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.
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. 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. 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. 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. 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 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
