[gmx-developers] combine neighborlist

Szilárd Páll pall.szilard at gmail.com
Thu Jun 25 04:00:15 CEST 2015


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.


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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