Thanks! Looking at the log file, as I guessed earlier, you can see the following:
- Given that you have a rather low-end GPU and a fairly fast workstation CPU the run is *very* GPU-bound: the CPU spends 16.4 + 54.2 = 70.6% waiting for the GPU (see lines 628 and 630) - this means that the default behavior of offloading both the nonbonded and PME tasks to the GPU is not beneficial (try the other parallel modes) - mdrun is still using 8 cores / 16 threads *for the parts of the run that require it* (Bonded forces (2.7%), Integration / Constraints (2.6 % / 4.9 %) etc.), but as this takes <30% of the runtime, that gives you your average of 4.5 utilization (0.3*16 = 4.8). That you "see" 9 threads active is just the averaging/sampling effect of from your minitoring tools. Cheers, -- Szilárd On Wed, Feb 28, 2018 at 10:12 PM, Mahmood Naderan <nt_mahm...@yahoo.com> wrote: > >The list does not accept attachments, so please use a file sharing or > content sharing website so >everyone can see your data and has the context. > > I uploaded here > > https://pastebin.com/RCkkFXPx > > > > Regards, > Mahmood > > -- 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.
