GROMACS version: 2020.04
GROMACS modification: Yes/No
Here post your question
i am trying to do MDS for the protein only.
When i tried at 2021 version there is no error exist but i’m downgrade GROMACS version for GPU utilization and stability. so this time i run the command with gmx mdrun -v deffnm em or gmx mdrun -v deffnm -nb gpu and I am getting error like this
:-) GROMACS - gmx mdrun, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2019, 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 2020.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/user/Desktop/kyoungpyo/gromacs_data
Command line:
gmx mdrun -v -deffnm em -nb gpu
Reading file em.tpr, VERSION 2020.4 (single precision)
Program: gmx mdrun, version 2020.4
Source file: src/gromacs/domdec/domdec_setup.cpp (line 789)
MPI rank: 6 (out of 14)
Fatal error:
The number of ranks selected for particle-particle work (14) contains a large
prime factor 7. In most cases this will lead to bad performance. Choose a
number with smaller prime factors or set the decomposition (option -dd)
manually.
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
Please help me to fix the error.
Thanks in advance.