[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder
gmx3 at hotmail.com
Thu Jan 22 10:10:32 CET 2009
It seems that I have only tested the cylinder option after the very first implementation
of the domain decomposition.
There are two obvious bugs:
On line 967 of src/mdlib/pull.c ind_loc should be snew'ed instead of ind.
On line 170 of src/mdlib/pullutil.c the loop should go to 1+pull->ngrp, not 1+pull->ngrp+1.
With those changes it runs for me.
But please check that your results are correct, I have not properly tested the cylinder option.
> Date: Wed, 21 Jan 2009 15:50:06 -0500
> From: fiedler at umich.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder
> Dear all,
> On transitioning from Gromacs version 3.3.3 to 4.0.3, I have encountered
> a segmentation fault (output below) preprocessing a constraint force
> calculation, while using the pull code with the "pull_geometry =
> cylinder" option in the mdp file. This problem appears is reproducible
> on 32 and 64 bit architecture systems, and is present using both single
> and double precision versions of the grompp executable. Alternative
> pull options (constraint, umbrella, and constant_force) also generated
> this error. This calculation can be successfully run using Gromacs
> version 3.3.3 with the below ppa file options.
> Suggestions would be appreciated.
> Thank you,
> Steve Fiedler
> Gromacs 4.0.3 mdp pull options:
> pull = constraint
> pull_geometry = cylinder
> pull_r1 = 1
> pull_r0 = 1.5
> pull_dim = N N Y
> pull_vec1 = 0 0 1
> pull_group1 = Buk
> pull_group0 = Ref
> pull_init1 = .4
> Gromacs 3.3.3 ppa file:
> runtype = constraint
> reftype = dynamic
> r = 1.
> rc = 1.5
> pull_dim = N N Y
> constraint_direction = 0 0 1
> group_1 = BUK
> reference_group = Ref
> constraint_distance1 = 0.400
> Preprocessing output for Gromacs 4.0.3 calculation:
> bash-3.2$ grompp_d -n index.ndx
> :-) G R O M A C S (-:
> Grunge ROck MAChoS
> :-) VERSION 4.0.3 (-:
> 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.
> :-) grompp_d (double precision) (-:
> Option Filename Type Description
> -f grompp.mdp Input, Opt. grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt! Index file
> -p topol.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o topol.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
> Option Type Value Description
> -[no]h bool no Print help info and quit
> -nice int 0 Set the nicelevel
> -[no]v bool yes Be loud and noisy
> -time real -1 Take frame at or first after this time.
> -[no]rmvsbds bool yes Remove constant bonded interactions with
> -maxwarn int 0 Number of allowed warnings during input
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> Ignoring obsolete mdp entry 'title'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> checking input for internal consistency...
> processing topology...
> Generated 224 of the 378 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.125
> Generated 377 of the 378 1-4 parameter combinations
> Excluding 1 bonded neighbours molecule type 'ADMP'
> Excluding 1 bonded neighbours molecule type 'ACHO'
> Excluding 1 bonded neighbours molecule type 'AWAT'
> Excluding 3 bonded neighbours molecule type 'BUKY'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Making dummy/rest group for T-Coupling containing 6848 elements
> Pull group 0 'Ref' has 2266 atoms
> Pull group 1 'Buk' has 60 atoms
> Making dummy/rest group for Acceleration containing 6848 elements
> Making dummy/rest group for Freeze containing 6848 elements
> Making dummy/rest group for Energy Mon. containing 6848 elements
> Making dummy/rest group for VCM containing 6848 elements
> Number of degrees of freedom in T-Coupling group rest is 13752.00
> Making dummy/rest group for User1 containing 6848 elements
> Making dummy/rest group for User2 containing 6848 elements
> Making dummy/rest group for XTC containing 6848 elements
> Making dummy/rest group for Or. Res. Fit containing 6848 elements
> Making dummy/rest group for QMMM containing 6848 elements
> T-Coupling has 1 element(s): rest
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120
> Segmentation fault
> Steve Fiedler, Ph.D.
> Research Fellow
> Department of Mechanical Engineering
> The University of Michigan
> 2024 G.G. Brown
> 2350 Hayward St.
> Ann Arbor, MI 48109-2125
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