[gmx-users] distance restraints and domain decomposition
Berk Hess
gmx3 at hotmail.com
Mon Dec 8 16:12:00 CET 2008
Hi,
Is this the only output you got?
There is no error message at all?
If there was no error message and you get the error quickly
(i.e. not after hours of simulations),
please file a bugzilla entry, give the exact command line
of mpirun and mdrun and attach your tpr file.
Berk
> Date: Fri, 5 Dec 2008 14:33:30 -0500
> From: map110+ at pitt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] distance restraints and domain decomposition
>
> Hi All,
>
> I am trying to run a simulation on a 13 residue peptide fragment with
> distance restraints in parallel and I'm getting a fatal error when I try
> to implement mdrun. Here is my nohup.out file:
>
> :-) G R O M A C S (-:
>
> Giving Russians Opium May Alter Current Situation
>
> :-) VERSION 4.0 (-:
>
>
> 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.
>
> :-) mdrunmpi (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s md.tpr Input Run input file: tpr tpb tpa
> -o md.trr Output Full precision trajectory: trr trj cpt
> -x md.xtc Output, Opt! Compressed trajectory (portable xdr format)
> -cpi state.cpt Input, Opt. Checkpoint file
> -cpo state.cpt Output, Opt. Checkpoint file
> -c md.gro Output Structure file: gro g96 pdb
> -e md.edr Output Energy file: edr ene
> -g md.log Output Log file
> -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr file
> -table table.xvg Input, Opt. xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> -tableb table.xvg Input, Opt. xvgr/xmgr file
> -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
> -ei sam.edi Input, Opt. ED sampling input
> -eo sam.edo Output, Opt. ED sampling output
> -j wham.gct Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt. General coupling stuff
> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -px pullx.xvg Output, Opt. xvgr/xmgr file
> -pf pullf.xvg Output, Opt. xvgr/xmgr file
> -mtx nm.mtx Output, Opt. Hessian matrix
> -dn dipole.ndx Output, Opt. Index file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 0 Set the nicelevel
> -deffnm string Set the default filename for all file options
> -[no]xvgr bool yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -[no]pd bool no Use particle decompostion
> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
> -npme int -1 Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum interleave DD node order: interleave, pp_pme or
> cartesian
> -[no]ddcheck bool yes Check for all bonded interactions with DD
> -rdd real 0 The maximum distance for bonded interactions with
> DD (nm), 0 is determine from initial coordinates
> -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
> -dlb enum auto Dynamic load balancing (with DD): auto, no or yes
> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> -[no]sum bool yes Sum the energies at every step
> -[no]v bool no Be loud and noisy
> -[no]compact bool yes Write a compact log file
> -[no]seppot bool no Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -pforce real -1 Print all forces larger than this (kJ/mol nm)
> -[no]reprod bool no Try to avoid optimizations that affect binary
> reproducibility
> -cpt real 15 Checkpoint interval (minutes)
> -[no]append bool no Append to previous output files when restarting
> from checkpoint
> -maxh real -1 Terminate after 0.99 times this time (hours)
> -multi int 0 Do multiple simulations in parallel
> -replex int 0 Attempt replica exchange every # steps
> -reseed int -1 Seed for replica exchange, -1 is generate a seed
> -[no]glas bool no Do glass simulation with special long range
> corrections
> -[no]ionize bool no Do a simulation including the effect of an X-Ray
> bombardment on your system
>
>
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file md.tpr, VERSION 4.0 (single precision)
>
> NOTE: atoms involved in distance restraints should be within the longest
> cut-off distance, if this is not the case mdrun generates a fatal error,
> in that case use particle decomposition (mdrun option -pd)
>
>
> WARNING: Can not write distance restraint data to energy file with domain
> decomposition
> rank 0 in job 55 chong06.chem.pitt.edu_35438 caused collective abort of
> all ranks
> exit status of rank 0: killed by signal 9
>
>
>
> All my restraints are within the 1.0 cutoff so I'm not sure why that note
> is showing up and I don't know what to do about this issue with the domain
> decomposition. I checked the mailing lists and noticed that there have
> been glitches with distance restraints and domain decomposition in the
> past and I was wondering if anyone has experienced similar problems. I'm
> attaching my mdp file with the cut offs and my topology file with the
> restraints.
>
> Any guidance would be greatly appreciated.
>
> Thanks a lot in advance!
>
> Maria
>
>
>
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