[Bioclusters] Submitting SGE jobs as nobody

david speed (RI) bioclusters@bioinformatics.org
Wed, 29 Oct 2003 11:53:10 -0000

Hi All,

I recently submitted this query to the SGE users list, it was suggested that it might be better to post it here.

Hi All,

We have installed SGE onto our 15-node Linux (Red Hat 7.1) cluster (30 Intel CPUs). There is an NFS export mounted from the head node to each slave node solely to contain the SGE tools and directories.  We have installed the ncbi blast tools and the databases to be blasted against locally on each node.

We also have installed SGE onto an old Linux (Red Hat 7.2) box using the same NFS export

We are working on a web interface that allows users to submit a blast job to SGE by pasting in fasta sequences to a form with the option to add some of the basic blast parameters.

The separate Linux box is a submit host only which has the web server /interface installed on it, the blast jobs are run on the cluster nodes which are all execution hosts.

The Linux box and the cluster nodes are all reading and writing to a shared area.

We have encountered a strange problem when testing our prototype, the web interface will fail with this error message

Can't exec "/local/SGE/bin/glinux/qsub": Input/output error

However if we try to run again the error message changes to ( and stays the same for subsequent attempts)

Can't exec "/local/SGE/bin/glinux/qsub": Permission denied

I've been able to able to temporarily fix this problem by running qsub on the command line while logged into my own account on the machine.  

After I do this the web interface submits jobs as expected (even typing qsub then ctrl-c to escape while its waiting for stdin works) for the remainder of the working day,  however the fix 'wears off' sometime between when I go home at night and get back here in the morning when I have to use my qsub command line fix to get things working again.

Has anyone seem this problem before?

Any help in identifying / resolving the problem so that user nobody jobs are submitted as expected without any weirdness will be appreciated

Thanks for your time.


David Speed
Roslin Institute
Bioinformatics Group
EH25 9PS, 
Telephone: +44 (0)131 527 4200 (switchboard) 
Fax: +44 (0)131 440 0434

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