Re: [AMBER-Developers] pmemd external force

From: Ross Walker <>
Date: Mon, 2 Oct 2017 07:32:55 -0400

Hi Sergio,

I see Josh already responded but in addition to what he said note that the use of gpu_download and gpu_upload are really intended just to be used for simplifying development / debugging. They are not designed to be used in production code since it adds a huge amount of overhead and puts computation load on the CPU - which is, by design, only serial. Plus we encourage people when building machines for AMBER GPU to spec them with low end CPUs to save on cost so you cannot assume that a machine running AMBER on GPUs will have fast CPUs.

The correct approach is to get the basic elements working and check an algorithmic approach is valid using the download / upload routines and then to write a CUDA kernel for the method, call that instead of the upload and download and then remove the upload and download routines.

All the best

> On Oct 2, 2017, at 04:35, Sergio Decherchi at IIT <> wrote:
> Dear Amber Developers,
> I would like to add an external force to the pmemd program.
> I am looking at the pme_force.F90 source file and it seems a suitable
> location where
> to add an external force because I see that there, for instance, scaled
> md is applied.
> Is this correct?
> Also I am calling gpu_download_crd and gpu_download_frc to download
> coordinates and forces
> and I update them upon computation via gpu_upload_frc. Is this the right
> approach? Which
> are the units of the forces and coordinates used by thoose functions and
> which is the memory layout of those arrays?
> Is there a more lightweight way to retrieve forces/coordinates from GPU,
> because I observed a significant slow down
> when using those functions at each time step.
> Last, in case one may envision to add the force directly on the GPU (to
> make it faster) which is the memory layout of the forces on the GPU and
> which are the variables that should be updated/read (e.g. coordinates,
> forces)?
> Many thanks,
> Sergio Decherchi
> _______________________________________________
> AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Mon Oct 02 2017 - 05:00:02 PDT
Custom Search