[gmx-users] Version error running mdrun

Jordi Camps jcamps at lsi.upc.edu
Sat Mar 19 18:46:31 CET 2005


I just compiled FFTW and GROMACS from scratch on a system like:
	-PPC970 (G5)
	-GM (Myrinet)
	-IBM compilers

Now I'm trying to run gmxdemo and the benchmarcks but keep obtaining a very
strange complaint bout the version of the files used. Mdrun say that the
*.tpr files are of a version of gromacs older than 2.0, but I just generated
this files with my own compiled version of grompp V.3.2.1. And if I execute
a "strings topol.tpr | head -1" I get the next string: "VERSION 3.2.1". It
seems that the file has the correct extension.

I compiled mdrun with MPI support, so I must execute mdrun with mpirun.

The log of the mdrun (using only one processor) is this:

NNODES=1, MYRANK=0, HOSTNAME=s41c3b12-gigabit1.mn
                         :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                            :-)  VERSION 3.2.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, 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.

              :-)  /home/bsc23089/installed/gromacs/bin/mdrun  (-:

Option     Filename  Type         Description
  -s      topol.tpr  Input        Generic run input: tpr tpb tpa xml
  -o       traj.trr  Output       Full precision trajectory: trr trj
  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr
  -c    confout.gro  Output       Generic structure: gro g96 pdb xml
  -e       ener.edr  Output       Generic energy: 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
-rerun    rerun.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96
 -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
 -pi       pull.ppa  Input, Opt.  Pull parameters
 -po    pullout.ppa  Output, Opt. Pull parameters
 -pd       pull.pdo  Output, Opt. Pull data output
 -pn       pull.ndx  Input, Opt.  Index 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
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
     -deffnm string         Set the default filename for all file options
         -np    int      1  Number of nodes, must be the same as used for
         -nt    int      1  Number of threads to start on each node
      -[no]v   bool     no  Be loud and noisy
-[no]compact   bool    yes  Write a compact log file
  -[no]multi   bool     no  Do multiple simulations in parallel (only with
                            -np > 1)
   -[no]glas   bool     no  Do glass simulation with special long range
 -[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#
Fatal error: Can not read file topol.tpr,
             this file is from a Gromacs version which is older than 2.0
             Make a new one with grompp or use a gro or pdb file, if
[0] MPI Abort by user Aborting program !
[0] Aborting program!

Thanks for your help and advises :-)

Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
c/. Jordi Girona 1-3              
Modul C6-E201                     Tel.  : 934 011 650
E-08034 Barcelona                 Fax   : 934 017 014
Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu

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