[GE users] Dytran: Works from command line, not through SGE

Gerhard Venter gventer at sun.ac.za
Thu May 22 12:34:47 BST 2008


Thanks for the feedback.  Unfortunately, I get the same error.  I few
other things I've tried in the mean time:

1.  Made sure I am mounting my work directory (on the head node) with
the sync option to NFS
2.  Made sure the time is set consistent among all nodes
3.  Tried running the script with ssh (something like "ssh
comp002 /home/blah/script") and it works without any issues
4.  Tried qrsh and I get the same errors as with qsub

Many thanks,
Gerhard

On Thu, 2008-05-22 at 10:24 +0200, Reuti wrote:
> Am 19.05.2008 um 18:43 schrieb Gerhard Venter:
> 
> > I am very new to SGE and ran into an issue that I hope somebody could
> > help me with - I hope I am posting on the correct mailing list.
> >
> > We are trying to run Dytran from MSC Software on our cluster.  When I
> > launch Dytran from the command line (on the head node or any of the
> > compute nodes) it works without any problems.  However, when I launch
> > Dytran using SGE, I get an error message that states "Error closing
> > file".  We are using SGE 6.0 and OpenSuse 10.3 as the OS.
> >
> > My submit script is very simple, and looks something like this:
> > #!/bin/bash
> > #$ -cwd
> > /apps/msc/dytran2007r1/bin/dytran jid=Klep72
> >
> > As mentioned, I can run this script directly from the command line
> > without any issues.
> >
> > I am not an Dytran expert, but it seems that Dytran creates a csh  
> > script
> > on the fly that it starts.  Could this be part of the problem?  I
> > cannot seem to find much help on using Dytran with SGE on the web.  I
> > did try to explicitly set my limits in my submit script to be the same
> > as from the command line (as mentioned in the FAQ on this website)
> > without any success.
> 
> When this application creates a new job script on the fly, it might  
> indeed jump out of SGE's control. But I never heard about such an  
> error when closing a file. Maybe Dytran is using $TMPDIR which is  
> removed after the job (but even then it's just like unlinking a file  
> and it should just disappear - unless they meaning "appending some to  
> the file to mark it as closed" or so.)
> 
> To avoid the creation of an additonal shell (csh as kid of bash),  
> maybe you can try the small adjustment and prepend an exec:
> 
> exec /apps/msc/dytran2007r1/bin/dytran jid=Klep72
> 
> This will replace the bash with your application, so one process less  
> in the process tree.
> 
> -- Reuti
> > Any help will be greatly appreciated.
> >
> > Best regards,
> > Gerhard
> > -- 
> > +------------------------------------------------------------------+
> > || Prof. Gerhard Venter
> > ||
> > || Departement Meganiese en        |  Department of Mechanical and
> > ||   Megatroniese Ingenieurswese   |    Mechatronic Engineering
> > || Universiteit Stellenbosch       |  Stellenbosch  University
> > || Privaat Sak X1 Matieland 7602   |  Private Bag X1 Matieland 7602
> > || Suid-Afrika                     |  South Africa
> > ||
> > || Tel: +27 21 808 3560
> > || E-Mail: gventer at sun.ac.za          Web: www.eng.sun.ac.za
> > +------------------------------------------------------------------+
> >
> >
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-- 
+------------------------------------------------------------------+
|| Prof. Gerhard Venter
||
|| Departement Meganiese en        |  Department of Mechanical and
||   Megatroniese Ingenieurswese   |    Mechatronic Engineering
|| Universiteit Stellenbosch       |  Stellenbosch  University
|| Privaat Sak X1 Matieland 7602   |  Private Bag X1 Matieland 7602  
|| Suid-Afrika                     |  South Africa
||
|| Tel: +27 21 808 3560
|| E-Mail: gventer at sun.ac.za          Web: www.eng.sun.ac.za
+------------------------------------------------------------------+


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