[Bioclusters] error while running mpiblast

[James Cuff]

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...

*sigh*

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:

 Shared=/home/kalyani/toolkit/ncbi
 Local=/tmp/kalyani_mpiblast/

(or as Joe maybe put better)

 Shared=/home/kalyani/toolkit/ncbi
 Local=/mylocalfilesystemthatnoonewillmesswith/kalyani_mpiblast/

 WFM, YMMV..

Best,

J.

--
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