I have tested with 8, 16, 24 and 32 cpus. Only parallel with 8 and 16 cpus works, and the other cases (24 and 32) are even much slower than 8 cpus' case.
Any idea about this? On Nov 24, 2007 11:42 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Myunggi Yi wrote: > > Thank you for the answer. > > > > I compiled gmx with gcc and gnu onpempi. > > > > I have seen very good performance with 16 cpus (about 12,000 atoms). > > > > +++++++++++++++++++++++++++++++++++ > > (Mnbf/s) (GFlops) (ns/day) (hour/ns) > > Performance: 50.828 19.920 14.648 1.638 > > Total Scaling: 95% of max performance > > +++++++++++++++++++++++++++++++++++ > > > > Now I just submit a job with 32 cpus (about 48,000 atoms). > > It looks very very slow. > > > > > > Would you recommend the optimal numer of cpus? > No. You have to test for yourself (as you are doing right now). > It is very dependent on simulation size, network etc. > > > > > > > > > > > On Nov 24, 2007 10:53 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > >> Myunggi Yi wrote: > >>> Sorry. Here is more information. > >>> > >>> > >>> GNU C/C++ 3.4.6 > >>> Intel C/C++ 10.0.026 > >>> and > >>> OpenMPI GNU 1.2.4 > >>> OpenMPI Intel 1.2.4 > >> Everything will probably be easier with the gcc compiler, and the > >> performance difference is negligible for gromacs. > >> > >>> > >>> > >>> On Nov 24, 2007 10:31 AM, Myunggi Yi <[EMAIL PROTECTED]> wrote: > >>>> Dear gromacs users, > >>>> > >>>> I'm a beginner. > >>>> I'm trying to compile gromacs 3.3.1 or 3.3.2 on the following linux > >>>> cluster (centOS). > >>>> Dual, Dual-Core 2220 2.8 GHz Opterons, 2 GB RAM per core, 64-bit. > >>>> I will use 16 to 32 (64) cpus for the parallel simulations. > >>>> > >>>> I tested mpich2, but there is a problem with infiniband communications. > >>>> > >>>> I have intel and GNU compilers and openMPI. > >>>> > >>>> Which option will give me the best performance? > >>>> > >>>> Have a nice weekend. > >>>> > >>>> > >>>> -- > >>>> Best wishes, > >>>> > >>>> MYUNGGI YI > >>>> ================================== > >>>> KLB 419 > >>>> Institute of Molecular Biophysics > >>>> Florida State University > >>>> Tallahassee, FL 32306 > >>>> > >>>> Office: (850) 645-1334 > >>>> http://www.scs.fsu.edu/~myunggi > >>>> > >>> > >>> > >> > >> -- > >> David. > >> ________________________________________________________________________ > >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > >> Dept. of Cell and Molecular Biology, Uppsala University. > >> Husargatan 3, Box 596, 75124 Uppsala, Sweden > >> phone: 46 18 471 4205 fax: 46 18 511 755 > >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Best wishes, MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
