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From "Hoeftberger, Johann" <Johann_Hoeftber...@DFCI.HARVARD.EDU>
Subject Re: Taverna and SGE
Date Wed, 26 Nov 2014 18:50:44 GMT
On 11/26/2014 10:56 AM, alaninmcr wrote:
> On 26/11/2014 15:14, Hoeftberger, Johann wrote:
>> On 11/26/2014 08:55 AM, alaninmcr wrote:
>>> On 25/11/2014 16:36, Hoeftberger, Johann wrote:
>>>> Can Taverna make use of a Sun Grid Engine Cluster and is there a good
>>>> explanation how to do that?
>>>
>>> What do you mean by "make use of" ? Do you want to have a workflow be
>>> run on a node in the cluster or to have individual steps within a
>>> workflow run be executed on nodes in the cluster?
>>
>> I think both.
>> The most important need for me seems to be to have the ability that
>> individual steps within a workflow run on our SGE cluster transparently
>> for the user which uses the workflow. So those workflow steps should be
>> executed on nodes of the SGE cluster, the whole handshake for the usage
>> of those steps should be done by the Taverna system itself.
>
> What is the normal interface for "talking" to the SGE?

That's the question whose answer I hoped the SGE integration in Taverna 
would give.
(For our current jobs we use qsub and related tools.)

It seems currently there doesn't exist a real integration of a SGE Grid 
Engine in Taverna. And the only available solution is over Tool Service, 
SSH and qsub commands.
Although I don't have any experience with that I see the theoretical 
approach behind it. But this results in a polling strategy of the Grid 
results from a workflow engine perspectice. I thought / hoped there 
exists a tighter integrated solution for the connection between Taverna 
and SGE.


> A quick way to try things would be use the tool service to run qsub (and
> related) commands to your SGE. Then you could group the choreography of
> submit -> poll * -> retrieve results, into a component.

Yes, that's the best I could found and you confirm that somehow.


> Alternatively, if there is a Java library, you could write an equivalent
> Beanshell.

I also find very interesting the "Tool Activity pluggable execution 
point" Alan mentioned in his last post. But this would take a much 
bigger development approach I guess. I have to figure out what fits best 
in our situation.

Thank you all for your suggestions so far.


Regards,
Johann


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