[Bioclusters] Submitting SGE jobs as nobody

[david speed (RI)]

Hi Joe, Farul,

Thanks for the replies,

As per Robert Findlay's (the sys admin here) post, I made an error in my original post
the NFS exported SGE tools are not on the head node - they are on a seperate machine and mounted on each
of the compute farm nodes and the Linux box.

Joe the output from ls -alF /local/SGE/bin/glinux/qsub was 

-rwxrwxrwx    1 root     root       985098 Jul 24 14:53 /local/SGE/bin/glinux/qsub*

We've changed the permission to 4755 as per Joe's mail and this seems to have fixed the problem.

Thanks again for your help

David

-----Original Message-----
From: Joseph Landman [mailto:landman@scalableinformatics.com]
Sent: Wednesday, October 29, 2003 12:15 PM
To: biocluster
Subject: RE: [Bioclusters] Submitting SGE jobs as nobody


Are the NFS directories exported with no_root_squash as the export
option?

On Wed, 2003-10-29 at 08:01, robert findlay (RI) wrote:
> David
> 
> The NFS exported directories are not on the head node - they are on the pineapple.  Remember we changed this in an attempt to stop the nodes hanging
> 
> Robert
> 
> -----Original Message-----
> From: david speed (RI) [mailto:David.Speed@bbsrc.ac.uk]
> Sent: 29 October 2003 11:53
> To: 'Bioclusters@bioinformatics.org'
> Subject: [Bioclusters] Submitting SGE jobs as nobody
> 
> 
> 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
> 
> 
> 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
> 
> The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute.
> 
> 
> _______________________________________________
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> https://bioinformatics.org/mailman/listinfo/bioclusters
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
-- 
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615


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