[Bioclusters] Re: new on using clusters: problem running mpiblast (2)

Joe Landman landman at scalableinformatics.com
Thu Sep 20 16:13:50 EDT 2007

Zhiliang Hu wrote:

> ---------------------------------------
> bash: orted: command not found
> bash: orted: command not found


Could you do a

	which orted

on the head node from where you launch the mpiblast, and then

	ssh node001 which orted

and report that back?

> [ansci.iastate.edu:03916] ERROR: A daemon on node node001 failed to
> start as expected.

This suggests that a) orted wasn't found, and b) since that is required
to let OpenMPI set up the remote process, the remote process doesn't get

> [ansci.iastate.edu:03916] ERROR: There may be more information available
> from
> [ansci.iastate.edu:03916] ERROR: the remote shell (see above).
> [ansci.iastate.edu:03916] ERROR: The daemon exited unexpectedly with
> status 127.

If you don't see orted on the remote system, you might need to contact
your systems administrator to make sure the right path is mounted on the
remote node.

If you built OpenMPI yourself, you need to make sure your path variable
includes the $openmpi/bin  directory.

Basically this looks like OpenMPI is not in your path, which is why it
can't find orted, and this is why mpiblast isn't booting up on the node.

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  : +1 866 888 3112
cell : +1 734 612 4615

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