[GE users] Managing the Queue + Nodes

reuti reuti at staff.uni-marburg.de
Wed Nov 4 00:09:55 GMT 2009

Hi Roger,

Am 03.11.2009 um 11:02 schrieb scu98rkr:

> Hi Reuti,
> Thanks for your ideas, but I seem to be having a similar problem
> following your instructions as I get when reading the manual.

which chapter is unclearly written? There is also a wiki: http:// 

> In that I
> dont really know what they mean.
> First you suggest
> qconf -msconf`: max_reservation 25
> what does this mean what is a reservation is it the amount of jobs  
> queued?

man sched_conf

> qsub -R y ...

man qsub

> Sorry really no idea what does this flag do ?
> Also what is a share tree ?


man sge_priority

It's one of the three SGE policies. When you want to honor only  
actual usage, you don't need a share tree policy. The functional will  
do, and you can define functional shares also for users.

-- Reuti

> Thanks Roger
>> Hi,
>> Am 02.11.2009 um 17:12 schrieb scu98rkr:
>>> We have a 64 node cluster consisting of 32 dual node machines.
>>> There are
>>> about 3 users. 2 of the users run single processor jobs that usually
>>> last between 7 hours and 1-2 days and they tend to queue up a  
>>> batch of
>>> test cases ie up 70 jobs each.
>>> Im running Gaussian and run many different types of jobs 1-2  
>>> hours or
>>> composite calculations several days. Recently I've started running
>>> dual
>>> processor open mp2 jobs. I tend to just run a few jobs at a time.
>>> Although I occasionally will run batches.
>>> We've never really come to a satisfactory conclusion of how to  
>>> manage
>>> the resources most efficiently. Quite often 1-2 users will not be
>>> using
>>> the node so I want the all of the resources open to every one. I've
>>> set
>>> up the share policy to 33% each so Queued jobs will be order  
>>> according
>>> to how much computing power each user is using on the cluster.
>>> Which is
>>> good but it still means the user with the least jobs has to wait  
>>> till
>>> the previous jobs have finished until their (possibly 1 hour job)
>>> will run.
>>> Also as I mentioned earlier I've started running dual processor  
>>> jobs.
>>> I've just come back over the weekend to find none of my jobs have  
>>> ran
>>> even after being at the front of the queue because at no point  
>>> have 2
>>> nodes on the same machine been free ( rather unsurprisingly)(I can
>>> pretend the jobs only uses 1 processor but I've noticed if you
>>> specify 2
>>> processors and some one else starts a job on the same machine the
>>> computation time become much slower than if you'd specified 1
>>> processor)
>>> What I really need SGE to do is monitor the usage of each user
>>> check if
>>> any user is using more than 33% of the cluster. If there are  
>>> currently
>>> any other jobs queued it needs to suspend the user over 33% jobs and
>>> replace them with the queued jobs. SGE doesnt seem to have any  
>>> problem
>>> suspending jobs so can it running other jobs in that suspended  
>>> space.
>>> I dont want limit peoples access to queues because I want the whole
>>> cluster available to 1 user if there is space.
>> a) as I read between the lines, you defined a PE with allocation_rule
>> $pe_slots and request two slots. What you need to avoid serial jobs
>> slipping in, is to turn on resource reservation in the scheduler
>> configuration `qconf -msconf`:
>> max_reservation 25
>> (or a more appropriate value)
>> and submit jobs with: qsub -R y ...
>> b) a share tree will honor the past usage, but AFAICS you request
>> only to honor the usage of the cluster right now:
>> http://gridengine.info/2006/01/17/easy-setup-of-equal-user-fairshare-
>> policy
>> -- Reuti
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> -- 
> "He made him ride on the high places of the earth, that he might  
> eat the increase of the fields"
> Deuteronomy 32:13
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