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

Berk Hess gmx3 at hotmail.com
Fri Jan 23 10:37:17 CET 2009


Hi,

For my test system it works with those modfications.

Can you file a bugzilla entry and attach all the files necessary
for running grompp?

Berk

> Date: Thu, 22 Jan 2009 21:48:41 -0500
> From: fiedler at umich.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Segmentation fault preprocessing with pull_geometry =	cylinder
> 
> Hi,
> 
> I modified the changes to the source code as suggested by Dr. Hess and 
> recompiled Gromacs.  The grompp output appears to have advanced by one 
> line (output below), however the process still terminates with a 
> segmentation fault.  Additional suggestions or ideas for diagnostics 
> would be appreciated.
> 
> Thank you,
> 
>     Steve Fiedler
> 
> Bottom 3 lines of grompp output:
> Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120
> Pull group  natoms  pbc atom  distance at start     reference at t=0
> Segmentation fault
> 
> 
> 
> > *Berk Hess* gmx3 at hotmail.com 
> > <mailto:gmx-users%40gromacs.org?Subject=%5Bgmx-users%5D%20Segmentation%20fault%20preprocessing%20with%20pull_geometry%0A%09%3D%09cylinder&In-Reply-To=49778A7E.9010804%40umich.edu>
> > /Thu Jan 22 10:10:32 CET 2009/
> >
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> >       with pull_geometry = cylinder
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> >
> >
> > ------------------------------------------------------------------------
> > 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 <http://www.gromacs.org/mailman/listinfo/gmx-users>
> > />/ To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
> > />/ 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>
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> >   
> 
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