) that are
>>> provided in the 2018 tarball
>>> I know that the GPU ( GTX1080) is installed properly in that it works
>>> with Schrodinger and the Nvidia self tests. Gromacs runs the MD from the
>>> University of Baltimore lysozyme example normally
>>> but only on the 8 threads of the CPU
>> The tutorial explicitly addresses this. See
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html>
>>> Make test indicates that it sees the GPU, but
>>> 1) is there a way to definitively determine if the make commands were run
>>> properly or that Gromacs was installed properly with the GPU
>> To know that a simulation ran on the GPU, you must inspect the log file
>> that it wrote.
>>> 2) for a linux desktop system with one GPU, a/the proper command to run
>>> the lysozyme . I ask since there is indication that with one GPU (0) it
>>> will be dedicated to graphics.
>> If the display is sharing the GPU, then it shares the GPU (and performance
>> of either the display or the simulation might be affected). With only one
>> GPU, there's no option (unless your motherboard has a built-in GPU that
>> you'd prefer to use for the display).
>>> 3) is there an up to data set of install instructions for Gromacs 2018
>>> and Nvidia 9.1 toolkit, 384.11 drivers ?
>> No, there's nothing unusual about that, so the generic instructions apply.
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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