On Sat, Mar 9, 2013 at 6:53 AM, Christopher Neale < [email protected]> wrote:
> Dear users: > > I am seeing a 140% performance boost when moving from gromacs 4.5.5 to > 4.6.1 when I run a simulation on a single node. However, I am "only" seeing > a 110% performance boost when running on multiple nodes. Does anyone else > see this? Note that I am not using the verlet cutoff scheme. > What's the processor and network for those runs? I'm not sure that this is a problem, but I was surprised to see how big the > difference was between 1 and 2 nodes, while for 2-10 nodes I saw a reliable > 10% performance boost. > Not sure what you mean by "reliable 10% performance boost." Reporting actual ns/day rates would be clearer. Is a "140% performance boost" a factor of 1.4 more ns/day or a factor of 2.4 more ns/day? Please note that, while I compiled the fftw (with sse2) and gromacs 4.6.1, > I did not compile the 4.5.5 version that I am comparing to (or its fftw) so > the difference might be in compilation options. Indeed. > Still, I wonder why the benefits of 4.6.1 are so fantastic on 1 node but > fall off to good-but-not-amazing on > 1 node. > Finding the answer would start by examining the changes in the timing breakdowns in your .log files. Switching from using in-memory MPI to network MPI is a significant cost on busy/weak networks. The system is about 43K atoms. I have not tested this with other systems or > cutoffs. > > My mdp file follows. Thank you for any advice. > Your system is probably not calculating energies very much. 4.6 uses force-only kernels if that's all you need from it. Mark Chris. > > constraints = all-bonds > lincs-iter = 1 > lincs-order = 6 > constraint_algorithm = lincs > integrator = sd > dt = 0.002 > tinit = 0 > nsteps = 2500000000 > nstcomm = 1 > nstxout = 2500000000 > nstvout = 2500000000 > nstfout = 2500000000 > nstxtcout = 50000 > nstenergy = 50000 > nstlist = 10 > nstlog=0 > ns_type = grid > vdwtype = switch > rlist = 1.0 > rlistlong = 1.6 > rvdw = 1.5 > rvdw-switch = 1.4 > rcoulomb = 1.0 > coulombtype = PME > ewald-rtol = 1e-5 > optimize_fft = yes > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > tc_grps = System > tau_t = 1.0 > ld_seed = -1 > ref_t = 310 > gen_temp = 310 > gen_vel = yes > unconstrained_start = no > gen_seed = -1 > Pcoupl = berendsen > pcoupltype = semiisotropic > tau_p = 4 4 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > dispcorr = EnerPres > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
