Re: MD Simulation of accelerated MD using GPU

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Fri Oct 16 2015 - 08:25:29 CDT

You need to add idlepoll in regular namd command line.
I use following command:

charmrun +p16 namd2 +idlepoll x.conf > x.log

On Fri, Oct 16, 2015 at 9:18 AM, Nikhil Maroli <scinikhil_at_gmail.com> wrote:

> Hi
> i also recently own a GPU Tesla k20c with 16 core processor ,i also wanted
> to check the speed of my gpu and cpu,could you please tel me how to give
> input in GPU for NAMD
> thanks
>
> i think sometimes cpu alon run faster than gpu!!
>
> On Tue, Oct 13, 2015 at 3:49 AM, 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
>>
>>
>
>
> --
> Ragards,
> Nikhil Maroli
>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:07 CST