[gmx-users] mdrun on multiple nodes

Szilárd Páll pall.szilard at gmail.com
Thu Apr 21 02:52:23 CEST 2016 

On Thu, Apr 21, 2016 at 2:20 AM, Husen R <hus3nr at gmail.com> wrote:
> Hi,
>
>
> Thank a lot for the information.
>
> in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not
> recognized as a gromacs command.

Just as expected; the binary is suffixed, not the comand and you built
a full gmx build which is not too useful with my BTW:
http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#building-only-mdrun

>
> Regards,
>
>
> Husen
>
>
> On Wed, Apr 20, 2016 at 6:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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
>> > > > --
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