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.