[gmx-users] mdrun on multiple nodes
Husen R
hus3nr at gmail.com
Wed Apr 20 13:33:13 CEST 2016
Hi Mark,
I'm wondering why in this link
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
'gmx' is used to run mdrun on more than one node instead of 'gmx_mpi' ?
Regards,
Husen
On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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> >
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