[Bioclusters] Re: new on using clusters: problem running mpiblast (2)

Joe Landman landman at scalableinformatics.com
Fri Sep 21 11:20:10 EDT 2007

Zhiliang Hu wrote:
> Thanks Joe!
> I tested with 'which' and 'whereis', they do find 'orted' on my system.
> So I tried again with full path to "mpirun" (i am sorry I should have
> done this earlier):
>> /opt/openmpi.gcc/bin/mpirun -np 3 -machinefile machines 
> /home/local/bin/mpiblast -p blastp -i ./bait.fasta -d ecoli.aa

Lets have you add '-d 4' to the mpirun line in both cases.

Also, I might suggest forcing it to use the ethernet if possible.  You
would need to add in

	-mca btl tcp

to make that happen.

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

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