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Re: [ESPResSo-devel] Porting Interaction Calculations to CUDA

From: Peter Toson
Subject: Re: [ESPResSo-devel] Porting Interaction Calculations to CUDA
Date: Sat, 28 Apr 2012 00:09:39 +0200
User-agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:11.0) Gecko/20120327 Thunderbird/11.0.1

Yes, i ment the bonded interactions. Looks like I have to gather them
from the particles to transfer the bonded interactions to the GPU...

Thanks, Peter

Am 27.04.2012 19:51, schrieb Axel Arnold:
Sorry, but what do you mean by interactions? If you mean the bonded
interactions, they are indeed only stored with the particles, more precisely,
with one of the particles involved in the bond (so, for a bond, only one
partner knows about this bond!). There is no local or global list of these,
since we don't need it. We anyways loop the particles once to calculate the
nonbonded interactions, and during that course, we also add the bonded

For the nonbonded short ranged interactions a local Verlet list is kept with
all the interacting pairs per pair of cells, but that does not include the
pairs you probably need.

Many regards,
On Friday 27 April 2012, Peter Toson wrote:

Thanks for the quick reply and pointing me to that code - you've saved
me a lot
of work.

Now I have a follow-up question: is there an array for all (local)
interactions as well?
Or can I get the interaction information only from particles?

-- Peter

Am 24.04.2012 16:38, schrieb Axel Arnold:

If I didn't missunderstand you, you basically want to do the same as the
LB- GPU code. That code also copies the positions and velocities to the
GPU and gets the forces back. The interesting parts for you are
lbgpu_cfile.c, lb_calc_particle_lattice_ia_gpu and lb_send_forces_gpu.
These also handle the gathering of the parallely distributed particle

There are some minor issues with the C++/C interfacing since CUDA is
inherently C++, but that can be solved using "extern "C" {}" constructs.
In any case, you don't need to recompile the whole code, just your GPU
code and of course linking.


On Tuesday 24 April 2012, Toson Peter wrote:

I am trying to port the force calculation of some self-implemented
bonded interactions to CUDA. For a beginning, I would like to write
isolated tests (for performance and correctness) comparing
the CPU and GPU calculations.

The tests should look something like this:

build Particles
build Interactions

for each Particle P {

      for each Interaction I of P {

          add force cause by I to P



convert Particle and Interaction data to a GPU-friendly format
do force calculation on GPU

compare results and times

What would be the best way to do it, without compiling whole ESPResSo
after any change to the GPU-Implementation?

"Only" using the Particle and Interaction structs from ESPResSo? Is
that even possible considering the many includes in particle_data.h/c?

Implementing fake Particle and Interaction structs containing only the
members needed for the force calculation?

Some other way I did not think of?

Peter Toson
Industrial Simulation
St. Poelten University of Applied Sciences

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