[gmx-developers] combine neighborlist
mashayak at votca.org
Tue Jun 30 21:57:40 CEST 2015
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.
On Wed, Jun 24, 2015 at 8:00 PM, Szilárd Páll <pall.szilard at gmail.com>
> 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>
> > 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
> > one for simple 4*4 type neighborlist?
> > Thanks,
> > Sikandar
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