[gmx-users] Gromacs 2018 and GPU
paul buscemi
pbuscemi at q.com
Sat May 5 00:53:25 CEST 2018
Justin,
Here is the install script and a snippit from the log file .
Gromacs runs normally with this ( fresh ) install but without GPU use
Paul
cmake .. -DGMX_BUILD_OWN_FFTW=ON \
-DGMX_GPU=on \
-DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit \
-DGMX_USE_OPENCL=on
Command line:
gmx mdrun -deffnm md_0_1
GROMACS version: VERSION 5.1.2
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
OpenCL support: disabled
invsqrt routine: gmx_software_invsqrt(x)
SIMD instructions: SSE2
FFT library: fftw-3.3.4-sse2-avx
RDTSCP usage: enabled
C++11 compilation: enabled
TNG support: enabled
Tracing support: disable…..
> On May 4, 2018, at 1:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 5/4/18 2:11 PM, paul buscemi wrote:
>> Thank you Justin.
>>
>> Not at the linux system at the moment, but is there anything in particular I should look for in the log file ?
>
> Just look for "GPU" and you'll find it.
>
> -Justin
>
>> Paul
>>
>>> On 4,May 2018, at 12:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> 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.
>>>
>>> -Justin
>>>
>>>> thanks
>>>> Paul
>>>>
>>>>> On 4,May 2018, at 11:57 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> 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
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
>>>>>> <
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
>>>>>> 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.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>>> Regards
>>>>>> Paul
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>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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