[BiO BB] mpiblast error.
landman at scalableinformatics.com
Wed May 18 10:24:23 EDT 2005
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
 MPI Abort by user Aborting program !
 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
> Our query:
> 1. Why is this happening?
> 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.
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
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