<div dir="ltr"><div><div><div>Thanks Szilard,<br><br></div>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. <br><br></div>Thanks,<br></div>Sikandar<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 24, 2015 at 8:00 PM, Szilárd Páll <span dir="ltr"><<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I think it should be supported if not out of the box, perhaps with<br>
small code changes. I know we have discussed decoupling the search<br>
form the force compute to allow executing them on different number of<br>
executors/tasks. Also, I'm not entirely sure if the implementation<br>
allows searchig on N tasks and merging simple CPU-style lists into a<br>
single list output.<br>
<br>
Try looking into the nbnxn_init_pairlist_set() function which gets<br>
passed a boolean that tells whether to combine lists or not.<br>
<br>
Note that you can control the number of tasks (=OpenMP threads) in<br>
different parts of the code through the gmx_omp module which reads<br>
environment variables in the form of GMX_*_NUM_THREADS.<br>
<br>
Cheers,<br>
--<br>
Szilárd<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Thu, Jun 25, 2015 at 1:06 AM, Sikandar Mashayak <<a href="mailto:mashayak@votca.org">mashayak@votca.org</a>> wrote:<br>
> Hi,<br>
><br>
> I want to use pairlist with M = 4 and N = 4 i and j cluster sizes. I<br>
> understand, that with OpenMP threads enabled, gromacs builds ntomp, i.e.,<br>
> nthreads, neighborlists. I understand, for 8*8*8 kernel type, these<br>
> neighborlists are combined and superclusters are built.<br>
><br>
> I am wondering, is there a way to combine all the nthreads neighborlist into<br>
> one for simple 4*4 type neighborlist?<br>
><br>
> Thanks,<br>
> Sikandar<br>
><br>
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