[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

Berk Hess gmx3 at hotmail.com
Thu Jan 22 10:10:32 CET 2009 

Hi,

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.

Berk

> 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 
> virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input 
> processing
> -[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
>                             atomtypes
>  
> 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
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
See all the ways you can stay connected to friends and family
http://www.microsoft.com/windows/windowslive/default.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090122/51e13adc/attachment.html>

More information about the gromacs.org_gmx-users mailing list