[gmx-developers] How to parallel Gromacs with multi-thread?

[Szilárd Páll]

> Hi, the architecture of my machine is like CPU+GPU which are both on
chip.

What exactly is this hardware you are talking about? Intel CPU+iGPU or AMD
APU?

--
Szilárd

On Tue, Nov 24, 2015 at 3:57 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Please don't reply to a digest, because that is confusing for everybody...
> (and for a mailing list with O(1) posts per day, in which you want to
> participate in discussion, please subscribe in non-digest mode!)
>
> Vincent said
>
> > 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?
>
> Such loops do O(100k) operations, which is far too small to think about
> accelerating with offloading to a device with maybe hundreds of cores,
> unless maybe your GPU shares L3 cache.
>
> You would do well to consider reading some of the published work about the
> parallelization of GROMACS, e.g.
> http://www.sciencedirect.com/science/article/pii/S0010465513001975.
> There's already an OpenCL port in GROMACS, too.
>
> What is your objective? Why is parallelising GROMACS on some mystery
> hardware with neither SIMD nor OpenMP a good thing to do for someone
> learning about GROMACS?
>
> Mark
>
> On Tue, Nov 24, 2015 at 9:25 AM Berk Hess <hess at kth.se> wrote:
>
>> 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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