Thanks Glen and Kip for your instructions. We could troubleshoot the earlier troubles.While working with pvm we found contirb-pvm is installed in the frontend and no pvm was installed in the slave nodes. So we installed the normal pvm present in the distro and it is working fine. Now we are trying to run blast on the cluster. We could ran the normal blast without any hiccups. But the problem started with mpiblast. We have downloaded some of the example scripts from http://www.llnl.gov/computing/tutorials/mpi/samples/C/. Compiled the programs with "/usr/bin/mpicc", created the machines file (with only two nodes, compute-0-0, compute-0-1), started up ssh-agent and ran the sample program. That ran fine in all the compute nodes without any error. As we try to run the mpiBlast with the following command: [andrew at frontend-0 mpi_test_blast]$ /usr/local/mpich-vmi2/bin/mpirun -np 2 -machinefile ../machines /opt/BioBrew/NCBI/6.1.0/bin/mpiblast --config-file=/opt/BioBrew/NCBI/6.1.0/etc/mpiblast.conf -p blastp -d ../db/nr -i test.seq We get the error as bellow: Sorry, mpiBLAST must be run on 2 or more nodes. With Regards, Soumyadeep __________________________________ Do you Yahoo!? Yahoo! Search - Find what youre looking for faster http://search.yahoo.com