I seem to have found a combination of resource quotas that is preventing
the scheduler from scheduling parallel jobs across multiple queues.
I have multiple queues for jobs with different run times: veryshort.q, short.q
,
long.q, and verylong.q. Each of these queues has an increasing 'h_rt' limit and
an increasing sequence number (I have the scheduler sort by sequence
numbers). Each of these queues also has a decreasing number slots available.
Jobs are then submitted with an h_rt value and the shortest queue with an
open slot is used. I also have a parallel environment "mpi" that is enabled in
all of these queues.
The problem only occurs if I use resource quota sets to both limit the total
number of slots for the queues and limit the number of slots on each node.
For example:
{
name nodelimit
description NONE
enabled TRUE
limit queues !debug.q hosts {*} to slots=$num_proc
}
{
name shortlimit
description NONE
enabled TRUE
limit queues short.q hosts * to slots=32
}
{
name longlimit
description NONE
enabled TRUE
limit queues long.q hosts * to slots=16
}
{
name verylonglimit
description NONE
enabled TRUE
limit queues verylong.q hosts * to slots=4
}
{
name urgentlimit
description NONE
enabled TRUE
limit users {*} queues urgent.q hosts * to slots=1
}
{
name debuglimit
description NONE
enabled TRUE
limit users {*} queues debug.q hosts {*} to slots=1
}
This will cause a parallel job across multiple queues to never schedule. If
I get rid of the "nodelimit" and instead set the number of slots using
the complex value in the host configuration, then everything works (except
my debug queue).
Below I give an example of a hanging job (with the scheduler output enabled).
I set h_rt to 3:50:00 as this will allow the queues short.q, long.q, and
verylong.q. I request 40 slots as that will have to span multiple queues.
$ qsub -w e -l h_rt=3:50:00 -pe mpi 40 test.sh
Your job 13280 ("test.sh") has been submitted
$ qstat -u '*'
job-ID prior name user state submit/start at queue
slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
13280 0.00000 test.sh moloney qw 01/11/2012 21:21:32
40
$ qstat -j 13280
==============================================================
job_number: 13280
exec_file: job_scripts/13280
submission_time: Wed Jan 11 21:21:32 2012
owner: moloney
...
scheduling info: cannot run in queue "debug.q" because PE "mpi" is
not in pe list
cannot run in queue "urgent.q" because PE "mpi" is
not in pe list
cannot run because it exceeds limit "////piggy/" in
rule "nodelimit/1"
cannot run because it exceeds limit "////piggy/" in
rule "nodelimit/1"
cannot run because it exceeds limit "////piggy/" in
rule "nodelimit/1"
cannot run because it exceeds limit "////piggy/" in
rule "nodelimit/1"
cannot run because it exceeds limit "////kermit/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////kermit/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////kermit/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////kermit/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////animal/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////animal/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////animal/"
in rule "nodelimit/1"
cannot run because it exceeds limit "////animal/"
in rule "nodelimit/1"
cannot run in PE "mpi" because it only offers 0
slots
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