[Bioclusters] mpiblast on the smallest possible cluster

Lucas Carey bioclusters@bioinformatics.org
Wed, 28 Jan 2004 09:54:26 -0500

You should be fine using -np 3 instead of -np2. MPICH will start up the third process on the master. Also, try the cvs version if you have any troubles, as it contains a lot of bugfixes. You can get a nightly tarball from:

On Fri, Jan 23, 2004 at 05:34:58PM -0300, Fernan Aguero wrote:
> Hi!
> I'm trying mpiblast for the first time, and I'm testing it
> in a small (hmm, indeed very small) cluster. Actually, you
> wouldn't call it a cluster :)
> I have two machines. A master node, and a slave node. I have
> installed mpich-1.2.5 and mpiblast-1.2.0 on both. 
> All the tests I've performed (from reading the docs) pass.
> However, all the jobs run on the slave. The master just sits
> down quietly waiting for the slave to finish with one
> segment, before feeding the next. I suppose that this
> is the desired behaviour when you have a big cluster --
> you'll want to use the master node for managing the nodes,
> and not run any job.
> But what about small clusters of workstations? I would want
> the jobs to be run also by the master host. Is this
> impossible to do with the current state of the tools? I
> imagine that for a small number of nodes, and if the master
> is not managing anything else (sge or other mpi jobs), it
> should be possible to run blast jobs on the master without
> affecting its ability to manage the slaves. Am i right here?
> Thanks in advance for any tip/suggestion,
> Fernan
> -- 
> F e r n a n   A g u e r o
> http://genoma.unsam.edu.ar/~fernan
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