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. Regards, Husen On Wed, Apr 20, 2016 at 6:42 PM, Mark Abraham <mark.j.abra...@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 <hus...@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.abra...@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 <hus...@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=hus...@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 > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? 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