[gmx-users] Simulations on GPU
Francesco Oteri
francesco.oteri at gmail.com
Tue Jan 4 15:16:23 CET 2011
Maybe the used force-field is wrong.
mdrun-gpu is able to use the AMBER forcefield, but it is not possible
using gromos force-field.
When gromos force-field is used, the output is full of NaN
Il 12/10/2010 03:00, Igor Leontyev ha scritto:
> Now I am able to run simulations on GPU but the output is weird. For
> example, temperature drops down to 270K while ref_t=298
> (Tcoupl=andersen). Moreover, after several hours of simulations
> mdrun-gpu starts to output "NAN" energies and hangs up. Pre-run and
> post-run GPU memory test is always passed. The graphics card is that
> provided with HP desktops (might be MSI) NVIDIA GTX260 with 1.8Gb
> memory. The output of mdrun and mdrun-gpu versions of Gromacs is given
> bellow. Any ideas? Thanks.
>
> Igor
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////
>
> Log file opened on Fri Oct 8 14:46:51 2010
> Host: powerpc pid: 32083 nodeid: 0 nnodes: 4
> The Gromacs distribution was built Thu Sep 30 14:42:48 PDT 2010 by
> leontyev at powerpc (Linux 2.6.32-22-generic x86_64)
>
>
> :-) G R O M A C S (-:
>
> Gromacs Runs One Microsecond At Cannonball Speeds
>
> :-) VERSION 4.5.1 (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> 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.
>
> :-) /usr/local/opt/bin/gromacs/gromacs-4.5.1/bin/mdrun_mpich2 (-:
>
>
>
> Input Parameters:
> integrator = md
> nsteps = 10000
> init_step = 0
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 1003
> comm_mode = Linear
> nstlog = 1000
> nstxout = 5000
> nstvout = 10000000
> nstfout = 0
> nstcalcenergy = 10
> nstenergy = 1000
> nstxtcout = 0
> init_t = 0
> delta_t = 0.001
> xtcprec = 1000
> nkx = 54
> nky = 60
> nkz = 90
> pme_order = 6
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Andersen
> nsttcouple = 10
> epc = Berendsen
> epctype = Isotropic
> nstpcouple = 10
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+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 = 1.2
> rlistlong = 1.2
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.2
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1.2
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 1
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = No
> sa_surface_tension = 2.092
> DispCorr = EnerPres
> free_energy = no
> init_lambda = 0
> delta_lambda = 0
> n_foreign_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> sc_sigma_min = 0.3
> nstdhdl = 10
> separate_dhdl_file = yes
> dhdl_derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> 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 = 8
> lincs_warnangle = 30
> lincs_iter = 4
> 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: 99021
> ref_t: 298.15
> tau_t: 0.3
> anneal: No
> ann_npoints: 0
> acc: 0 0 0
> nfreeze: Y Y Y N N N
> energygrp_flags[ 0]: 0 0
> energygrp_flags[ 1]: 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
>
> Initializing Domain Decomposition on 4 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 0.585 nm, LJ-14, atoms 10901 11433
> multi-body bonded interactions: 0.482 nm, Ryckaert-Bell., atoms 11431
> 11935
> Minimum cell size due to bonded interactions: 0.530 nm
> Maximum distance for 9 constraints, at 120 deg. angles, all-trans:
> 0.218 nm
> Estimated maximum distance required for P-LINCS: 0.218 nm
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 4 cells with a minimum initial size of
> 0.663 nm
> The maximum allowed number of cells is: X 9 Y 10 Z 16
> Domain decomposition grid 1 x 4 x 1, separate PME nodes 0
> PME domain decomposition: 1 x 4 x 1
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
> Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
> Long Range LJ corr.: <C6> 4.0351e-04
> System total charge: -0.000
> Generated table with 1100 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 11505 molecules.
>
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
> Removing pbc first time
>
> Initializing Parallel LINear Constraint Solver
>
> Linking all bonded interactions to atoms
> There are 65716 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: Y 1
> The initial domain decomposition cell size is: Y 1.77 nm
>
> The maximum allowed distance for charge groups involved in
> interactions is:
> non-bonded interactions 1.200 nm
> (the following are initial values, they could change due to box
> deformation)
> two-body bonded interactions (-rdd) 1.200 nm
> multi-body bonded interactions (-rdd) 1.200 nm
> atoms separated by up to 9 constraints (-rcon) 1.773 nm
>
> When dynamic load balancing gets turned on, these settings will change
> to:
> The maximum number of communication pulses is: Y 1
> The minimum size for domain decomposition cells is 1.200 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: Y 0.68
> The maximum allowed distance for charge groups involved in
> interactions is:
> non-bonded interactions 1.200 nm
> two-body bonded interactions (-rdd) 1.200 nm
> multi-body bonded interactions (-rdd) 1.200 nm
> atoms separated by up to 9 constraints (-rcon) 1.200 nm
>
>
> Making 1D domain decomposition grid 1 x 4 x 1, home cell index 0 0 0
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> There are: 46503 Atoms
> Charge group distribution at step 0: 4533 7043 7334 4581
> Grid: 10 x 6 x 17 cells
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 7.96e-07
> Initial temperature: 297.745 K
>
> Started mdrun on node 0 Fri Oct 8 14:46:51 2010
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Ryckaert-Bell.
> LJ-14
> 9.26629e+03 2.53358e+04 1.36779e+03 2.97600e+04
> 1.20809e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> recip.
> 1.40505e+05 3.83498e+04 -2.30989e+03 -5.95333e+05
> -1.96357e+05
> Potential Kinetic En. Total Energy Temperature Pres. DC
> (bar)
> -5.37334e+05 1.22595e+05 -4.14739e+05 2.97810e+02
> -1.67546e+02
> Pressure (bar) Constr. rmsd
> 2.67468e+00 1.03652e-06
>
> DD step 9 load imb.: force 19.9%
>
> At step 10 the performance loss due to force load imbalance is 9.3 %
>
> NOTE: Turning on dynamic load balancing
>
> DD step 999 vol min/aver 0.777 load imb.: force 0.1%
>
> Step Time Lambda
> 1000 1.00000 0.00000
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Ryckaert-Bell.
> LJ-14
> 9.29054e+03 2.49530e+04 1.43296e+03 2.96188e+04
> 1.19777e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> recip.
> 1.40496e+05 3.99112e+04 -2.30308e+03 -5.96482e+05
> -1.96429e+05
> Potential Kinetic En. Total Energy Temperature Pres. DC
> (bar)
> -5.37533e+05 1.22974e+05 -4.14560e+05 2.98729e+02
> -1.66560e+02
> Pressure (bar) Constr. rmsd
> -1.40877e+02 1.04647e-06
>
> DD step 1999 vol min/aver 0.773 load imb.: force 0.1%
>
> ................................................................................
>
>
> Step Time Lambda
> 10000 10.00000 0.00000
>
> Writing checkpoint, step 10000 at Fri Oct 8 14:58:26 2010
>
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Ryckaert-Bell.
> LJ-14
> 9.00658e+03 2.52059e+04 1.34920e+03 2.95995e+04
> 1.19606e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> recip.
> 1.40474e+05 4.00471e+04 -2.30290e+03 -5.96601e+05
> -1.96374e+05
> Potential Kinetic En. Total Energy Temperature Pres. DC
> (bar)
> -5.37636e+05 1.22577e+05 -4.15059e+05 2.97765e+02
> -1.66533e+02
> Pressure (bar) Constr. rmsd
> -5.69272e+01 1.04191e-06
>
> <====== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
>
> Statistics over 10001 steps using 1001 frames
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Ryckaert-Bell.
> LJ-14
> 9.11274e+03 2.49545e+04 1.36688e+03 2.96269e+04
> 1.20386e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul.
> recip.
> 1.40680e+05 3.95513e+04 -2.30457e+03 -5.95701e+05
> -1.96403e+05
> Potential Kinetic En. Total Energy Temperature Pres. DC
> (bar)
> -5.37077e+05 1.22248e+05 -4.14829e+05 2.96967e+02
> -1.66776e+02
> Pressure (bar) Constr. rmsd
> 4.32167e+00 0.00000e+00
>
> Box-X Box-Y Box-Z
> 6.01417e+00 7.09874e+00 1.07493e+01
>
> Total Virial (kJ/mol)
> 4.10242e+04 -9.05005e+00 -2.30129e+02
> -1.20791e+01 4.05914e+04 1.71615e+02
> -2.13770e+02 1.99254e+02 4.04540e+04
>
> Pressure (bar)
> -1.22617e+01 -8.98547e-01 1.93020e+01
> -6.78561e-01 2.15880e+01 -8.68094e+00
> 1.81194e+01 -1.06823e+01 3.63870e+00
>
> Total Dipole (D)
> 4.73145e+02 -1.30311e+03 -2.15240e+02
>
> Epot (kJ/mol) Coul-SR LJ-SR Coul-14
> LJ-14
> glu242side-glu242side 2.99268e+00 0.00000e+00 -1.85865e+02
> 1.35027e+00
> glu242side-rest -5.15085e+01 -2.83484e+01 2.08195e+01
> 4.24614e+00
> rest-rest -5.95653e+05 3.95797e+04 1.40846e+05
> 1.20330e+04
>
>
> M E G A - F L O P S A C C O U N T I N G
>
> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
> NF=No Forces
>
> Computing: M-Number M-Flops %
> Flops
> -----------------------------------------------------------------------------
>
> Coul(T) 10781.556318 452825.365 4.6
> Coul(T) [W3] 70.655819 8831.977 0.1
> Coul(T) + LJ 34247.547832 1883615.131 18.9
> Coul(T) + LJ [W3] 4684.616330 646477.054 6.5
> Coul(T) + LJ [W3-W3] 12244.355656 4677343.861 47.0
> Outer nonbonded loop 2334.588434 23345.884 0.2
> 1,4 nonbonded interactions 314.111408 28270.027 0.3
> Calc Weights 1395.229509 50228.262 0.5
> Spread Q Bspline 100456.524648 200913.049 2.0
> Gather F Bspline 100456.524648 602739.148 6.1
> 3D-FFT 105882.547196 847060.378 8.5
> Solve PME 1490.549040 95395.139 1.0
> NS-Pairs 12131.757207 254766.901 2.6
> Reset In Box 23.514491 70.543 0.0
> CG-CoM 46.596006 139.788 0.0
> Bonds 61.886188 3651.285 0.0
> Angles 219.991997 36958.655 0.4
> Propers 23.872387 5466.777 0.1
> RB-Dihedrals 253.765374 62680.047 0.6
> Virial 46.729683 841.134 0.0
> Stop-CM 0.465030 4.650 0.0
> P-Coupling 465.076503 2790.459 0.0
> Calc-Ekin 465.123006 12558.321 0.1
> Lincs 62.989618 3779.377 0.0
> Lincs-Mat 569.895960 2279.584 0.0
> Constraint-V 471.185790 3769.486 0.0
> Constraint-Vir 40.852892 980.469 0.0
> Settle 115.084515 37172.298 0.4
> -----------------------------------------------------------------------------
>
> Total 9944955.052 100.0
> -----------------------------------------------------------------------------
>
>
>
> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>
> av. #atoms communicated per step for force: 2 x 31556.3
> av. #atoms communicated per step for LINCS: 5 x 512.1
>
> Average load imbalance: 0.5 %
> Part of the total run time spent waiting due to load imbalance: 0.3 %
> Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> Y 0 %
>
>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Number G-Cycles Seconds %
> -----------------------------------------------------------------------
> Domain decomp. 4 1001 56.954 21.4 0.8
> DD comm. load 4 1000 0.206 0.1 0.0
> DD comm. bounds 4 1000 2.836 1.1 0.0
> Comm. coord. 4 10001 30.480 11.5 0.4
> Neighbor search 4 1001 579.978 218.1 7.8
> Force 4 10001 4548.315 1710.0 61.5
> Wait + Comm. F 4 10001 17.520 6.6 0.2
> PME mesh 4 10001 1897.783 713.5 25.7
> Write traj. 4 3 0.668 0.3 0.0
> Update 4 10001 45.142 17.0 0.6
> Constraints 4 10001 181.826 68.4 2.5
> Comm. energies 4 1011 3.026 1.1 0.0
> Rest 4 31.895 12.0 0.4
> -----------------------------------------------------------------------
> Total 4 7396.630 2780.9 100.0
> -----------------------------------------------------------------------
> -----------------------------------------------------------------------
> PME redist. X/F 4 20002 208.454 78.4 2.8
> PME spread/gather 4 20002 1440.827 541.7 19.5
> PME 3D-FFT 4 20002 203.508 76.5 2.8
> PME solve 4 10001 44.697 16.8 0.6
> -----------------------------------------------------------------------
>
> Parallel run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 695.218 695.218 100.0
> 11:35
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
> Performance: 243.800 14.305 1.243 19.310
> Finished mdrun on node 0 Fri Oct 8 14:58:27 2010
>
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////
>
> :-) G R O M A C S (-:
>
> Groningen Machine for Chemical Simulation
>
> :-) VERSION 4.5.1-dev-20101006-d3b58 (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> 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/leontyev/programs/bin/gromacs/gromacs-4.5.1-gpu/bin/mdrun-gpu (-:
>
> Input Parameters:
> integrator = md
> nsteps = 10000
> init_step = 0
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 1003
> comm_mode = Linear
> nstlog = 1000
> nstxout = 5000
> nstvout = 10000000
> nstfout = 0
> nstcalcenergy = 10
> nstenergy = 1000
> nstxtcout = 0
> init_t = 0
> delta_t = 0.001
> xtcprec = 1000
> nkx = 54
> nky = 60
> nkz = 90
> pme_order = 6
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Andersen
> nsttcouple = 10
> epc = Berendsen
> epctype = Isotropic
> nstpcouple = 10
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+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 = 1.2
> rlistlong = 1.2
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.2
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1.2
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 1
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = Ace-approximation
> sa_surface_tension = 2.092
> DispCorr = EnerPres
> free_energy = no
> init_lambda = 0
> delta_lambda = 0
> n_foreign_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> sc_sigma_min = 0.3
> nstdhdl = 10
> separate_dhdl_file = yes
> dhdl_derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> 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 = 8
> lincs_warnangle = 30
> lincs_iter = 4
> 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: 99021
> ref_t: 298.15
> tau_t: 0.3
> anneal: No
> ann_npoints: 0
> acc: 0 0 0
> nfreeze: Y Y Y N N N
> energygrp_flags[ 0]: 0 0
> energygrp_flags[ 1]: 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.
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
> Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
> Long Range LJ corr.: <C6> 4.0351e-04
> System total charge: -0.000
> Generated table with 1100 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 11505 molecules.
>
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
>
>
> Removing pbc first time
>
> Initializing LINear Constraint Solver
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> Max number of connections per atom is 91
> Total number of connections is 387700
> Max number of graph edges per atom is 6
> Total number of graph edges is 70330
>
> OpenMM plugins loaded from directory
> /home/leontyev/programs/bin/gromacs/OpenMM2.0-Linux64/lib/plugins:
> libOpenMMCuda.so, libOpenMMOpenCL.so,
> The combination rule of the used force field matches the one used by
> OpenMM.
> Gromacs will use the OpenMM platform: Cuda
> Gromacs will run on the GPU #0 (GeForce GTX 260).
> Pre-simulation ~15s memtest in progress...
> Memory test completed without errors.
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> Initial temperature: 0 K
>
> Started mdrun on node 0 Fri Oct 8 16:54:04 2010
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.34934e+05 1.22629e+05 -4.12305e+05 2.97883e+02
> 1.03777e-06
>
> Step Time Lambda
> 1000 1.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.42963e+05 1.16609e+05 -4.26354e+05 2.83260e+02
> 1.03777e-06
>
> Step Time Lambda
> 2000 2.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.49782e+05 1.14408e+05 -4.35374e+05 2.77912e+02
> 1.03777e-06
>
> Step Time Lambda
> 3000 3.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.51337e+05 1.12705e+05 -4.38631e+05 2.73777e+02
> 1.03777e-06
>
> Step Time Lambda
> 4000 4.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.52340e+05 1.12827e+05 -4.39513e+05 2.74073e+02
> 1.03777e-06
>
> Step Time Lambda
> 5000 5.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.52599e+05 1.13543e+05 -4.39056e+05 2.75812e+02
> 1.03777e-06
>
> Step Time Lambda
> 6000 6.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.52946e+05 1.14271e+05 -4.38675e+05 2.77580e+02
> 1.03777e-06
>
> Step Time Lambda
> 7000 7.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.51992e+05 1.13521e+05 -4.38471e+05 2.75759e+02
> 1.03777e-06
>
> Step Time Lambda
> 8000 8.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.52834e+05 1.14111e+05 -4.38723e+05 2.77192e+02
> 1.03777e-06
>
> Step Time Lambda
> 9000 9.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.52806e+05 1.13783e+05 -4.39022e+05 2.76396e+02
> 1.03777e-06
>
> Step Time Lambda
> 10000 10.00000 0.00000
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.53230e+05 1.12594e+05 -4.40636e+05 2.73506e+02
> 1.03777e-06
>
> Writing checkpoint, step 10000 at Fri Oct 8 17:06:02 2010
>
>
> <====== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
>
> Statistics over 11 steps using 11 frames
>
> Energies (kJ/mol)
> Potential Kinetic En. Total Energy Temperature Constr.
> rmsd
> -5.49797e+05 1.14636e+05 -4.35160e+05 2.78468e+02
> 0.00000e+00
>
> Box-X Box-Y Box-Z
> 1.73572e+12 1.19301e-40 2.31720e+11
>
> Total Virial (kJ/mol)
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
>
> Pressure (bar)
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0.00000e+00
>
> Total Dipole (D)
> 0.00000e+00 0.00000e+00 0.00000e+00
>
> Epot (kJ/mol) Coul-SR LJ-SR Coul-14
> LJ-14
> glu242side-glu242side 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00
> glu242side-rest 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00
> rest-rest 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00
>
> Post-simulation ~15s memtest in progress...
> Memory test completed without errors.
>
> M E G A - F L O P S A C C O U N T I N G
>
> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
> NF=No Forces
>
> Computing: M-Number M-Flops %
> Flops
> -----------------------------------------------------------------------------
>
> Lincs 0.011934 0.716 8.0
> Lincs-Mat 0.106200 0.425 4.7
> Constraint-V 0.046449 0.372 4.2
> Settle 0.023010 7.432 83.1
> -----------------------------------------------------------------------------
>
> Total 8.945 100.0
> -----------------------------------------------------------------------------
>
>
>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Number G-Cycles Seconds %
> -----------------------------------------------------------------------
> Write traj. 1 11 3.033 1.1 0.2
> Rest 1 1978.521 716.9 99.8
> -----------------------------------------------------------------------
> Total 1 1981.554 718.0 100.0
> -----------------------------------------------------------------------
>
> OpenMM run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 717.970 717.970 100.0
> 11:57
> (Mnbf/s) (MFlops) (ns/day) (hour/ns)
> Performance: 0.000 0.012 1.204 19.942
> Finished mdrun on node 0 Fri Oct 8 17:06:02 2010
> ////////////////////////////////////////////////////////////////////////////////////////////////////
>
>
>> Igor Leontyev wrote:
>>
>> Finally, I compiled and ran simulations with gpu version of
>> gromacs-4.5.1.
>> There were several issues:
>>
>> 1) Precompiled OpenMM2.0 libraries and headers must be downloaded (which
>> requires registration on their web page) and installed, otherwise cmake
>> doesn't find some source files.
>>
>> 2) cmake should be called outside the original source directory with the
>> path of the directory as an argument.
>>
>> 3) To run the obtained mdrun-gpu binary the CUDA dev driver should be
>> installed, otherwise the program does not find 'CUDA'. This step
>> appeared to
>> be the most problematic for me. According to OpenMM manual the driver
>> must
>> be installed with turned off x-windows service which can be done by the
>> command "init 3". In Ubuntu this command has no effect, while
>> switching the
>> graphical interface off/on is done by
>>
>> "sudo service gdm stop/start"
>>
>> It turned out that in Ubuntu-10.04 the CUDA driver installation
>> script does
>> not work properly even with turned off gdm. This issue and its
>> solution is
>> described at http://ubuntuforums.org/showthread.php?t=1467074
>>
>> Thank you for comments,
>>
>> Igor
>>>
>>>
>>> Szilárd Páll wrote:
>>> Dear Igor,
>>>
>>> Your output look _very_ weird, it seems as if CMake internal
>>> variable(s) were not initialized, which I have no clue how could have
>>> happened - the build generator works just fine for me. The only thing
>>> I can think of is that maybe your CMakeCache is corrupted.
>>>
>>> Could you please rerun cmake in a _clean_ build directory? Also, are
>>> you able to run cmake for CPU build (no -D options)?
>>>
>>> --
>>> Szilárd
>>>
>>>> Szilárd wrote:
>>>>>
>>>>> The beta versions are all outdated, could you please use the latest
>>>>> source distribution (4.5.1) instead (or git from the
>>>>> release-4-5-patches branch)?
>>>>
>>>> The result is the same for both the distribution 4.5.1 and git from
>>>> the
>>>> release-4-5-patches. See the output bellow.
>>>> =========================================
>>>>
>>>> PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>>>>
>>>> LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64:
>>>>
>>>> CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include
>>>> -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include
>>>> LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib
>>>> -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib
>>>> OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm
>>>>
>>>>
>>>> cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>>>> -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git
>>>>
>>>> CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties):
>>>> set_target_properties called with incorrect number of arguments.
>>>>
>>>>
>>>> CMake Error at gmxlib/CMakeLists.txt:126 (install):
>>>> install TARGETS given no ARCHIVE DESTINATION for static library target
>>>> "gmx".
>>>>
>>>>
>>>> CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
>>>> set_target_properties called with incorrect number of arguments.
>>>>
>>>>
>>>> CMake Error at mdlib/CMakeLists.txt:13 (install):
>>>> install TARGETS given no ARCHIVE DESTINATION for static library target
>>>> "md".
>>>>
>>>>
>>>> CMake Error at kernel/CMakeLists.txt:43 (set_target_properties):
>>>> set_target_properties called with incorrect number of arguments.
>>>>
>>>>
>>>> CMake Error at kernel/CMakeLists.txt:44 (set_target_properties):
>>>> set_target_properties called with incorrect number of arguments.
>>>>
>>>>
>>>> CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18
>>>> (CUDA_INCLUDE_DIRECTORIES):
>>>> Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".
>>>>
>>>>
>>>> CMake Warning (dev) in CMakeLists.txt:
>>>> No cmake_minimum_required command is present. A line of code such as
>>>>
>>>> cmake_minimum_required(VERSION 2.8)
>>>>
>>>> should be added at the top of the file. The version specified may be
>>>> lower
>>>> if you wish to support older CMake versions for this project. For more
>>>> information run "cmake --help-policy CMP0000".
>>>> This warning is for project developers. Use -Wno-dev to suppress it.
>>>>
>>>> -- Configuring incomplete, errors occurred!
>
>
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