[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder
Steve Fiedler
fiedler at umich.edu
Fri Jan 23 03:48:41 CET 2009
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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> ------------------------------------------------------------------------
> 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
> />/
> />/
> />/ _______________________________________________
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