[GE users] How to move resultfiles from execute host back to submitter

Daniel Templeton Dan.Templeton at Sun.COM
Fri Dec 14 17:57:10 GMT 2007


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Atle,

 From what machine are you submitting the job?  I'm really confused as 
to how the SSH login window has any idea *where* to pop up.

Just to double-check, I set up an epilog script that scp's a file across 
the network.  When I submit a job with my id in the authorized_keys 
file, everything works fine.  When I submit a job without my id in the 
authorized_keys file, I get the following line in the job's error file:

Permission denied 
(gssapi-keyex,gssapi-with-mic,publickey,keyboard-interactive).

and qacct says the job failed in the epilog, which is also correct behavior.

So, the question is, what in your environment is causing the odd 
behavior?  What happens if you leave out the epilog and submit a job 
that tries to do an scp?

Daniel

Atle Rudshaug wrote:
> It works just fine when executing the script by hand on the execution
> hosts. Everything is transferred without problems. However, when
> submitting a job from a terminal window inside Gnome X, an OpenSSH
> dialog appears and wants me to enter my password for each file
> transfer. However, if submitting from command promt outside X (Ctrl +
> Alt + F1), the files are transferres successfully without promting for
> password as I want it to.
>
> - Atle
>
> On 12/14/07, Daniel Templeton <Dan.Templeton at sun.com> wrote:
>   
>> The epilog script is just a script.  There shouldn't be any strange
>> behavior.  It's executed as the user who submitted the job on the host
>> where the job will be run.  What happens when you run the script by hand
>> on the execution host?
>>
>> Daniel
>>
>> Atle Rudshaug wrote:
>>     
>>> Well the epilog script starts. I had forgotten to make it executable.
>>> Now I get another problem with SSH. An OpenSSH dialog appears on the
>>> submit host and asks for my password for each file. An error dialog in
>>> the background says that the SSH password dialog could not grab the
>>> keyboard input.
>>>
>>> scp works fine manually when I run the epilog script from the execute
>>> hosts. Why do these dialog boxes appear for every file when run it in
>>> the epilog script? Is this a known problem? RCP just hangs if I try
>>> that.
>>>
>>> - Atle
>>>
>>> On 12/14/07, Daniel Templeton <Dan.Templeton at sun.com> wrote:
>>>
>>>       
>>>> Harald,
>>>>
>>>> Hmmm...  You added that feature, and you wrote the howto page, but I'm
>>>> going to be bold and disagree with you.  My understanding is that
>>>> delegated file staging is really just a switch that lets you tell the
>>>> qmaster that you have configured your own epilog and prolog scripts to
>>>> enable file staging, so that the DRMAA transfer_files optional attribute
>>>> is accepted for DRMAA applications.  It that's true, then it doesn't
>>>> help Atle set up the epilog script in the first place.  Delegated File
>>>> Staging is the step *after* solving Atle's problem, so that a DRMAA
>>>> application could take advantage of the solution.
>>>>
>>>> Do I have it wrong?
>>>>
>>>> Daniel
>>>>
>>>> Harald Pollinger wrote:
>>>>
>>>>         
>>>>> Hi Atle,
>>>>>
>>>>> there is a mechanism called "delegated file staging" in SGE. It's
>>>>> called "delegated" because it just provides all necessary
>>>>> informations, the real work is delegated to the prolog/epilog scripts.
>>>>>
>>>>> Please see the man page sge_conf(5) how to enable and how to use this
>>>>> mechanism, search terms in this page are "delegated_file_staging" and
>>>>> "$fs_", and
>>>>> http://gridengine.sunsource.net/howto/filestaging/filestaging6.html
>>>>> for a howto.
>>>>>
>>>>> Regards,
>>>>> Harald
>>>>>
>>>>> Atle Rudshaug wrote:
>>>>>
>>>>>           
>>>>>> Hi!
>>>>>>
>>>>>> I am doing some tests with SGE and Condor on 3 nodes only. What I need
>>>>>> is to get the result files for SGE back to my home dir on the submit
>>>>>> host. I don't have the home directories on NFS and don't have time to
>>>>>> set that up before a deadline. Condor does this automatically. Is
>>>>>> there some automatic way for SGE? Do I have to use a epilogue script?
>>>>>> If so, how?
>>>>>>
>>>>>> - Atle
>>>>>>
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>>     
>
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