[Bioclusters] error on qsub/mpirun jobs

Zhiliang Hu zhu at iastate.edu
Tue Sep 9 13:22:27 EDT 2008


Thank you for the hints as where to look for the errors.  That's helpful.


At 11:35 AM 9/8/2008 -0400, Michael Edwards wrote:
>On Fri, Sep 5, 2008 at 4:55 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> ----------------------------------------------------------
>> Unable to copy file /var/spool/torque/spool/658.nagrp2..ER to
>> hu at hist:/raid/pub/ncbi/blast/www/mpiblast.tmp
>> >>> error from copy
>> Host key verification failed.
>> lost connection
>> >>> end error output
>> Output retained on that host in:
>> /var/spool/torque/undelivered/658.nagrp2..ER
>> ----------------------------------------------------------
>> Note: When manually check, the "retained" file is not there:
>> "/var/spool/torque/undelivered/658.nagrp2..ER"
>qsub opens a shell to the selected compute node and runs the script from
>that node.  So the retained file would not be on the head node, but on the
>local file system on which the node was trying to run.
>If you are trying to run qsub, the code has to be present on all the compute
>nodes in the same place.  The easiest way to do this is using a shared file
>Bioclusters maillist  -  Bioclusters at bioinformatics.org

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