Note: forwarded message attached.
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P.Sravana Kumar.
Laboratory of Molecular Genetics.
Center for DNA Fingerprinting and Diagnostics.
ECIL road, Nacharam.
Hyderabad 500 076.
Ph: 91-40-27151344-1102.
Ph: 91-40-27151344-1209.
e-mail: sravan_at_[hidden],sravan_mar_at_[hidden]
==============================================
---------- Forwarded message ----------
Date: Wed, 18 May 2005 07:41:37 -0700
From: P Sravan Kumar. PAsst <sravan_at_[hidden]>
To: mpiblast-users_at_[hidden]
Cc: lam_at_[hidden], bio_bulletin_board_at_[hidden]
Subject: mpiblast error.
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.
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.
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 ).
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?
Please assist us in proper integration and running of mpiblast
tool. We appreciate your early suggestions.
Regards.
Sravan.
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