Hello, On 15.04.2010, at 16:18, Mark Abraham wrote:
> On 16/04/2010 12:02 AM, Shuangxing Dai wrote: >> Hi, gmx-users: >> I am using latest version of gromacs and found it was really slow. I >> was wondering anyone got the same experience and can point out where the >> problem is. >> I was running double precision for MD. But for each dynamics >> simulation, it takes 4 days. I should only take two or three hours. > > Well, double precisions is slower - possibly very much so. You need twice the > bus and cache bandwidth because you are throwing around twice the memory. > Otherwise, we can't say much because we don't know anything about your > hardware or where you got your benchmark from. > > Other comments below. It looks very much like you've gone and made a bunch of > semi-random changes to things. That's not normally a good idea. > >> Here is the .mdp file: >> define = >> ; RUN CONTROL PARAMETERS = >> integrator = sd >> ; start time and timestep in ps = >> tinit = 0 >> dt = 0.001 >> nsteps = 200000 >> ; number of steps for center of mass motion removal = >> nstcomm = 100 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 100 >> nstenergy = 100 >> ; Output frequency and precision for xtc file = >> nstxtcout = 100 >> xtc-precision = 1000 >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 50 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> >> ;OPTIONS FOR PRESSURE COUPLING >> Pcoupl = berendsen >> tau_p = 1 >> compressibility = 4.5e-05 >> ref_p = 0.1 >> ;OPTIONS FOR TEMPERATURE COUPLING >> tc_grps = system >> tau_t = 0.1 >> ref_t = 300 >> ; OPTIONS FOR BONDS = >> constraints = hbonds >> ; Type of constraint algorithm = >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration = >> unconstrained-start = no >> ; Relative tolerance of shake = >> shake-tol = 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 12 > > That's huge, and the use of lincs is somewhat inconsistent with a 1fs > timestep. > >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> ; Periodic boundary conditions: xyz, no, xy >> pbc = xyz >> periodic_molecules = no >> ; nblist cut-off >> rlist = 1 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = Ewald > > This could be a correct decision, but it's unlikely. > >> rcoulomb = 1 >> ; Method for doing Van der Waals >> vdw-type = Cut-off >> ; cut-off lengths >> rvdw = 1 >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters >> pme_order = 6 >> ewald_rtol = 1e-4 > > Again, could be correct, or could just be killing you. > This is definitely killing you, because you can run Ewald just in serial and not in parallel. Cheers, Flo >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = no > > Mark > -- > 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/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/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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