<div class="im" style><b><br></b><br>Hello gmx-users 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 <b>one master and two slaves machine</b>, 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 <b>openmpi-bin, openmpi-doc, openmpi-dev and gromacs-openmpi (VERSION - 4.5.4</b>)on all three( 1M & 2S) machines. For making cluster i followed this tutorial - <br>
<br><a href="http://randomusefulnotes.blogspot.in/2010/12/setting-up-mpi-cluster-on-ubuntu.html" target="_blank" style="color:rgb(17,85,204)">http://randomusefulnotes.blogspot.in/2010/12/setting-up-mpi-cluster-on-ubuntu.html</a><br>
<br>After setting up that cluster i had transfered my input file to all 3 computers in their home directories. <br>Each pc configuration-<br>3 GB ram and Intel core2duo 2.9 GHz processor<br><br>hostfile-{2 slave ips}<br>192.168.42.130<br>
192.168.42.131<br><br></div><span style>Now problem start, </span><span style>My aim is to combine all power and decrease the run time.I</span><span style> had tested following 3 commands on master computer.</span><div><font color="#222222" face="arial, sans-serif"><br>
</font><div class="im HOEnZb adL" style><br>1- mdrun_mpi --hostfile hostfile -np 4 -s input.tpr <br> This command starts mdrun on all the nodes and they are generating same output file in their home directories. so no use.<br>
<br><br>2- mpirun --hostfile hostfile -np 4 mdrun_mpi -s input.tpr <br> This command does nothing just shows the hostname of 2 slave computers and remain silent.<br><br><br>3- mpirun -np 4 mdrun_mpi --hostfile hostfile -s input.tpr<br>
This command runs mdrun only on master computer, i doesn't even detect other nodes.<br><br>Please someone help me, what mistake i am doing??? </div><div class="im HOEnZb adL" style>Please suggest.</div>
<div>Sorry for posting this problem twice.</div>-- <br><font style="font-family:georgia,serif" size="4">Dharmendra Kumar Verma</font><br><font style="font-family:georgia,serif" size="2">B-Tech Bioinformatics<br>VIT University, TN (India)<br>
Web- <a href="http://www.dkvermalinux.in" target="_blank">http://www.dkvermalinux.in</a></font><br><br>
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