[BioBrew Users] Trouble running mpiBlast

Glen Otero gotero at linuxprophet.com
Wed Mar 10 20:10:25 EST 2004

Hmmm...I'm getting the same error. I'll need some time to look into 
this. Anyone else seen this problem, or running mpiBLAST properly with 
a different mpi (like lam)?


On Mar 9, 2004, at 11:16 PM, Soumyadeep nandi wrote:

> 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
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Glen Otero, Ph.D.
Linux Prophet

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