[gmx-users] Problem with the mdrun_openmpi on cluster

Smith, Micholas D. smithmd at ornl.gov
Mon Mar 14 17:22:51 CET 2016

What is your box size (x, y, z)? 

What happens if you use half that number of nodes? 

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of James Starlight <jmsstarlight at gmail.com>
Sent: Monday, March 14, 2016 12:19 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Problem with the mdrun_openmpi on cluster


I am trying to submit job on 64 nodes on mu local cluster using below
combination of software

DO="mpiexec -np 64"

$DO $PROG -deffnm sim

obtaining error

Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 64 nodes that is compatible with
the given box and a minimum cell size of 2.6255 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings

Could someone provide me trivial sollution/


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