[gmx-users] GPU acceleration

[יוכבד]

but still shouldn't I see some acceleration?
The other process is not using the GPUs at all only CPUs

On Mon, Jun 27, 2016 at 4:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/27/16 9:12 AM, יוכבד wrote:
>
>> here's a link to the log file
>>
>> https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing
>>
>> The  computer is 4GPUs and 32 CPUs but some GPUs were in use hence only
>> 15-16 were used.
>>
>>
> That's not what
>
> gmx mdrun -v -deffnm nvt_New -nb gpu
>
> will do.  That command will attempt to use all resources available on the
> machine, all 32 CPU and all 4 GPU.  The .log file confirms this is the
> case.  If you're running multiple processes on the same machine, you need
> to appropriately define what should be used for each run, using -pin,
> -pinoffset, -gpu_id, -nt, -ntmpi, etc as needed, otherwise they're all
> going to try to use everything, and end up fighting each other, slowing
> everything down.
>
> -Justin
>
>
> Thanks
>>
>> On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/27/16 8:49 AM, יוכבד wrote:
>>>
>>> Hi
>>>> I've recently installed GROMACS 5.1.2.
>>>> I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
>>>> using 4GPUs and 32 CPU and I got the performances of ~330ns/day
>>>>
>>>> Now I'm tring to run my system but I don't see any acceleration (a 500ps
>>>> nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs
>>>> and
>>>> 15 CPUs.
>>>>
>>>> What am I missing here?
>>>>
>>>> attached is my mdp file and the command used was
>>>>
>>>>
>>> The list does not accept attachments.  The .log files are the most
>>> informative as the end contains a full performance breakdown; if you wish
>>> to share them, upload them to a file sharing service and provide a URL.
>>>
>>> The actual performance depends largely on the content/size of the system.
>>> Perhaps you have a bottleneck due to the size of the system such that you
>>> cannot efficiently utilize all 4 GPU and 15 CPUs (an odd combination,
>>> anyway) simultaneously.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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