[gmx-users] GPU acceleration

[Justin Lemkul]

On 6/27/16 9:37 AM, יוכבד wrote:
> but still shouldn't I see some acceleration?
> The other process is not using the GPUs at all only CPUs
>

And your GPU run is trying to use the CPUs to do PME; you'll note from the .log 
file that a large amount of time is being spent doing PME, which then becomes a 
limiting factor in the progress of the GPU simulation.  As I said, you need to 
properly allocate the resources.

-Justin

> 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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-- 
==================================================

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

==================================================