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uchicago-bio / 2015-Autumn-Forum

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mpiblast single node single thread #55

Closed bdallen-uchicago closed 9 years ago

bdallen-uchicago commented 9 years ago

I get the following error when trying to run mpiblast 1x1:

Sorry, mpiBLAST must be run on 3 or more nodes

I tried running mpiblast directly, without mpirun, with same result. Should we be using blastp directly instead?

tabinks commented 9 years ago

Remember that mpiblast needs at least three nodes for super master, master and worker. For speedup measurement you should be using just blastp. This would give the base serial runtime.

If you used 3 nodes (i.e. 1 worker) the runtime should be similar, but there would be quite a bit of overhead from the master and super master nodes.