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

Reuti reuti at staff.uni-marburg.de
Thu May 22 16:41:08 BST 2008


Am 22.05.2008 um 15:48 schrieb Gerhard Venter:

> 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.

Funny :-)

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

Maybe strace is forking the processes in a different way :-/

You can try to limit the output with "-e trace=file" or so. Maybe we  
can get a clue, what is failing when we know the type of a call at  
least.

-- Reuti


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