[Bioclusters] error while running mpiblast

James Cuff jcuff at broad.mit.edu
Wed Mar 2 00:02:23 EST 2005

On Wed, 2 Mar 2005, kalyani goli wrote:

> Iam running this on SGI multiprocessor(numa). So, everything is
> visible to all the processors. Thats why i gave the directory where
> ncbi is installed ,and gave it same for both shared and local.

...  gurgh?

mpiblast will (and I have seen it, with my own eyes) scale 'super linear'
on high latency, multiply interconnected servers.  Aaron did a really
sensible and good job to make this scale across nodes.

However, as you describe:

"Iam running this on SGI multiprocessor(numa)",

you are running on a single shared (well near unified, and SGI do this
very, very well) memory server with, as you said and appear to understand
shared storage...


What on earth are you going to gain from MPI?  Standard NCBI threads
should do for you just fine, or maybe I've been smoking the funny stuff.

If you _do_ happen to have multiple NUMA's in a cluster, (1) you are very
lucky and (2) you should the still listen to Joe's advice...  Local is
only local so far, try:


(or as Joe maybe put better)





James Cuff, D. Phil.
Group Leader, Applied Production Systems
Broad Institute of MIT and Harvard. 320 Charles Street,
Cambridge, MA. 02141.  Tel: 617-252-1925  Fax: 617-258-0903

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