Hi, you might want to use g_tune_pme to find out the optimal number of PME nodes for 4.6 and 5.0.
Carsten On 05 Sep 2014, at 15:39, David McGiven <davidmcgiv...@gmail.com> wrote: > What is even more strange is that I tried with 10 pme nodes (mdrun -ntmpi > 48 -v -c TEST_md.gro -npme 16), got a 15,8% performance loss and ns/day are > very similar : 33 ns/day > > D. > > 2014-09-05 14:54 GMT+02:00 David McGiven <davidmcgiv...@gmail.com>: > >> Hi Abhi, >> >> Yes I noticed that imbalance but I thought gromacs knew better than the >> user how to split PP/PME!! >> >> How is it possible that 4.6.5 guesses better than 5.0 ? >> >> Anyway, I tried : >> mdrun -nt 48 -v -c test.out >> >> Exits with an error "You need to explicitly specify the number of MPI >> threads (-ntmpi) when using separate PME ranks" >> >> Then: >> mdrun -ntmpi 48 -v -c TEST_md.gro -npme 12 >> >> Then again 35 ns/day with the warning : >> NOTE: 8.5 % performance was lost because the PME ranks >> had less work to do than the PP ranks. >> You might want to decrease the number of PME ranks >> or decrease the cut-off and the grid spacing. >> >> >> I don't know much about Gromacs so I am puzzled. >> >> >> >> >> 2014-09-05 14:32 GMT+02:00 Abhi Acharya <abhi117acha...@gmail.com>: >> >>> Hello, >>> >>> From the log files it is clear that out of 48 cores, the 5.0 run had 8 >>> cores allocated to PME while the 4.6.5 run had 12 cores. This seems to >>> have >>> caused a greater load imbalance in case of the 5.0 run. >>> >>> If you notice the last table in both .mdp files, you will notice that the >>> PME spread/gather wall time values for 5.0 is more than double the wall >>> time value in case of the 4.6.5. >>> >>> Try running the simulation by explicitly setting the -npme flag as 12. >>> >>> Regards, >>> Abhishek Acharya >>> >>> >>> On Fri, Sep 5, 2014 at 4:43 PM, David McGiven <davidmcgiv...@gmail.com> >>> wrote: >>> >>>> Thanks Szilard, here it goes! : >>>> >>>> 4.6.5 : http://pastebin.com/nqBn3FKs >>>> 5.0 : http://pastebin.com/kR4ntHtK >>>> >>>> 2014-09-05 12:47 GMT+02:00 Szilárd Páll <pall.szil...@gmail.com>: >>>> >>>>> mdrun writes a log file, named md.log by default, which contains among >>>>> other things results of hardware detection and performance >>>>> measurements. The list does not accept attachments, please upload it >>>>> somewhere (dropbox, pastebin, etc.) and post a link. >>>>> >>>>> Cheers, >>>>> -- >>>>> Szilárd >>>>> >>>>> >>>>> On Fri, Sep 5, 2014 at 12:37 PM, David McGiven < >>> davidmcgiv...@gmail.com> >>>>> wrote: >>>>>> Command line in both cases is : >>>>>> 1st : grompp -f grompp.mdp -c conf.gro -n index.ndx >>>>>> 2nd : mdrun -nt 48 -v -c test.out >>>>>> >>>>>> Log file you mean the standard output/error ? Attached to the email >>> ? >>>>>> >>>>>> Thanks >>>>>> >>>>>> 2014-09-05 12:30 GMT+02:00 Szilárd Páll <pall.szil...@gmail.com>: >>>>>> >>>>>>> Please post the command lines you used to invoke mdrun as well as >>> the >>>>>>> log files of the runs you are comparing. >>>>>>> >>>>>>> Cheers, >>>>>>> -- >>>>>>> Szilárd >>>>>>> >>>>>>> >>>>>>> On Fri, Sep 5, 2014 at 12:10 PM, David McGiven < >>>> davidmcgiv...@gmail.com >>>>>> >>>>>>> wrote: >>>>>>>> Dear Gromacs users, >>>>>>>> >>>>>>>> I just compiled gromacs 5.0 with the same compiler (gcc 4.7.2), >>> same >>>>> OS >>>>>>>> (RHEL 6) same configuration options and basically everything >>> than my >>>>>>>> previous gromacs 4.6.5 compilation and when doing one of our >>> typical >>>>>>>> simulations, I get worst performance. >>>>>>>> >>>>>>>> 4.6.5 does 45 ns/day >>>>>>>> 5.0 does 35 ns/day >>>>>>>> >>>>>>>> Do you have any idea of what could be happening ? >>>>>>>> >>>>>>>> Thanks. >>>>>>>> >>>>>>>> Best Regards, >>>>>>>> D. >>>>>>>> -- >>>>>>>> Gromacs Users mailing list >>>>>>>> >>>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>>> >>>>>>>> * Can't post? 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