[BiO BB] mpiblast error.

Joe Landman landman at scalableinformatics.com
Wed May 18 10:29:07 EDT 2005

Hi Sravan:

   Since you are using the RPMs we built, maybe I can help.

P Sravan Kumar. PAsst wrote:

 > We need assistance from the users of mpiblast regarding the execution on
 > AMD64 grid environment.
 > 1.System Configuration:
 > ---------------------
 > Operating System:
 > Red Hat Enterprise Linux 3.0 for AMD 64 Architecture
 > Sun Fire v20z machine
 > Bio Clusture Grid Engine
 > 2. We have downloaded the NCBI-2.2.10-1.x86_64.rpm and
 > mpiblast-1.3.0-1.x86_64.rpm from scalableinformatics.com. When we
 > installed NCBI: all the binaries like blastall are loaded onto /usr/bin.
 > and mpiblast: all the binaries are loaded onto /usr/local/bin ex:
 > mpiblast, mpiformatdb.

Good.  These binaries are built against mpich-1.2.6.  I have not done a 
build against LAM yet, though I would like to.  This is relevant a 
little later on in the error message portion.

 > 3. We have created one common blastdb in /apps/Databases/blastdb/ using
 > mpiformatdb -i scaffolds --nfrags=250 N 250 -p F. ( 250 fragments have
 > been created).


 > 4. Lamboot and lamnodes are also working fine as we checked by running
 > clustalmpi.sh through mpirun command.

Since mpiblast (from the RPM) is not using LAM, this is going to be an 
issue when you try to run it.

 > 5. But we are unable to run mpiblast through mpirun script as it 
gives the
 > follwing error:
 >   ( I am attaching a file containing the script and the error message ).

execution: ./mpiblast.sh on the masternode (silk-node 7 n0)
Wed May 18 14:29:55 IST 2005
Sorry, mpiBLAST must be run on 3 or more nodes
[0] MPI Abort by user Aborting program !
[0] Aborting program!

Yes.  Makes sense (oddly enough), as this version of the mpiblast RPM 
was built against mpich-1.2.6.  I would be happy to build against LAM (I 
have 7.0.3, 7.0.6, and 7.1.1 installed on my build machine), though it 
might take a little while.

Unfortunately, MPI != MPI.  I cannot take a LAM compiled binary and run 
it on an MPICH system, nor can I take an MPICH compiled binary and run 
it on an LAM system.  I would like us to get there, but this requires an 
MPI ABI, and a few other bits (agreement on how MPI processes are 
started, etc).

 > Our query:
 > ---------
 > 1. Why is this happening?

See above.

 > 2. Is there an NCBI.TAR.GZ pacakge that supports AMD64(X86_64) for RH
 > Enterprise WS 3.0?


 > 3. While installing NCBI rpms we were able to find only binary files. We
 > did not find the data files of NCBI ex: blosum, pam etc in any path in
 >  Is there any specific path they may be located?

I did not include them in the RPM.  Would you like a separate RPM with 
the data files?

 >     Please assist us in proper integration and running of mpiblast
 > tool. We appreciate your early suggestions.


 > Regards.
 > Sravan.
 > ------------------------------------------------------------------------
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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  : +1 734 786 8452
cell : +1 734 612 4615

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