Hi Mark, Yes I have compared the runtime for single as well as 8 processor . Could you please tell me the right steps to configure GROMACS-MPI version?.
Thanks. thamu 2009/6/11 <[email protected]> > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 11 Jun 2009 13:56:15 +0000 (GMT) > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow > speed > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > On 06/11/09, Thamu <[email protected]> wrote: > > > > Hi Mark, > > > > The top md.log is below. The mdrun command was "mpirun -np 8 > ~/software/bin/mdrun_mpi -deffnm md" > In my experience, correctly-configured MPI gromacs running in parallel > reports information about the number of nodes and the identity of the node > writing the .log file. This is missing, so something is wrong with your > setup. > > I've assumed that you've compared this "8-processor" runtime with a > single-processor runtime and found them comparable... > > Mark > > > > > > > > > :-) G R O M A C S (-: > > > > GROup of MAchos and Cynical Suckers > > > > :-) VERSION 4.0.5 (-: > > > > > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and > others. > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2008, The GROMACS development team, > > check out http://www.gromacs.org (http://www.gromacs.org) > for more information. > > > > This program is free software; you can redistribute it and/or > > modify it under the terms of the GNU General Public License > > as published by the Free Software Foundation; either version 2 > > of the License, or (at your option) any later version. > > > > :-) /home/thamu/software/bin/mdrun_mpi (-: > > > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl > > GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable > > molecular simulation > > J. Chem. Theory Comput. 4 (2008) pp. 435-447 > > -------- -------- --- Thank You --- -------- -------- > > > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. > C. > > Berendsen > > GROMACS: Fast, Flexible and Free > > J. Comp. Chem. 26 (2005) pp. 1701-1719 > > -------- -------- --- Thank You --- -------- -------- > > > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > E. Lindahl and B. Hess and D. van der Spoel > > GROMACS 3.0: A package for molecular simulation and trajectory analysis > > J. Mol. Mod. 7 (2001) pp. 306-317 > > -------- -------- --- Thank You --- -------- -------- > > > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > H. J. C. Berendsen, D. van der Spoel and R. van Drunen > > GROMACS: A message-passing parallel molecular dynamics implementation > > Comp. Phys. Comm. 91 (1995) pp. 43-56 > > -------- -------- --- Thank You --- -------- -------- > > > > Input Parameters: > > integrator = md > > nsteps = 10000000 > > init_step = 0 > > ns_type = Grid > > nstlist = 10 > > ndelta = 2 > > nstcomm = 1 > > comm_mode = Linear > > nstlog = 100 > > nstxout = 1000 > > nstvout = 0 > > nstfout = 0 > > nstenergy = 100 > > nstxtcout = 0 > > init_t = 0 > > delta_t = 0.002 > > xtcprec = 1000 > > nkx = 70 > > nky = 70 > > nkz = 70 > > pme_order = 4 > > ewald_rtol = 1e-05 > > ewald_geometry = 0 > > epsilon_surface = 0 > > optimize_fft = TRUE > > ePBC = xyz > > bPeriodicMols = FALSE > > bContinuation = FALSE > > bShakeSOR = FALSE > > etc = V-rescale > > epc = Parrinello-Rahman > > epctype = Isotropic > > tau_p = 0.5 > > ref_p (3x3): > > ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} > > ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} > > ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} > > compress (3x3): > > compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} > > compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} > > compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} > > refcoord_scaling = No > > posres_com (3): > > posres_com[0]= 0.00000e+00 > > posres_com[1]= 0.00000e+00 > > posres_com[2]= 0.00000e+00 > > posres_comB (3): > > posres_comB[0]= 0.00000e+00 > > posres_comB[1]= 0.00000e+00 > > posres_comB[2]= 0.00000e+00 > > andersen_seed = 815131 > > rlist = 1 > > rtpi = 0.05 > > coulombtype = PME > > rcoulomb_switch = 0 > > rcoulomb = 1 > > vdwtype = Cut-off > > rvdw_switch = 0 > > rvdw = 1.4 > > epsilon_r = 1 > > epsilon_rf = 1 > > tabext = 1 > > implicit_solvent = No > > gb_algorithm = Still > > gb_epsilon_solvent = 80 > > nstgbradii = 1 > > rgbradii = 2 > > gb_saltconc = 0 > > gb_obc_alpha = 1 > > gb_obc_beta = 0.8 > > gb_obc_gamma = 4.85 > > sa_surface_tension = 2.092 > > DispCorr = No > > free_energy = no > > init_lambda = 0 > > sc_alpha = 0 > > sc_power = 0 > > sc_sigma = 0.3 > > delta_lambda = 0 > > nwall = 0 > > wall_type = 9-3 > > wall_atomtype[0] = -1 > > wall_atomtype[1] = -1 > > wall_density[0] = 0 > > wall_density[1] = 0 > > wall_ewald_zfac = 3 > > pull = no > > disre = No > > disre_weighting = Conservative > > disre_mixed = FALSE > > dr_fc = 1000 > > dr_tau = 0 > > nstdisreout = 100 > > orires_fc = 0 > > orires_tau = 0 > > nstorireout = 100 > > dihre-fc = 1000 > > em_stepsize = 0.01 > > em_tol = 10 > > niter = 20 > > fc_stepsize = 0 > > nstcgsteep = 1000 > > nbfgscorr = 10 > > ConstAlg = Lincs > > shake_tol = 0.0001 > > lincs_order = 4 > > lincs_warnangle = 30 > > lincs_iter = 1 > > bd_fric = 0 > > ld_seed = 1993 > > cos_accel = 0 > > deform (3x3): > > deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > > deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > > deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > > userint1 = 0 > > userint2 = 0 > > userint3 = 0 > > userint4 = 0 > > userreal1 = 0 > > userreal2 = 0 > > userreal3 = 0 > > userreal4 = 0 > > grpopts: > > nrdf: 6706.82 106800 > > ref_t: 300 300 > > tau_t: 0.1 0.1 > > anneal: No No > > ann_npoints: 0 0 > > acc: 0 0 0 > > nfreeze: N N N > > energygrp_flags[ 0]: 0 0 0 > > energygrp_flags[ 1]: 0 0 0 > > energygrp_flags[ 2]: 0 0 0 > > efield-x: > > n = 0 > > efield-xt: > > n = 0 > > efield-y: > > n = 0 > > efield-yt: > > n = 0 > > efield-z: > > n = 0 > > efield-zt: > > n = 0 > > bQMMM = FALSE > > QMconstraints = 0 > > QMMMscheme = 0 > > scalefactor = 1 > > qm_opts: > > ngQM = 0 > > Table routines are used for coulomb: TRUE > > Table routines are used for vdw: FALSE > > Will do PME sum in reciprocal space. > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. > Pedersen > > A smooth particle mesh Ewald method > > J. Chem. Phys. 103 (1995) pp. 8577-8592 > > -------- -------- --- Thank You --- -------- -------- > > > > Using a Gaussian width (1/beta) of 0.320163 nm for Ewald > > Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4 > > System total charge: -0.000 > > Generated table with 1200 data points for Ewald. > > Tabscale = 500 points/nm > > Generated table with 1200 data points for LJ6. > > Tabscale = 500 points/nm > > Generated table with 1200 data points for LJ12. > > Tabscale = 500 points/nm > > Generated table with 1200 data points for 1-4 COUL. > > Tabscale = 500 points/nm > > Generated table with 1200 data points for 1-4 LJ6. > > Tabscale = 500 points/nm > > Generated table with 1200 data points for 1-4 LJ12. > > Tabscale = 500 points/nm > > > > Enabling TIP4p water optimization for 17798 molecules. > > > > Configuring nonbonded kernels... > > Testing x86_64 SSE support... present. > > > > > > Removing pbc first time > > > > Initializing LINear Constraint Solver > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije > > LINCS: A Linear Constraint Solver for molecular simulations > > J. Comp. Chem. 18 (1997) pp. 1463-1472 > > -------- -------- --- Thank You --- -------- -------- > > > > The number of constraints is 3439 > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > S. Miyamoto and P. A. Kollman > > SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for > Rigid > > Water Models > > J. Comp. Chem. 13 (1992) pp. 952-962 > > -------- -------- --- Thank You --- -------- -------- > > > > Center of mass motion removal mode is Linear > > We have the following groups for center of mass motion removal: > > 0: rest > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > G. Bussi, D. Donadio and M. Parrinello > > Canonical sampling through velocity rescaling > > J. Chem. Phys. 126 (2007) pp. 014101 > > -------- -------- --- Thank You --- -------- -------- > > > > There are: 56781 Atoms > > There are: 17798 VSites > > Max number of connections per atom is 59 > > Total number of connections is 216528 > > Max number of graph edges per atom is 4 > > Total number of graph edges is 113666 > > > > Constraining the starting coordinates (step 0) > > > > Constraining the coordinates at t0-dt (step 0) > > RMS relative constraint deviation after constraining: 3.77e-05 > > Initial temperature: 299.838 K > > > > > > > > Recently I successfully installed the gromacs-4.0.5 mpi version. > > > > I could run in 8 cpu. but the speed is very slow. > > > > Total number of atoms in the system is 78424. > > > > while running all 8 cpu showing 95-100% CPU. > > > > > > > > How to speed up the calculation. > > > > > > > > Thanks > > > > > > > > > > > That's normal for a system that atoms/cpu ratio. > > > What's your system and what mdp file are you using? > > > -- > > > ------------------------------------------------------ > > > You haven't given us any diagnostic information. The problem could be > > > that you're not running an MPI GROMACS (show us your configure line, > > > your mdrun command line and the top 50 lines of your .log file). > > > > > > Mark > > > > > > > > > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090611/b60097b8/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 62, Issue 57 > ***************************************** >
_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
