[Bioclusters] new on using clusters: problem running mpiblast

Joe Landman landman at scalableinformatics.com
Sat Aug 25 22:12:37 EDT 2007

Zhiliang Hu wrote:
> I am new on using clusters.
> I have just installed mpiblast 1.4.0 with ncbi toolbox (June 2005)
> from source codes on a linux cluster [x86_64/x86_64 (GNU/Linux), CentOS].
> The installation seemed to be successful.
> Now when I try the following:
>> /opt/openmpi.gcc/bin/mpirun -np 14
>       /usr/local/bin/mpiblast -p blastn
>                               -i /raid/pub/ncbi/blast/db/BTrsSNP
>                               -d bta.genome.chr
>                               -o out1
>                               -e 0.0000000001
>                               -W 38 -v 1 -b 1

There are many possibilities.  One of the best things to do is to run
with the verbose/debug flags for MPI.

I have found that most of the problems people encounter with mpiBLAST
and MPI-HMMer are that MPI isn't being launched (correctly), or there is
something non-functional with the MPI stack.  I usually suggest some
basic "hello world" tests to eliminate the MPI stack from consideration
as a source of a problem.

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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