[GE users] configure nodes to have a "head" node

Chris Dagdigian dag at sonsorol.org
Mon Mar 20 13:25:57 GMT 2006

Hi Davide,

For a cluster of only 10 nodes it is extremely common for the head  
node to serve double duty as both the user/submit node as well as the  
machine that runs the SGE qmaster and schedd daemons.  Most people  
construct their cluster networks such that the compute nodes are not  
accessible by end users except through the head node.

For your question #1 -- only you can really answer this since there  
is no correct answer for everyone on how user actions influence the  
performance of SGE qmaster and scheddd. It depends on how many active/ 
pending jobs you may have entering and exiting the system.  For a  
small cluster doing computational biology and bioinformatics the user  
induced load is probably not going to be all that huge. Bio people  
tend to run lots of IO intensive serial jobs rather than slamming SGE  
with hundreds of thousands of small parallel tasks.  Your biggest  
performance bottleneck will be storage and fileservers if you are  
doing bioinformatics on this system.

If you want to start experimenting with #1 consider adding an SGE  
queue instance with only a single job slot on it - see how the system  
handles its tasks along with a single grid job running.

For question #2 -- the mechanism you would use within Grid Engine to  
manually influence the order in which machines are picked is called  
"queue_sort" -- you can assign each of your queue instances an  
integer value and tell SGE to sort first on the queue number and then  
on load. The end result is you can control the order of machine  
dispatch and you can place your head node at the "back" of the line.

There are a few blog entries on queue sorting and you can also search  
the mailing lists for when these methods have been discussed:



On Mar 20, 2006, at 3:32 AM, Davide Cittaro wrote:

> Hi all, I'm pretty new to sge6. I have this 10 nodes cluster I set  
> up with sge6. One node is only for qmaster and qsched, there is no  
> user access, no work at all. The other 9 nodes are submit/execution  
> hosts.
> Now I have a problem. Some users would like that their works do not  
> migrate on node1 (the node tipically used to submit works) except  
> when the other 8 nodes are really full. In other words they would  
> like to have a "head" node.
> I'm thinking to two solutions and I need help for both:
> 1- let the qmaster node be used as the unique submit host. In this  
> case I would like to know how much the users activity on the node  
> influences the efficiency of the qmaster and qsched daemons...
> 2- let node1 being considered less "performant" or "important" so  
> that sge chooses to migrate works on nodes2-9 and, in the end,  
> node1. In this case I would like to know which parameters I can  
> tune. Consider that all 10 machines are hardware identical (2  
> opteron, 4Gb RAM).
> Thanks
> d
> /*
> Davide Cittaro
> Bioinformatics Systems @ Informatics Core
> IFOM - Istituto FIRC di Oncologia Molecolare
> via adamello, 16
> 20139 Milano
> Italy
> tel.: +39(02)574303355
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */

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