[gmx-users] mdrun on multiple nodes
Mark Abraham
mark.j.abraham at gmail.com
Wed Apr 20 13:42:54 CEST 2016
Hi,
Well spotted. These should all be along the lines of
mpirun -np 2 gmx_mpi mdrun
or
mpirun -np 2 mdrun_mpi
if the admins have done an mdrun-only installation.
I'll fix that for future versions
Mark
On Wed, 20 Apr 2016 13:34 Husen R <hus3nr at gmail.com> wrote:
> 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
> > > --
> > > Gromacs Users mailing list
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