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

Gerhard Venter gventer at sun.ac.za
Thu May 22 14:48:36 BST 2008


qrsh and qsub both result in the same error message.  However, when I
add strace -f to see where the problem is, the code runs!  Of course
strace then creates gigabytes worth of output.

The queue does not have any limits set that I am aware of.  The queue
definition is attached (obtained from qconf -sq default.q).

Gerhard


On Thu, 2008-05-22 at 14:41 +0200, Reuti wrote:
> Am 22.05.2008 um 13:34 schrieb Gerhard Venter:
> 
> > 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
> 
> As qrsh is working, can you try to run it via "strace" - maybe you  
> can get some hint where it's crashing and why?
> 
> Is there any limit in SGE on this particular queue (h_vmem...) set?
> 
> -- Reuti
> 
> 
> > 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
> >>> +------------------------------------------------------------------+
> >>>
> >>>
> >>> -------------------------------------------------------------------- 
> >>> -
> >>> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
> >>> For additional commands, e-mail: users-help at gridengine.sunsource.net
> >>
> >>
> >> ---------------------------------------------------------------------
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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
> > +------------------------------------------------------------------+
> >
> >
> > ---------------------------------------------------------------------
> > To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
> > For additional commands, e-mail: users-help at gridengine.sunsource.net
> 
> 
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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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