[gmx-users] Simulation in clusters -reg

Meagha ramana kumar meaghar at gmail.com
Fri Sep 29 06:24:41 CEST 2017

Hi gmx-users,

I was trying to run my simulation in core cluster in my institute. It is
showing the following error. But it works completely fine in my
personal laptop.

*the cluster error:-*

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

*the gromacs error:-*

NOTE: Turning on dynamic load balancing

A list of missing interactions:
               LJ-14 of    479 missing      1

Molecule type 'Macromolecule'
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms  146  196           global   146   196

Program gmx mdrun, VERSION 5.1.2
Source code file:
/root/gromacs-5.1.2/src/gromacs/domdec/domdec_topology.cpp, line: 435

Fatal error:
1 of the 2886 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.18407 nm) or the two-body cut-off distance (2 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

thank you

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