[gmx-users] Gromacs using openmpi [mdrun_mpi]

Dharmendra Verma dkverma.vit at gmail.com
Mon Apr 30 19:09:25 CEST 2012

*                                                          How to use
gromacs using openmpi*

Hello all, i am an undergraduate student here at VIT University
Vellore,INDIA, I m trying to run mdrun on a cluster using openmpi, so for
that i have used Ubuntu 11.04 server edition , and made a cluster of *one
master and two slaves machine*, and configured the ssh between master and
slave so now i can ssh in to slave from master without password (one way),
then i had installed *openmpi-bin, openmpi-doc, openmpi-dev and
gromacs-openmpi (VERSION - 4.5.4*)on all three( 1M & 2S) machines. For
making cluster i followed this tutorial -


After setting up that cluster i had transfered my input file to all 3
computers in their home directories.
Each pc configuration-
3 GB ram and Intel core2duo 2.9 GHz processor

hostfile-{2 slave ips}

Now problem start, My aim is to combine all power and decrease the run
time.I had tested following 3 commands on master computer.
1- mdrun_mpi --hostfile hostfile -np 4 -s input.tpr
         This command starts mdrun on all the nodes and they are generating
same output file in their home directories. so no use.

2- mpirun --hostfile hostfile -np 4 mdrun_mpi -s input.tpr
                        This command does nothing just shows the hostname
of 2 slave computers and remain silent.

3- mpirun -np 4 mdrun_mpi --hostfile hostfile -s input.tpr
                         This command runs mdrun only on master computer, i
doesn't even detect other nodes.

Please someone help me, what mistake i am doing, please suggest.

Dharmendra Kumar Verma
B-Tech Bioinformatics
VIT University, TN (India)
Web- http://www.dkvermalinux.in
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