Dear all, I am trying to optimize runtimes/speed for a series of calculations i plan to do with a rather complex system. When looking at runtimes I observed one peculiar issue: the estimated runtime written to stderr by mdrun with the "-v" option keepsgrowing ... in my experience this estimate normally converges to a fairly accurate value within a few hundred steps. not so here .. for example, starting a job at 12:14 gromacs writes to stderr:
step 100, will finish Wed Apr 6 12:40:35 2011vol 0.97 imb F 1% step 200, will finish Wed Apr 6 12:39:42 2011vol 0.95 imb F 2% step 300, will finish Wed Apr 6 12:39:47 2011vol 0.95 imb F 1% step 400, will finish Wed Apr 6 12:39:52 2011vol 0.96 imb F 1% ... step 38400, will finish Wed Apr 6 14:09:11 2011vol 0.91 imb F 29% so the estimated run time grows steadily from 25 to 110 minutes within about one hour... this is mdrun_d (gmx-4.5.3) running on a linux PC with 2 processores/4 nodes/8 threads. There's a couple of other programs (X, editor, ...) running at the same time but none of them uses a lot of CPU. Anyway, what i see lets me expect there might be a way to speed up these calculations. I'd appreciate any suggestions! (below is my mdp file.) cheers, Michael mdp file: integrator = md ; dt = 0.001 tinit = 0 nsteps = 100000 nstxtcout = 0 nstxout = 1000 nstvout = 0 nstfout = 0 nstenergy = 1000 ; constraint_algorithm = lincs constraints = hbonds ; comm_mode = Linear nstcomm = 1 pbc = xyz nstlist = 10 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; coulombtype = PME vdwtype = User fourierspacing = 0.2 optimize_fft = yes ; Tcoupl = nose-hoover tc_grps = System ref_t = 300.0 tau_t = 0.4 gen_vel = yes gen_temp = 240.0 gen_seed = 222222 ; pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = f1 pull_group1 = f2 pull_rate1 = -0.015 pull_k1 = 1000 pull_nstxout = 100 pull_nstfout = 100 pull_pbcatom0 = 241 pull_pbcatom1 = 482 ; freezegrps = c1 c2 freezedim = Y Y N Y Y N ; energygrps = SOL CC CF energygrp_table = CF CF CF SOL CF CC -- 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
