[gmx-users] GPU Not Being Utilized during mdrun

[Szilárd Páll]

Hi,

If mdrun claims it's using the GPU and you see no errors (and results
look reasonable), the GPU is likely being used. That nvidia-smi is not
showing it is admittedly strange. However, this truncated log output
does not confirm much, e.g. it does not show the performance table and
the final performance.

Could you please run again and look at (and share if approapriate):
- the entire log, not just parts, in particular we want to see the
header, perf table
- the output of nvidia-smi dmon executing *during* mdrun's execution
(this monitors the device continuously)

Cheers,

--
Szilárd


On Thu, Jul 14, 2016 at 8:28 PM, Vito Spadavecchio
<spadavecchio at gmail.com> wrote:
> 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.