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Hi,<br><br>Is this the only output you got?<br>There is no error message at all?<br><br>If there was no error message and you get the error quickly<br>(i.e. not after hours of simulations),<br>please file a bugzilla entry, give the exact command line<br>of mpirun and mdrun and attach your tpr file.<br><br>Berk<br><br>> Date: Fri, 5 Dec 2008 14:33:30 -0500<br>> From: map110+@pitt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] distance restraints and domain decomposition<br>> <br>> Hi All,<br>> <br>> I am trying to run a simulation on a 13 residue peptide fragment with<br>> distance restraints in parallel and I'm getting a fatal error when I try<br>> to implement mdrun. Here is my nohup.out file:<br>> <br>> :-) G R O M A C S (-:<br>> <br>> Giving Russians Opium May Alter Current Situation<br>> <br>> :-) VERSION 4.0 (-:<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>> :-) mdrunmpi (-:<br>> <br>> Option Filename Type Description<br>> ------------------------------------------------------------<br>> -s md.tpr Input Run input file: tpr tpb tpa<br>> -o md.trr Output Full precision trajectory: trr trj cpt<br>> -x md.xtc Output, Opt! Compressed trajectory (portable xdr format)<br>> -cpi state.cpt Input, Opt. Checkpoint file<br>> -cpo state.cpt Output, Opt. Checkpoint file<br>> -c md.gro Output Structure file: gro g96 pdb<br>> -e md.edr Output Energy file: edr ene<br>> -g md.log Output Log file<br>> -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file<br>> -field field.xvg Output, Opt. xvgr/xmgr file<br>> -table table.xvg Input, Opt. xvgr/xmgr file<br>> -tablep tablep.xvg Input, Opt. xvgr/xmgr file<br>> -tableb table.xvg Input, Opt. xvgr/xmgr file<br>> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<br>> -tpi tpi.xvg Output, Opt. xvgr/xmgr file<br>> -tpid tpidist.xvg Output, Opt. xvgr/xmgr file<br>> -ei sam.edi Input, Opt. ED sampling input<br>> -eo sam.edo Output, Opt. ED sampling output<br>> -j wham.gct Input, Opt. General coupling stuff<br>> -jo bam.gct Output, Opt. General coupling stuff<br>> -ffout gct.xvg Output, Opt. xvgr/xmgr file<br>> -devout deviatie.xvg Output, Opt. xvgr/xmgr file<br>> -runav runaver.xvg Output, Opt. xvgr/xmgr file<br>> -px pullx.xvg Output, Opt. xvgr/xmgr file<br>> -pf pullf.xvg Output, Opt. xvgr/xmgr file<br>> -mtx nm.mtx Output, Opt. Hessian matrix<br>> -dn dipole.ndx Output, Opt. Index file<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>> -deffnm string Set the default filename for all file options<br>> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br>> xvg files for the xmgrace program<br>> -[no]pd bool no Use particle decompostion<br>> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize<br>> -npme int -1 Number of separate nodes to be used for PME, -1<br>> is guess<br>> -ddorder enum interleave DD node order: interleave, pp_pme or<br>> cartesian<br>> -[no]ddcheck bool yes Check for all bonded interactions with DD<br>> -rdd real 0 The maximum distance for bonded interactions with<br>> DD (nm), 0 is determine from initial coordinates<br>> -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate<br>> -dlb enum auto Dynamic load balancing (with DD): auto, no or yes<br>> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size<br>> -[no]sum bool yes Sum the energies at every step<br>> -[no]v bool no Be loud and noisy<br>> -[no]compact bool yes Write a compact log file<br>> -[no]seppot bool no Write separate V and dVdl terms for each<br>> interaction type and node to the log file(s)<br>> -pforce real -1 Print all forces larger than this (kJ/mol nm)<br>> -[no]reprod bool no Try to avoid optimizations that affect binary<br>> reproducibility<br>> -cpt real 15 Checkpoint interval (minutes)<br>> -[no]append bool no Append to previous output files when restarting<br>> from checkpoint<br>> -maxh real -1 Terminate after 0.99 times this time (hours)<br>> -multi int 0 Do multiple simulations in parallel<br>> -replex int 0 Attempt replica exchange every # steps<br>> -reseed int -1 Seed for replica exchange, -1 is generate a seed<br>> -[no]glas bool no Do glass simulation with special long range<br>> corrections<br>> -[no]ionize bool no Do a simulation including the effect of an X-Ray<br>> bombardment on your system<br>> <br>> <br>> Back Off! I just backed up md.log to ./#md.log.1#<br>> Reading file md.tpr, VERSION 4.0 (single precision)<br>> <br>> NOTE: atoms involved in distance restraints should be within the longest<br>> cut-off distance, if this is not the case mdrun generates a fatal error,<br>> in that case use particle decomposition (mdrun option -pd)<br>> <br>> <br>> WARNING: Can not write distance restraint data to energy file with domain<br>> decomposition<br>> rank 0 in job 55 chong06.chem.pitt.edu_35438 caused collective abort of<br>> all ranks<br>> exit status of rank 0: killed by signal 9<br>> <br>> <br>> <br>> All my restraints are within the 1.0 cutoff so I'm not sure why that note<br>> is showing up and I don't know what to do about this issue with the domain<br>> decomposition. I checked the mailing lists and noticed that there have<br>> been glitches with distance restraints and domain decomposition in the<br>> past and I was wondering if anyone has experienced similar problems. I'm<br>> attaching my mdp file with the cut offs and my topology file with the<br>> restraints.<br>> <br>> Any guidance would be greatly appreciated.<br>> <br>> Thanks a lot in advance!<br>> <br>> Maria<br>> <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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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