[gmx-developers] free energies on GPUs?

Berk Hess hess at kth.se
Wed Feb 22 10:10:28 CET 2017


The perturbed pair interactions are running on the CPU, so the more of 
the system you perturb, the more CPU limited you will be. Also when you 
use PME, the PME load nearly doubles and that's all on the CPU.

But GPU utilization of 1-2% must be incorrect. That means 2-4% in the 
non-FE runs, which is far too low.
What CPU vs GPU time per step gets reported at the end of the log file?



On 22/02/17 10:04 , Igor Leontyev wrote:
> Hi.
> I am having hard time with accelerating free energy (FE) simulations 
> on my high end GPU. Not sure is it normal for my smaller systems or I 
> am doing something wrong.
> The efficiency of GPU acceleration seems to decrease with the system 
> size, right? Typical sizes in FE simulations in water is 32x32x32 A^3 
> (~3.5K atoms) and in protein it is about 60x60x60A^3 (~25K atoms). 
> Requirement for larger MD box in FE simulation is rather rare.
> For my system (with 11K atoms) I am getting on 8 cpus and with GTX 
> 1080 gpu only up to 50% speedup. GPU utilization during simulation is 
> only 1-2%. Does it sound right? (I am using current gmx ver-2016.2 and 
> CUDA driver 8.0; by request will attach log-files with all the details.)
> BTW, regarding how much take perturbed interactions, in my case 
> simulation with "free_energy = no" running about TWICE faster.
> Igor
>> On 2/13/17, 1:32 AM, 
>> "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of 
>> Berk Hess" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on 
>> behalf of hess at kth.se> wrote:
>>     That depends on what you mean with this.
>>     With free-energy all non-perturbed non-bonded interactions can 
>> run on
>>     the GPU. The perturbed ones currently can not. For a large system 
>> with a
>>     few perturbed atoms this is no issue. For smaller systems the
>>     free-energy kernel can be the limiting factor. I think there is a 
>> lot of
>>     gain to be had in making the extremely complex CPU free-energy 
>> kernel
>>     faster. Initially I thought SIMD would not help there. But since any
>>     perturbed i-particle will have perturbed interactions with all 
>> j's, this
>>     will help a lot.
>>     Cheers,
>>     Berk
>>     On 2017-02-13 01:08, Michael R Shirts wrote:
>>     > What?s the current state of free energy code on GPU?s, and what 
>> are the roadblocks?
>>     >
>>     > Thanks!
>>     > ~~~~~~~~~~~~~~~~
>>     > Michael Shirts

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