On 29/12/11, "Peter C. Lai" <p...@uab.edu> wrote: > What performance are you getting that you want to improve more? > Here's a datapoint from the last simulation I ran: > > Currently running gromacs 4.5.4 built with icc+fftw+openmpi on infiniband > qdr and I get about 9.7ns/day on 64 PP nodes with 4 PME nodes (68 total > 2.66ghz X5650) on my 99113 atom system in single precision....
It is very likely you can do better by following grompp's advice about having one-third to one-quarter of your nodes doing PME. See manual 3.17.5. > > > I find that it is more important to optimize your PP/PME allocation than > microoptimizing the code... Yes, hence the existence of g_tune_pme and other tools. > I also find that at some point above 232 nodes (I don't remember what the > exact > number is), mdrun will complain about the overhead it takes to communicate > energies if am having it communicate energies every 5 steps; which is a > reflection on thea limitation of the infrastructure than the code too. I'd say this is more a reflection the limitations of the model you've asked it to use. Per manual 7.3.8 you can control this cost with suitable choices for the nst* variables. You can judge best whether you want faster performance or higher accuracy in the implementation of your approximate model... Mark > > > > On 2011-12-27 06:48:23AM -0600, Mark Abraham wrote: > > On 12/27/2011 11:18 PM, Sudip Roy wrote: > > > Gromacs users, > > > > > > Please let me know what is the best option for gromacs compilation > > > (looking for better performance in INFINIBAND QDR systems) > > > > > > 1. Intel composer XE i.e. Intel compilers, mkl but open MPI library > > > > > > 2. Intel studio i.e. Intel compilers, mkl, and Intel MPI library > > > > GROMACS is strongly CPU-bound in a way that is rather insensitive to > > compilers and libraries. I would expect no strong difference between the > > above two - and icc+MKL+OpenMPI was only a few percent faster than > > gcc+FFTW+OpenMPI when I tested them on such a machine about two years ago. > > > > Mark > > > > -- > > This message has been scanned for viruses and > > dangerous content by MailScanner, and is > > believed to be clean. > > > > -- > > 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 > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > 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 > >
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