Re: NAMD-CUDA GPU workload

From: Lewis J Martin (lewis.martin44_at_gmail.com)
Date: Thu Apr 05 2018 - 19:50:09 CDT

Hi Dave,

Do you have any preliminary indications as to the speedup of NAMD 2.13?
On any benchmarks or any system really

Cheers!

On 4/4/18 4:07 pm, namd-l digest wrote:
> ------------------------------
>
> Date: Mon, 2 Apr 2018 11:33:06 -0500
> From: David Hardy<dhardy_at_ks.uiuc.edu>
> Subject: Re: namd-l: NAMD-CUDA GPU workload
>
> Dear Yu,
>
> Part of the problem is that NAMD 2.12, to balance your fast GPU, requires a
> lot of CPU support, well beyond an AMD 8-core CPU.
>
> We will soon (within the next week or two) be releasing the first beta of NAMD
> 2.13. The new release will allow you to offload all of the force calculation
> to the GPU, which should increase your GPU usage.
>
> Best regards,
> Dave
>
> - --
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu,http://www.ks.uiuc.edu/~dhardy/
>
>
>> On Apr 2, 2018, at 10:11 AM, Yu Zhou<zylp2006_at_gmail.com> wrote:
>>
>> Dear NAMD users,
>>
>>
>> I was running simulation on an 70,000-atom system of an ion channel (KcsA)
> using NAMD 2.12 for Win64-multicore-CUDA on a desktop with an AMD 8-core CPU
> and a GTX-1080 graphic card by:
>> "NAMD2 +p8 kcsa.conf > kcsa.log". I noticed that the workload of GPU was
> only ~20% during the whole simulation process. I am wondering if there was any
> way I could increase the workload of GPU to accelerate simulation.
>> Thanks for your help.
>>
>>
>> Yu Zhou
>>
>> Dept. of Anesthesiology
>>
>> WUSM
>>
>>
> ------------------------------

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