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Hi,<br><br>For my test system it works with those modfications.<br><br>Can you file a bugzilla entry and attach all the files necessary<br>for running grompp?<br><br>Berk<br><br>> Date: Thu, 22 Jan 2009 21:48:41 -0500<br>> From: fiedler@umich.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Segmentation fault preprocessing with pull_geometry =        cylinder<br>> <br>> Hi,<br>> <br>> I modified the changes to the source code as suggested by Dr. Hess and <br>> recompiled Gromacs. The grompp output appears to have advanced by one <br>> line (output below), however the process still terminates with a <br>> segmentation fault. Additional suggestions or ideas for diagnostics <br>> would be appreciated.<br>> <br>> Thank you,<br>> <br>> Steve Fiedler<br>> <br>> Bottom 3 lines of grompp output:<br>> Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120<br>> Pull group natoms pbc atom distance at start reference at t=0<br>> Segmentation fault<br>> <br>> <br>> <br>> > *Berk Hess* gmx3 at hotmail.com <br>> > <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><br>> > /Thu Jan 22 10:10:32 CET 2009/<br>> ><br>> > * Previous message: [gmx-users] Segmentation fault preprocessing<br>> > with pull_geometry = cylinder<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/039119.html><br>> > * Next message: [gmx-users] Abu added you as a friend on<br>> > Reunion.com!<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/039121.html><br>> > * *Messages sorted by:* [ date ]<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/date.html#39126><br>> > [ thread ]<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/thread.html#39126><br>> > [ subject ]<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/subject.html#39126><br>> > [ author ]<br>> > <http://www.gromacs.org/pipermail/gmx-users/2009-January/author.html#39126><br>> ><br>> ><br>> > ------------------------------------------------------------------------<br>> > Hi,<br>> ><br>> > It seems that I have only tested the cylinder option after the very first implementation<br>> > of the domain decomposition.<br>> > There are two obvious bugs:<br>> > On line 967 of src/mdlib/pull.c ind_loc should be snew'ed instead of ind.<br>> > On line 170 of src/mdlib/pullutil.c the loop should go to 1+pull->ngrp, not 1+pull->ngrp+1.<br>> ><br>> > With those changes it runs for me.<br>> > But please check that your results are correct, I have not properly tested the cylinder option.<br>> ><br>> > Berk<br>> ><br>> > >/ Date: Wed, 21 Jan 2009 15:50:06 -0500<br>> > />/ From: fiedler at umich.edu <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> > />/ To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> > />/ Subject: [gmx-users] Segmentation fault preprocessing with pull_geometry =        cylinder<br>> > />/ <br>> > />/ Dear all,<br>> > />/ <br>> > />/ On transitioning from Gromacs version 3.3.3 to 4.0.3, I have encountered <br>> > />/ a segmentation fault (output below) preprocessing a constraint force <br>> > />/ calculation, while using the pull code with the "pull_geometry = <br>> > />/ cylinder" option in the mdp file. This problem appears is reproducible <br>> > />/ on 32 and 64 bit architecture systems, and is present using both single <br>> > />/ and double precision versions of the grompp executable. Alternative <br>> > />/ pull options (constraint, umbrella, and constant_force) also generated <br>> > />/ this error. This calculation can be successfully run using Gromacs <br>> > />/ version 3.3.3 with the below ppa file options.<br>> > />/ <br>> > />/ Suggestions would be appreciated. <br>> > />/ <br>> > />/ Thank you,<br>> > />/ <br>> > />/ Steve Fiedler<br>> > />/ <br>> > />/ <br>> > />/ Gromacs 4.0.3 mdp pull options:<br>> > />/ pull = constraint<br>> > />/ pull_geometry = cylinder<br>> > />/ pull_r1 = 1<br>> > />/ pull_r0 = 1.5<br>> > />/ pull_dim = N N Y<br>> > />/ pull_vec1 = 0 0 1<br>> > />/ pull_group1 = Buk<br>> > />/ pull_group0 = Ref<br>> > />/ pull_init1 = .4<br>> > />/ <br>> > />/ Gromacs 3.3.3 ppa file:<br>> > />/ runtype = constraint<br>> > />/ reftype = dynamic<br>> > />/ r = 1.<br>> > />/ rc = 1.5<br>> > />/ pull_dim = N N Y<br>> > />/ constraint_direction = 0 0 1<br>> > />/ group_1 = BUK<br>> > />/ reference_group = Ref<br>> > />/ constraint_distance1 = 0.400<br>> > />/ <br>> > />/ <br>> > />/ Preprocessing output for Gromacs 4.0.3 calculation:<br>> > />/ bash-3.2$ grompp_d -n index.ndx <br>> > />/ :-) G R O M A C S (-:<br>> > />/ <br>> > />/ Grunge ROck MAChoS<br>> > />/ <br>> > />/ :-) VERSION 4.0.3 (-:<br>> > />/ <br>> > />/ <br>> > />/ Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>> > />/ Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>> > />/ Copyright (c) 2001-2008, The GROMACS development team,<br>> > />/ check out http://www.gromacs.org for more information.<br>> > />/ <br>> > />/ This program is free software; you can redistribute it and/or<br>> > />/ modify it under the terms of the GNU General Public License<br>> > />/ as published by the Free Software Foundation; either version 2<br>> > />/ of the License, or (at your option) any later version.<br>> > />/ <br>> > />/ :-) grompp_d (double precision) (-:<br>> > />/ <br>> > />/ Option Filename Type Description<br>> > />/ ------------------------------------------------------------<br>> > />/ -f grompp.mdp Input, Opt. grompp input file with MD parameters<br>> > />/ -po mdout.mdp Output grompp input file with MD parameters<br>> > />/ -c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa<br>> > />/ -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>> > />/ -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>> > />/ -n index.ndx Input, Opt! Index file<br>> > />/ -p topol.top Input Topology file<br>> > />/ -pp processed.top Output, Opt. Topology file<br>> > />/ -o topol.tpr Output Run input file: tpr tpb tpa<br>> > />/ -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>> > />/ -e ener.edr Input, Opt. Energy file: edr ene<br>> > />/ <br>> > />/ Option Type Value Description<br>> > />/ ------------------------------------------------------<br>> > />/ -[no]h bool no Print help info and quit<br>> > />/ -nice int 0 Set the nicelevel<br>> > />/ -[no]v bool yes Be loud and noisy<br>> > />/ -time real -1 Take frame at or first after this time.<br>> > />/ -[no]rmvsbds bool yes Remove constant bonded interactions with <br>> > />/ virtual<br>> > />/ sites<br>> > />/ -maxwarn int 0 Number of allowed warnings during input <br>> > />/ processing<br>> > />/ -[no]zero bool no Set parameters for bonded interactions without<br>> > />/ defaults to zero instead of generating an error<br>> > />/ -[no]renum bool yes Renumber atomtypes and minimize number of<br>> > />/ atomtypes<br>> > />/ <br>> > />/ Ignoring obsolete mdp entry 'title'<br>> > />/ <br>> > />/ Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#<br>> > />/ checking input for internal consistency...<br>> > />/ processing topology...<br>> > />/ Generated 224 of the 378 non-bonded parameter combinations<br>> > />/ Generating 1-4 interactions: fudge = 0.125<br>> > />/ Generated 377 of the 378 1-4 parameter combinations<br>> > />/ Excluding 1 bonded neighbours molecule type 'ADMP'<br>> > />/ Excluding 1 bonded neighbours molecule type 'ACHO'<br>> > />/ Excluding 1 bonded neighbours molecule type 'AWAT'<br>> > />/ Excluding 3 bonded neighbours molecule type 'BUKY'<br>> > />/ processing coordinates...<br>> > />/ double-checking input for internal consistency...<br>> > />/ renumbering atomtypes...<br>> > />/ converting bonded parameters...<br>> > />/ initialising group options...<br>> > />/ processing index file...<br>> > />/ Making dummy/rest group for T-Coupling containing 6848 elements<br>> > />/ Pull group 0 'Ref' has 2266 atoms<br>> > />/ Pull group 1 'Buk' has 60 atoms<br>> > />/ Making dummy/rest group for Acceleration containing 6848 elements<br>> > />/ Making dummy/rest group for Freeze containing 6848 elements<br>> > />/ Making dummy/rest group for Energy Mon. containing 6848 elements<br>> > />/ Making dummy/rest group for VCM containing 6848 elements<br>> > />/ Number of degrees of freedom in T-Coupling group rest is 13752.00<br>> > />/ Making dummy/rest group for User1 containing 6848 elements<br>> > />/ Making dummy/rest group for User2 containing 6848 elements<br>> > />/ Making dummy/rest group for XTC containing 6848 elements<br>> > />/ Making dummy/rest group for Or. Res. Fit containing 6848 elements<br>> > />/ Making dummy/rest group for QMMM containing 6848 elements<br>> > />/ T-Coupling has 1 element(s): rest<br>> > />/ Energy Mon. has 1 element(s): rest<br>> > />/ Acceleration has 1 element(s): rest<br>> > />/ Freeze has 1 element(s): rest<br>> > />/ User1 has 1 element(s): rest<br>> > />/ User2 has 1 element(s): rest<br>> > />/ VCM has 1 element(s): rest<br>> > />/ XTC has 1 element(s): rest<br>> > />/ Or. Res. Fit has 1 element(s): rest<br>> > />/ QMMM has 1 element(s): rest<br>> > />/ Checking consistency between energy and charge groups...<br>> > />/ Calculating fourier grid dimensions for X Y Z<br>> > />/ Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120<br>> > />/ Segmentation fault<br>> > />/ <br>> > />/ <br>> > />/ <br>> > />/ <br>> > />/ -- <br>> > />/ Steve Fiedler, Ph.D.<br>> > />/ Research Fellow<br>> > />/ Department of Mechanical Engineering<br>> > />/ The University of Michigan<br>> > />/ 2024 G.G. Brown<br>> > />/ 2350 Hayward St.<br>> > />/ Ann Arbor, MI 48109-2125<br>> > />/ <br>> > />/ <br>> > />/ _______________________________________________<br>> > />/ gmx-users mailing list gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> > />/ http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > />/ Please search the archive at http://www.gromacs.org/search before posting!<br>> > />/ Please don't post (un)subscribe requests to the list. Use the <br>> > />/ www interface or send it to gmx-users-request at gromacs.org. <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> > />/ Can't post? 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