[gmx-users] Mdrun on 2 nodes

Tivadar Orban t.orban at csuohio.edu
Tue Sep 3 20:49:11 CEST 2002

I want to run a simulation on two nodes but I have the error a I'll describe
it bellow: 

grompp was ran with the option -np 2

after grompp I ran mdrun

>mpirun -np 2 mdrun -nice 4 -s 1FV4_em -o 1FV4_em -c 1FV4_b4pr -np 2

NODEID=0 argc=14
NODEID=1 argc=14
                         :-)  G  R  O  M  A  C  S  (-:

             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

                            :-)  VERSION 3.1.4  (-:

       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         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.

 :-)  /usr/apps/chemistry/gromacs-3.1.4/mips-sgi-irix6.5/r10000/bin/mdrun
mdrun  (-:

Option     Filename  Type          Description
  -s    1FV4_em.tpr  Input         Generic run input: tpr tpb tpa
  -o    1FV4_em.trr  Output        Full precision trajectory: trr trj
  -x       traj.xtc  Output, Opt.  Compressed trajectory (portable xdr
  -c  1FV4_b4pr.gro  Output        Generic structure: gro g96 pdb
  -e       ener.edr  Output        Generic energy: edr ene
  -g         md.log  Output        Log file
-dgdl      dgdl.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  Input, 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

      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      4  Set the nicelevel
     -deffnm string         Set the default filename for all file options
         -np    int      2  Number of nodes, must be the same as used for
      -[no]v   bool    yes  Be loud and noisy
-[no]compact   bool    yes  Write a compact log file
  -[no]multi   bool     no  Do multiple simulations in parallel (only with
                            > 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 md0.log to ./#md0.log.4#

Back Off! I just backed up md1.log to ./#md1.log.4#
Getting Loaded...
Reading file 1FV4_em.tpr, VERSION 3.1.4 (single precision)
Reading file 1FV4_em.tpr, VERSION 3.1.4 (single precision)
Loaded with Money

Back Off! I just backed up ener.edr to ./#ener.edr.4#
Steepest Descents:
   Tolerance         =  1.00000e+03
   Number of steps   =          100
MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
MPI: aborting job

Can someone tell me what is the problem here?

Tivadar, Orban

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