PS: Care to know what can you do? - as noted above try offloading only the nonbondeds (or possibly the hybrid PME mode -pmefft cpu) - check if your GPU has application clocks that can be bumped - if you have the means, consider getting a bit faster GPU; the Quadro M2000 in your machine is both slightly dated and low-end similar board as the GTX 950
-- Szilárd On Wed, Feb 28, 2018 at 10:26 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > 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.