[gmx-developers] combine neighborlist

[Sikandar Mashayak]

Hi,

I am trying to understand how a SIMD-based kernel distributes the work
across OpenMP threads. I found that, given n threads, n neighborlists are
built, each OpenMP thread is assigned a neighborlist and for each
neighborlist outer and inner loop computations are performed using SIMD
instructions.

My question is, whether building n neibhorlists and assigning 1 list to
each thread is same (from performance considerations) as creating 1
neighborlist and dividing i-clusters among n threads (nci/n per thread)?

Thanks,
Sikandar

On Tue, Jun 30, 2015 at 1:57 PM, Sikandar Mashayak <mashayak at votca.org>
wrote:

> Thanks Szilard,
>
> Yeah, I guess with some coding merging neighborlists into a single simple
> CPU-style list is possible. For now, I am manually setting number of
> neighborlist to 1 independent of openmp threads.
>
> Thanks,
> Sikandar
>
> On Wed, Jun 24, 2015 at 8:00 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
>> Hi,
>>
>> I think it should be supported if not out of the box, perhaps with
>> small code changes. I know we have discussed decoupling the search
>> form the force compute to allow executing them on different number of
>> executors/tasks. Also, I'm not entirely sure if the implementation
>> allows searchig on N tasks and merging simple CPU-style lists into a
>> single list output.
>>
>> Try looking into the nbnxn_init_pairlist_set() function which gets
>> passed a boolean that tells whether to combine lists or not.
>>
>> Note that you can control the number of tasks (=OpenMP threads) in
>> different parts of the code through the gmx_omp module which reads
>> environment variables in the form of GMX_*_NUM_THREADS.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Thu, Jun 25, 2015 at 1:06 AM, Sikandar Mashayak <mashayak at votca.org>
>> wrote:
>> > Hi,
>> >
>> > I want to use pairlist with M = 4 and N = 4 i and j cluster sizes. I
>> > understand, that with OpenMP threads enabled, gromacs builds ntomp,
>> i.e.,
>> > nthreads, neighborlists. I understand, for 8*8*8 kernel type, these
>> > neighborlists are combined and superclusters are built.
>> >
>> > I am wondering, is there a way to combine all the nthreads neighborlist
>> into
>> > one for simple 4*4 type neighborlist?
>> >
>> > Thanks,
>> > Sikandar
>> >
>> > --
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