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

Steve Fiedler fiedler at umich.edu
Mon Jan 26 17:15:14 CET 2009 

Hi,

This issue is resolved.  Using code compiled from the CVS source: 
VERSION 4.0.99_development_20090120, grompp successively ran to 
completion for this system.
Thank you Berk.

 -Steve

Berk Hess wrote:
> Hi,
>
> I found many bugs in the cylinder pulling code.
> I fixed them all for the upcoming 4.0.4 release.
> I now tested and checked everything properly and it should really be 
> correct.
> If you want to use 4.0 now, check out the 4.0 release branch from cvs.
>
> Berk
>
> ------------------------------------------------------------------------
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Segmentation fault preprocessing with 
> pull_geometry = cylinder
> Date: Fri, 23 Jan 2009 10:37:17 +0100
>
> 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/
> > >
> > > * Previous message: [gmx-users] Segmentation fault preprocessing
> > > with pull_geometry = cylinder
> > > <http://www.gromacs.org/pipermail/gmx-users/2009-January/039119.html>
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> <http://www.gromacs.org/pipermail/gmx-users/2009-January/date.html#39126>
> > > [ thread ]
> > > 
> <http://www.gromacs.org/pipermail/gmx-users/2009-January/thread.html#39126>
> > > [ subject ]
> > > 
> <http://www.gromacs.org/pipermail/gmx-users/2009-January/subject.html#39126>
> > > [ author ]
> > > 
> <http://www.gromacs.org/pipermail/gmx-users/2009-January/author.html#39126>
> > >
> > >
> > > 
> ------------------------------------------------------------------------
> > > 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 
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> >
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