[Bioclusters] Queue Problems / Dead Processes

[Ron Chen]

Did you try to logon to the machine and kill the job
or daemons by hand?

 -Ron

--- "david speed (RI)" <David.Speed@bbsrc.ac.uk>
wrote:
> The problem we are having is that when we submit a
> number of blast jobs to Grid Engine sometimes a
> queue that is being used will go into an alarm
> state.   The qstat -alarm command displays this
> error message: no load value for threshold
> np_load_avg and the job on the node will continue to
> use 99.9 of process time.  
> 
> Attempts to kill the job process or shutdown /
> restart the Grid Engine daemons are ignored by the
> machine and the only method we have found to reset
> the node is to power it down.
> 
> Has anyone seen this problem before?  We are not
> sure if it is a problem with our installation of
> Grid Engine or a problem with standalone blast if so
> any suggestions or pointers to relevant
> documentation would be appreciated.
> 
> Thanks
> 
> David
> 
> David Speed
> Programmer
> Roslin Institute
> Bioinformatics Group
> Roslin, 
> Midlothian, 
> EH25 9PS, 
> UK
> Telephone: +44 (0)131 527 4200 (switchboard) 
> Fax: +44 (0)131 440 0434
> 
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> 
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>
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