From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Wed Oct 14 2015 - 16:21:36 CDT
Thank you Brian and Kenneth for sharing your ideas.
On Mon, Oct 12, 2015 at 9:09 PM, Kenneth Huang <kennethneltharion_at_gmail.com>
wrote:
> Hi,
>
> I'm not an expert on the subject, but my understanding is that running any
> MD or any sort of calculation with more than 1 CPU per GPU tends to cause a
> bottleneck- each iteration has to pass from the GPU to the CPU to
> communicate the information, which then has to go back to the GPU, which
> compounds significantly the more CPUs you introduce. Whereas if you're just
> running by 1 GPU/CPU, then you only need to communicate once as opposed to
> 16 times.
>
> 20 ns/day for a system of your size seems kind of slow, so I'd try it
> first with just 1 CPU and 1 GPU, and see if you can't get some sort of
> speed up that way, or just running solely on CPU. It also does depend on
> what type of GPU you're using, since some have noticeable improvements over
> others.
>
> Best,
>
> Kenneth
>
> On Mon, Oct 12, 2015 at 6:07 PM, jeevan gc <gcjeevanbdr_at_gmail.com> wrote:
>
>> Dear all,
>>
>> In my protein membrane system of 121416 atoms,
>> When I use 16 CPU +1 GPU, the total time is 3 days for 20ns for the regular MD.
>> For the same system it takes 6 days to run 20ns accelerated MD.
>>
>> Why accelerated MD is slow in GPU? I am using NAMD2.10
>>
>> Thank you.
>>
>>
>>
>>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
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