[GE users] Better explaination on what I need to test with.

Andreas.Haas at Sun.COM Andreas.Haas at Sun.COM
Mon Mar 12 10:37:45 GMT 2007


On Tue, 6 Mar 2007, Joe Landman wrote:

> Hi Trey:
>
> Trey wrote:
>> I tried to ask this before, but in my haste I confused a ton of people and 
>> lost track of what exactly I was needing to ask myself.
>
> Was on vacation last week, and tried responding once, but it didn't make it.

Same with me but one week later now ;-)

>
>> What we have is a piece of software that you do molecular modeling with as 
>> well as calculations with.  These calculations if done on a single work 
>> station will quite often bog down the PC if not lock it up, if the 
>> resources are not enough and the calculation is far to larger.  So with the 
>> Scientific community gravitating more and more to Linux clusters to do the 
>> work, we are attempting to gravitate some form of our product to meet this 
>> need.
>
> Excellent.
>
>> We will have a windows GUI that you will draw the molecule and then 
>> initiate the calculation, then send it to the cluster to do the work. In 
>
> Ah... Hyperchem.  I remember playing with it a long time ago.
>
>> our software we already have some sort of ability to call other servers to 
>> do this via the IP address/Name.  We are going to develop linux backends to 
>> do the calculations themselves.  Once the calculation is complete it will 
>> then send it back to the windows GUI.
>
> Good.
>
>> What I need is some sort of script that will issue qsub commands via a some 
>> custom service/listener that translate the client's request into a qsub 
>> command.  then once it is done, will send it back to the windows 
>
> Ok.  This is a more general problem than SGE solves.  If you want to talk 
> about this offline, we have built a few codes like this in the past, mostly 
> for informatics, some for chemical visualization.

Joe/Trey consider one of the DRMAA scripting language bindings could
be base for this. It comes with a DRM indepenent job abstraction and 
lets one wait for jobs to finish very much as with waitpid(5) system
call. For an illustration with the Ruby language binding see

    http://drmaa4ruby.sunsource.net/source/browse/drmaa4ruby/src/samples/example.rb?view=markup

note there are examples that can do much more than this and it will
work with any DRM that supports the DRMAA base operations.

Regards,
Andreas

>> GUI.  Knowing that SGE isn't the only clustering software out there, we are 
>> trying to come up with a custom generic script to function on SGE as what 
>> we need and then use that to help come up with one that can move to the 
>> forms of clustering software.  Hence the reason we cant use a direct qsub 
>> call in the software itself.  We need something on the cluster side itself.
>
> Yup.  Understood.
>
>> 
>> Knowing I am far from a Linux expert, I am working on this far from the 
>> time we actually need it done.  The learning curve is a big one on my side 
>> since I am the only one on it and need as much help as I can get.
>
> One of the nicer aspects of this is, if it is done right, it can work on many 
> different incarnations of cluster.  Again, probably worth an offline 
> conversation.
>
>> 
>> 
>> Thank you in advance.
>> 
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>
> -- 
>
> Joseph Landman, Ph.D
> Founder and CEO
> Scalable Informatics LLC,
> email: landman at scalableinformatics.com
> web  : http://www.scalableinformatics.com
> phone: +1 734 786 8423
> fax  : +1 734 786 8452 or +1 866 888 3112
> cell : +1 734 612 4615
>
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