[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Hi 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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
On Thu, 2009-06-11 at 14:35 +0800, Thamu wrote: Hi 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. That's normal for a system that atoms/cpu ratio. What's your system and what mdp file are you using? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-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
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Thamu wrote: Hi Recently I successfully installed the gromacs-4.0.5 mpi version. Possibly. 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. 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 ___ gmx-users mailing listgmx-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
[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Hi Mark, The top md.log is below. The mdrun command was mpirun -np 8 ~/software/bin/mdrun_mpi -deffnm md :-) 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 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 = 1000 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]={ 1.0e+00, 0.0e+00, 0.0e+00} ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00} ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00} compress (3x3): compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00} compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00} compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05} refcoord_scaling = No posres_com (3): posres_com[0]= 0.0e+00 posres_com[1]= 0.0e+00 posres_com[2]= 0.0e+00 posres_comB (3): posres_comB[0]= 0.0e+00 posres_comB[1]= 0.0e+00 posres_comB[2]= 0.0e+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 =
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
On 06/11/09, Thamu asth...@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 = 1000 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]={ 1.0e+00, 0.0e+00, 0.0e+00} ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00} ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00} compress (3x3): compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00} compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00} compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05} refcoord_scaling = No posres_com (3): posres_com[0]= 0.0e+00 posres_com[1]= 0.0e+00 posres_com[2]= 0.0e+00 posres_comB (3): posres_comB[0]= 0.0e+00 posres_comB[1]= 0.0e+00 posres_comB[2]= 0.0e+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
RE: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Mark is correct. You should see node information at the top of the md log file if you are truly running in parallel. Apparently the default host (or machines) file (which contains the list of available nodes on your cluster) has not been /is not being populated correctly. Your can build your own hosts file and then rerun the job using the command line: mpirun -np 8 -hostfile hostfile ~/software/bin/mdrun_mpi -deffnm md The content and structure of the hostfile will depend on what version of MPI you are using. Hopefully, you are not using MPICH 1 but instead are using OpenMPI, MPICH2, or Intel MPI. Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Thamu Sent: Thursday, June 11, 2009 9:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed Hi Mark, The top md.log is below. The mdrun command was mpirun -np 8 ~/software/bin/mdrun_mpi -deffnm md :-) 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 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 = 1000 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]={ 1.0e+00, 0.0e+00, 0.0e+00} ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00} ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00} compress (3x3): compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00} compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00} compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05} refcoord_scaling = No posres_com (3): posres_com[0]= 0.0e+00 posres_com[1]= 0.0e+00 posres_com[2]= 0.0e+00 posres_comB (3): posres_comB[0]= 0.0e+00 posres_comB[1]= 0.0e+00 posres_comB[2]= 0.0e+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