[gmx-users] mdrun on multiple nodes

Husen R hus3nr at gmail.com
Wed Apr 20 11:55:02 CEST 2016


Hi Mark,

I have configured gromacs with mpi support (using -DGMX_MPI=on):

tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Currently, I tried to use gmx_mpi (as you said) instead of gmx and it works !
Using htop command, I can see that Each node has 8 processes running
"gmx_mpi mdrun -cpt 15 -deffnm md_0_1".
I can not wait to see the results.
Thank a lot.

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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