[gmx-users] mdrun on multiple nodes

[Husen R]

Hi all,

I tried to run mdrun on more than one node using the command available in
this url
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
.
The following is my sbatch job :

###########################SBATCH################
#!/bin/bash
#SBATCH -J sim
#SBATCH -o md-%j.out
#SBATCH -A pro
#SBATCH -N 3
#SBATCH -n 24
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus3nr at gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx mdrun -cpt 15 -deffnm md_0_1

#########################SBATCH END################

I open the output file to see the result. It contains something repeatedly
as shown below:

#########################OUTPUT###################
......
......
......
                           *GROMACS is written by:*
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
Bjelkmar
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner

    Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
   Roland Schulz     Alexey Shvetsov     Michael Shirts  Executable:
/usr/local/gromacs/bin/gmx
   Alfons Sijbers
   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

                   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

                           * GROMACS is written by:*
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
Bjelkmar
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner

    Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers
   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -cpt 15 -deffnm md_0_1

......
......
......

########################OUTPUT END###################

Is it normal for output file to have such content?

in addition, as we can see from my sbatch script, I use 3 nodes and 24
processes. Using that configuration, I hope each node will have 8 processes
running "gmx mdrun -cpt 15 -deffnm md_0_1".
However, when I see running processes in each node using htop command, each
node has more than 60 processes running "gmx mdrun -cpt 15 -deffnm md_0_1".
why is this happened ? I need help.

Thank you in advance.


regards,


Husen