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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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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