Custom Search
-- Jason M. Swails > On Jun 4, 2016, at 1:52 PM, B. Lachele Foley <lfoley.ccrc.uga.edu> wrote: > > Our queue was filled from the time this came out until just now. But, we finally tested, and do see a decent speed-up (~2x) in parallel, with a possible slight performance hit in serial. 149,500 atoms. > > :-) Lachele > > Dr. B. Lachele Foley > Associate Research Scientist > Complex Carbohydrate Research Center > The University of Georgia > Athens, GA USA > lfoley.uga.edu > http://glycam.org > > ________________________________________ > From: Charles Lin <clin92.ucsd.edu> > Sent: Friday, June 3, 2016 3:15:30 PM > To: AMBER Developers Mailing List > Subject: Re: [AMBER-Developers] AMBER Master Branch > > So there are performance enhancements for non-KNL systems primarily due to much better vectorization and hybrid MPI/OpenMP implementations. > > KNL specific improvements are under the -mic2 switch. We also add in the SPDP version (experimental) which is similar to SPFP on cuda which also increases performance (uses -mic2_SPDP switch). > > In particular for the latest Broadwell (36 core system) processors the proper input now will be: > PME: # of cores (36) & OMP_NUM_THREADS=2 > GB: # of sockets (2) & OMP_NUM_THREADS=# of cores per socket (18) > > Charlie > ________________________________________ > From: Hai Nguyen [nhai.qn.gmail.com] > Sent: Friday, June 03, 2016 12:11 PM > To: AMBER Developers Mailing List > Subject: Re: [AMBER-Developers] AMBER Master Branch > > hi Benny, > > I am confused here. Ross said "Performance changes here will be minimal for > pre V4 (Broadwell) hardware and most of the changes are focused on Knights > Landing Xeon Phi (to be released soon)." > > Does this mean we need to wait and buy Knights Landing Xeon Phi to see the > difference? Or something else. thanks > > Hai > >> On Fri, Jun 3, 2016 at 6:30 AM, Benny1 M <benny1.m.tcs.com> wrote: >> >> OpenMP does not come into play in PME on host and hence there is not much >> change in performance, >> or in the way the AMBER is run. >> >> Running PME: >> export I_MPI_PIN_MODE=pm >> export I_MPI_PIN_DOMAIN=auto >> mpirun -np NSOCKETS * NCORES_PER_SOCKET \ >> $AMBERHOME/bin/pmemd.MPI >> >> On the other hand MPI-communication in GB workload has been reduced by >> using minimal MPI ranks and >> more OpenMP threads. This improves single node performance as well as >> helps in scaling across nodes. >> Improvement is seen in mid to large size workloads like nucleosome(~25K >> atoms) and rubisco( ~75K atoms). >> Try using IntelMPI + OpenMP and let us know if any issues are faced. >> >> Running GB: >> export I_MPI_PIN_MODE=pm >> export I_MPI_PIN_DOMAIN=auto >> mpirun -np NSOCKETS \ >> -env OMP_NUM_THREADS=NCORES_PER_SOCKET*2 \ >> -env KMP_AFFINITY="scatter,granularity=core" \ >> -env KMP_STACKSIZE=10M \ >> $AMBERHOME/bin/pmemd.MPI >> >> >> - Benny >> >> >> >> From: Jason Swails <jason.swails.gmail.com> >> To: AMBER Developers Mailing List <amber-developers.ambermd.org> >> Date: 03-06-2016 07:20 >> Subject: Re: [AMBER-Developers] AMBER Master Branch >> >> >> >> It has something to do with OpenMP too, right? And then you have to be >> careful to count total threads as MPI*OMP threads to avoid thrashing. Do >> you only see the perf boost with OMP-MPI combo? That was my >> understanding... >> >> Is the exact recipe written down somewhere for how to take full advantage >> of this code? Because if Dave is having trouble using it "correctly", our >> users are highly unlikely to have better luck. >> >> -- >> Jason M. Swails >> >>> On Jun 2, 2016, at 8:54 PM, Ross Walker <ross.rosswalker.co.uk> wrote: >>> >>> Hi Dave, >>> >>> Performance changes here will be minimal for pre V4 (Broadwell) hardware >> and most of the changes are focused on Knights Landing Xeon Phi (to be >> released soon). >>> >>> All the best >>> Ross >>> >>>> On Jun 2, 2016, at 16:59, David A Case <david.case.rutgers.edu> wrote: >>>> >>>> On Thu, Jun 02, 2016, Charles Lin wrote: >>>>> >>>>> So the Intel code has been in master for about a month now. We plan >> on >>>>> releasing the patch within a week. >>>> >>>> Still not sure when I am supposed to see speedups. I've tried >> pmemd.MPI >>>> runs (using Intel 16.0.3 compilers + MKL + mvapich2) for various >> systems, up to 64 >>>> threads, and see no difference in speed for PME calculations. Have not >>>> tried any GB calculations. >>>> >>>> Is this only expected to speedup things when the -intelmpi (rather than >> -mpi) >>>> flag is set? >>>> >>>> Do you have specific examples of what systems one should expect >> speedups >>>> for? >>>> >>>> ...thx...dac >>>> >>>> >>>> _______________________________________________ >>>> AMBER-Developers mailing list >>>> AMBER-Developers.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber-developers >>> >>> >>> _______________________________________________ >>> AMBER-Developers mailing list >>> AMBER-Developers.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber-developers >> >> _______________________________________________ >> AMBER-Developers mailing list >> AMBER-Developers.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber-developers >> >> =====-----=====-----===== >> Notice: The information contained in this e-mail >> message and/or attachments to it may contain >> confidential or privileged information. If you are >> not the intended recipient, any dissemination, use, >> review, distribution, printing or copying of the >> information contained in this e-mail message >> and/or attachments to it are strictly prohibited. If >> you have received this communication in error, >> please notify us by reply e-mail or telephone and >> immediately and permanently delete the message >> and any attachments. Thank you >> >> >> _______________________________________________ >> AMBER-Developers mailing list >> AMBER-Developers.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber-developers > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Sat Jun 04 2016 - 13:30:02 PDT