On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si <sjyz...@gmail.com> wrote:
> This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. > of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. > Since the first line and third line both have N*N Vdw [F], does the former > include the latter? > No, but there is no line with "N*N Vdw [F]". Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU > acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
