* * 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 *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 -
http://randomusefulnotes.blogspot.in/2010/12/setting-up-mpi-cluster-on-ubuntu.html 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} 192.168.42.130 192.168.42.131 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. Sorry for posting this problem twice. -- Dharmendra Kumar Verma B-Tech Bioinformatics VIT University, TN (India) Web- http://www.dkvermalinux.in
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