[gmx-developers] gromacs.org_gmx-developers Digest, Vol 139, Issue 12

[Vinson Leung]

Hi, the architecture of my machine is like CPU+GPU which are both on chip.
I can use MPI but it will only use the "CPU" part of my machine. So I want
to parallelize the hotspot by offload it to the "GPU" part. My idea is to
do some modification on the code to split the nblist which is like the
OpenMP version of the code. But for the lack of support of OpenMP, is there
anyway to split the nblist while compiling with OpenMP=OFF?

On Tue, Nov 24, 2015 at 7:00 PM, <
gromacs.org_gmx-developers-request at maillist.sys.kth.se> wrote:

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>    1. Re: How to parallel Gromacs with multi-thread? (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Nov 2015 09:23:19 +0100
> From: Berk Hess <hess at kth.se>
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] How to parallel Gromacs with
>         multi-thread?
> Message-ID: <56541E77.1000508 at kth.se>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi,
>
> Why not simply use MPI parallelization?
>
> But what (exotic) architecture does not support OpenMP and SIMD? If you
> don't have SIMD, I would think it's not worth using it for production.
> You get great performance from a cheap Intel CPU + NVidia GPU machine.
>
> Cheers,
>
> Berk
>
> On 2015-11-24 06:05, Vinson Leung wrote:
> > Hi everyone, I am new learner to Gromacs and I want to implement
> > Gromacs in a multi-core CPU machine which is  for my research. Because
> > the machine we use only support MPI (no openmp, no SIMD), so I
> > profiled the MPI-only version of Gromacs-5.0.4 and found that the
> > hotspot was nbnxn_kernel_ref() in src/gromacs/mdlib/nbnxn_kernel_ref.c
> > which occupied 80% of the total running time. Naturally I want to
> > accelerate the nbnxn_kernel_ref() by parallelization with
> > multi-thread. After I simply make some analysis and found that the
> > structure of nbnxn_kernel_ref() is like below:
> > ========================================================
> > for (nb = 0 ; nb < nnbl; nb++)
> > {
> > ......
> >       for( n = 0 ; n < nbl->nci ; n++ )  // defined in
> > nbnxn_kernel_ref_outer.h
> >       {
> >       ....
> >       }
> > ...h
> > }
> > ========================================================
> > So here is my quesion. When I compile with OpenMP=OFF, the value of
> > nnbl is 1 during the runtime.  So  can I  parallelize the inner loop
> > by just evenly separate the inner loop  ( nbl->nci )  to multi-core?
> > Or I found that when I compile with OpenMP=ON the value of nnbl is not
> > 1 which I can parallelize the outer loop with multi-thread. But my
> > machine does not support OpenMP. So is there any way to make some
> > modification in the code and compile with OpenMP=OFF to make the value
> > of nnbl is not 1?
> > Thanks.
> >
> >
> >
>
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