[GE users] how to throttle jobs into a queue

david zanella zanella at mayo.edu
Fri Aug 24 18:12:58 BST 2007

I agree that this will probably work, but it isn't exactly what I"m looking 

In my case, the users are submitting several thousand jobs at a time. They 
cannot predict (or don't want to take the time to) how much memory a job will 
use. If they flag each job as using 2G of memory, then the consumable resource 
will run out at 15 or 16 jobs. Using my current load thresholds, I'm getting 
22-27 jobs on each server. I lose a lot of throughput if I do this. 

Using qconf -msconf and changing job_load_adjustments from
np_load_avg=0.5 to np_load_avg=2.0 with a load_adjustment_decay_time of
15 minutes *SHOULD* do it (man sched_conf)...but it doesn't seem to be
having any affect. That is, upon each job submission, it should
artificially increase the np_load_avg to 2.0 (alarm is set at 1.75) and
then decay that setting down for 15 minutes. That should give the job
enough time to ramp up and start using memory and trip my memory and
swap triggers. 

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From: "Kogan, Felix" <Felix-Kogan at deshaw.com>
To: <users at gridengine.sunsource.net>
Subject: RE: [GE users] how to throttle jobs into a queue
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by hsrnfs-101.mayo.edu id 

I've had the same problem and came up with the following solution (still
in testing phase):

o Make mem_free a requestable and consumable attribute

	$ qconf -sc
	#name                                    shortcut
type        relop requestable consumable default  urgency
	mem_free                                 mf
MEMORY      <=    YES         YES        0        0

o Set the resource value to the real amount of RAM for each node
	qconf -mattr exechost complex_values mem_free=32G

Once this is done, users can use "-l mem_free=2G" to really reserve 2GB
of RAM. Mem_free reading of the host where this job is executed will
show 2GB less mem_free. If the job, in fact consumed 2.5GB, mem_free
will reflect that. I.e. SGE uses the smaller of two values - calculated
from internal accounting and received from the load sensor. This works
for all other standard or custom requestable and consumable attributes,
as long as custom load sensor is set for these (e.g. you can set this up
for /var/tmp space).

Hope that helps.

Felix Kogan

-----Original Message-----
From: david zanella [mailto:zanella at mayo.edu] 
Sent: Friday, August 24, 2007 11:46 AM
To: users at gridengine.sunsource.net
Subject: [GE users] how to throttle jobs into a queue

I have a group of users that are submitting jobs to my grid.  The jobs
do some sort of pedigree/chromosome calculations. It is impossible for
the user to predict or control the amount of memory for each job.
Consequently, some job will start out small and grow to be about 2G in
size and run for weeks, other jobs can be small as a few hundred meg
and finish up in an hour.

I have set up load thresholds that will suspend job submission if the
available mem_free < 2G or swap_used > 6G.  For the most part, this
works well.  I have 7 T2000's for execute hosts.

Here's the problem:

My T2000's have 32G of memory and I have 30 slots for each. With the
load thresholds in place, say the server is only running 20 jobs. A job
completes and the server is now below it's load threshold. The qmaster
sees this and immediately shoves 11 jobs at the server.  Pretty soon,
the jobs grow, I run out of memory and swap, and jobs start crashing.

What I need is some way to throttle the acceptance rate to the server.
To tell the server to accept one job, then re-evaluate in, say, 15 or
30 minutes. If the load thresholds give a green light, it'll accept
another job.

I've looked at sched_conf, and it has what appears to be what I need.
I've made various adjustments to job_load_adjustments and
load_adjustment_decay_time, but these have not had any effect.

Am I missing something? Is there a better way to accomplish what I'm
trying to do?

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