[gmx-users] distance restraints and domain decomposition

Berk Hess gmx3 at hotmail.com
Mon Dec 8 16:12:00 CET 2008


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.


> 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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