Thanks a lot for your reply.
Now the mpiblast run in only one node both inside and outside a torque job.
How could I setup a hostlist for open mpi? I haven't found this in the open mpi faq. Thanks.
the "ompi_info | grep tm" output is:
MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.1)
MCA ras: tm (MCA v2.0, API v2.0, Component v1.4.1)
MCA plm: tm (MCA v2.0, API v2.0, Component v1.4.1)
I also attached the "ompi_info --all" output with this email. Maybe you'd like help me to check it.
I have set the openmpi/bin to PATH and openmpi/lib to LD_LIBRARY_PATH and I think the mpiblast complier chose the right mpicc.
Are you running your job inside a torque job? If you don't, open mpi will not have a hostlist and will assume that it should launch everything on the localhost.
If you are launching inside a torque job, ensure that ompi was build with torque support properly - run
ompi_info | grep tm
If you see 1 or more tm plugins listed, ompi has torque support.
Finally, make sure you're using the right mpicc and mpirun, etc.
Sent from my PDA. No type good.
From: firstname.lastname@example.org <email@example.com>
To: firstname.lastname@example.org <email@example.com>
Sent: Thu Apr 01 02:07:08 2010
Subject: [OMPI users] mpiblast only run in one nodeHi,
I've installed Torque/Maui, Open MPI 1.4.1 and mpiBlast 1.6.0-beta1 in a linux Beowulf culster with 15 nodes (node1~15).
Open MPI, mpiBlast were installed and my home directory lies in a directory "/data" which was shared by all nodes.
Open Mpi was compiled with "--with-tm" to support Torque, and mpiBlast was compiled with
"--with-mpi" to the directory where Open MPI installed.
When I run mpiBlast by mpirun in command line, like
node1 $ /data/open-mpi/bin/mpirun -np 34 /data/mpiblast/bin/mpiblast -p blastp -d nr -i test.faa -o test.out
I noticed all 34 mpiBlast processes run on node1 only.
This would not change if I submit job to Torque.
I've searched the mailing list archives but it seems won't help.
How to resolve this problem?
Any suggestion will be appreciated!
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