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

Reuti reuti at staff.uni-marburg.de
Thu May 22 13:41:54 BST 2008


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
>>> +------------------------------------------------------------------+
>>>
>>>
>>> -------------------------------------------------------------------- 
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>>
>>
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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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> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
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