[gmx-users] Re: gmx-users Digest, Vol 62, Issue 57
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 11 16:50:29 CEST 2009
Thamu wrote:
> 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?.
>
The full installation procedure is here:
http://oldwww.gromacs.org/content/view/23/33/
...as well as Appendix A of the manual.
-Justin
> Thanks.
>
> thamu
>
> 2009/6/11 <gmx-users-request at gromacs.org
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> 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 <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
> Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow
> speed
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <fbe6b07c8ea.4a310cff at anu.edu.au
> <mailto:fbe6b07c8ea.4a310cff at anu.edu.au>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 06/11/09, Thamu <asthamu at gmail.com <mailto:asthamu at gmail.com>>
> 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
> > >
> > >
> > >
> >
> >
>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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