[gmx-users] Re: equilibrium stage runs for too long
Justin Lemkul
jalemkul at vt.edu
Thu Aug 23 23:43:59 CEST 2012
On 8/23/12 5:10 PM, Clare wrote:
> Dear Vitaly,
>
> here's the log file of the nvt simulation, and it was killed due to
> exceeding the wall time. Hopefully it could still provide some useful
> information. Thank you so much indeed!
>
> :-) G R O M A C S (-:
>
> Good ROcking Metal Altar for Chronical Sinners
>
> :-) VERSION 4.5.5 (-:
>
> 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 Schulz,
> 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.
>
> :-) 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
> ++++ 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 = 50000
> init_step = 0
> ns_type = Grid
> nstlist = 5
> ndelta = 2
> nstcomm = 10
> comm_mode = Linear
> nstlog = 100
> nstxout = 100
> nstvout = 100
> nstfout = 0
> nstcalcenergy = 5
> nstenergy = 100
> nstxtcout = 0
> init_t = 0
> delta_t = 0.002
> xtcprec = 1000
> nkx = 50
> nky = 50
> nkz = 100
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = V-rescale
> nsttcouple = 5
> epc = No
> epctype = Isotropic
> nstpcouple = -1
> tau_p = 1
> ref_p (3x3):
> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress (3x3):
> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> 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 = 0.9
> rlistlong = 0.9
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 0.9
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 0.9
> 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 = 2.05016
> 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 = 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: 13166.4 4039.82 51459.8
> ref_t: 300 300 300
> tau_t: 0.1 0.1 0.1
> anneal: No No No
> ann_npoints: 0 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_flags[ 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 48 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: 0.574 nm, LJ-14, atoms 661 682
> multi-body bonded interactions: 0.574 nm, Proper Dih., atoms 661 682
> Minimum cell size due to bonded interactions: 0.631 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.771 nm
> Estimated maximum distance required for P-LINCS: 0.771 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.58
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 48 cells with a minimum initial size of 0.964 nm
> The maximum allowed number of cells is: X 8 Y 8 Z 16
> Domain decomposition grid 6 x 4 x 2, separate PME nodes 0
> PME domain decomposition: 6 x 8 x 1
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Using two step summing over 6 groups of on average 8.0 processes
>
> 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. Essmann, L. Perera, 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 --- -------- --------
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
> Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
> Long Range LJ corr.: <C6> 9.2537e-04
> System total charge: 0.000
> Generated table with 950 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 950 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 950 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 950 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 950 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 950 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 8577 molecules.
>
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
> Removing pbc first time
>
> Initializing Parallel LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess
> P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 116-122
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 7603
> There are inter charge-group constraints,
> will communicate selected coordinates each lincs iteration
> ++++ 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 --- -------- --------
>
>
> Linking all bonded interactions to atoms
> There are 19808 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1 Y 1 Z 1
> The initial domain decomposition cell size is: X 1.33 nm Y 2.00 nm Z 8.00 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 0.900 nm
> two-body bonded interactions (-rdd) 0.900 nm
> multi-body bonded interactions (-rdd) 0.900 nm
> atoms separated by up to 5 constraints (-rcon) 1.333 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Y 1 Z 1
> The minimum size for domain decomposition cells is 0.900 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.67 Y 0.45 Z 0.11
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 0.900 nm
> two-body bonded interactions (-rdd) 0.900 nm
> multi-body bonded interactions (-rdd) 0.900 nm
> atoms separated by up to 5 constraints (-rcon) 0.900 nm
>
>
> Making 3D domain decomposition grid 6 x 4 x 2, 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
>
> ++++ 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 --- -------- --------
>
>
The log file indicates the job never even really started. Either mdrun_mpi is
defective, your MPI implementation in general does not work, or there was some
other error at the system level that halted the job. There are no errors from
Gromacs here, so the source of the problem is external to Gromacs. Try getting
simple example MPI programs to work and discuss with your sysadmins.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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