<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
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@umich.edu<br>> To: gmx-users@gromacs.org<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@gromacs.org<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@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
</html>