[BiO BB] mpiblast error.

[P Sravan Kumar. PAsst]

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.




-------------- next part --------------
script:
-----
#! /bin/sh
date
/usr/local/lam/bin/mpirun -np 5  /usr/local/bin/mpiblast  -p blastn -d /apps/Databases/blastdb/scaff
olds -i /home/sravan/demorun/blast/SW_ge2k_BGF.cds -o /home/sravan/demorun/blast/mpiblast.out
date
lamnodes: execution:
-------------------
n0      silk-node7:2:origin,this_node
n1      silk-node6:2:
n2      silk-node5:2:
n3      silk-node4:2:
n4      silk-node3:2:
n5      silk-node2:2:
n6      silk-node1:2:
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!
p0_15547:  p4_error: : 0
Sorry, mpiBLAST must be run on 3 or more nodes
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_15548:  p4_error: : 0
Sorry, mpiBLAST must be run on 3 or more nodes
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_5535:  p4_error: : 0
Sorry, mpiBLAST must be run on 3 or more nodes
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_5536:  p4_error: : 0
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
Wed May 18 14:29:58 IST 2005
================================================================================