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


From: Axel Arnold
Subject: Re: [ESPResSo-devel] Porting Interaction Calculations to CUDA
Date: Sat, 28 Apr 2012 21:08:10 +0200
User-agent: KMail/1.13.6 (Linux/2.6.38-14-generic; KDE/4.6.5; x86_64; ; )

On Saturday 28 April 2012, Peter Toson wrote:
> Yes, i ment the bonded interactions. Looks like I have to gather them
> from the particles to transfer the bonded interactions to the GPU...

If you also use other interactions, you could collect them during the regular 
bonded calculations, in add_bonded_force, forces.h. Or once in 
on_integration_start() in initialize.c, which is called when you enter the 
integration loop. After that, bonds only change if you use dynamic bonding. On 
the other hand, it might be easier to collect the positions only for the 
interaction every time step, and by that send them presorted to the GPU.

Many regards,
Axel

> 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 interactions.
> > 
> > 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,
> > Axel
> > 
> > On Friday 27 April 2012, Peter Toson wrote:
> >> Hallo!
> >> 
> >> 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:
> >>> Hi!
> >>> 
> >>> 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
> >>> data.
> >>> 
> >>> 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.
> >>> 
> >>> Axel
> >>> 
> >>> On Tuesday 24 April 2012, Toson Peter wrote:
> >>>> Hallo!
> >>>> 
> >>>> 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


-- 
JP Dr. Axel Arnold      Tel: +49 711 685 67609
ICP, Universit├Ąt Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany



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