[gmx-users] mdrun on multiple nodes

[Mark Abraham]

Hi,

Probably you haven't built gromacs with MPI support, else the name of the
binary would be gmx_mpi. You can get that confirmed if you look further
down the output .log files.

Mark

On Wed, 20 Apr 2016 10:09 Husen R <hus3nr at gmail.com> wrote:

> 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
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