On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole <x.peri...@rug.nl> wrote:
> > BG CPUs are generally much slower (clock whose) but scale better. > > You should try to run on 64 CPUs on the Blue gene too for faire comparison. > The number of CPUs per nodes is also an important factor: the more CPUs > per nodes the more communications needs to be done. I observed a > significant slow down while going from 16 to 32 CPUs nodes (recent intel) > but using the same number of CPUs. > Indeed. Moreover, there is not (yet) any instruction-level parallelism in the GROMACS kernels used on BG/Q, unlike for the x86 family. So there is a theoretical factor of four that is simply not being exploited. (And no, the compiler is not good enough to do it automatically ;-)) Mark > On Jun 4, 2013, at 4:02 PM, Jianguo Li <ljg...@yahoo.com.sg> wrote: > > > Dear All, > > > > > > Has anyone has Gromacs benchmark on Bluegene/Q? > > I recently installed gromacs-461 on BG/Q using the following command: > > cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ > > -DGMX_BUILD_OWN_FFTW=ON \ > > -DBUILD_SHARED_LIBS=OFF \ > > -DGMX_XML=OFF \ > > -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 > > make > > make install > > > > After that, I did a benchmark simulation using a box of pure water > containing 140k atoms. > > The command I used for the above test is: > > srun --ntasks-per-node=32 --overcommit > /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c > box_md1.gro -x box_md1.xtc -g md1.log >& job_md1 > > > > And I got the following performance: > > Num. cores hour/ns > > 128 9.860 > > 256 4.984 > > 512 2.706 > > 1024 1.544 > > 2048 0.978 > > 4092 0.677 > > > > The scaling seems ok, but the performance is far from what I expected. > In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other > clusters. For comparison, I also did the same simulation using 64 > processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly > equivalent to using 512 cores in BlueGene/Q. > > > > I am wondering if the above benchmark results are reasonable or not? Or > Am I doing something wrong in compiling? > > Any comments/suggestions are appreciated, thank you very much! > > > > Have a nice day! > > Jianguo > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
