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Some interesting SGE queue attributes

News SGE Queues Recommended Links qconf SGE hostgroups Most important optiona of qconf Parallel environment
Some interesting queue params queue_conf - Grid Engine queue configuration file format slots queue attribute Excluding SGE execution host from scheduling Restricting number of slots per server Slot hacking sge_types
Controlling Queues and Jobs qdel qhold qalter -- Change Job Priority qmod qsub qstat
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hostlist

seq_no

Use to influence exec host selection when all other things are equal

load_threshold

When threshold is exceeded, no new jobs are placed on host. Essentially it is the signal that the host is busy as determined by uptime

Can use iether built-in values or values reported by custom load sensors (example: ‘logged-in-users=5’).

Default value

np_load_avg=1.75 

lead to oversubscription of computational tasks. In many cases lower threshold such as 0.75 might be better. 

suspend_threshold, nsuspend, suspend_interval

Similar to load_threshold but running jobs will actually be suspended/stopped. The ‘nsuspend’ param determines how many jobs per interval get suspend signals.

 ‘suspend_interval’ defaults to 00:05:00.

pe_list

What parallel environment (PE) objects this queue supports. See SGE Parallel Environment

slots

Max number of tasks or jobs that this queue supports. It is not necessary number of CPUs on each computational node. Slots queue attribute is really a resource which specifies two things

It an be defined iether:

prolog & epilog

Custom scripts that run before/after a job

Trivial epilog usage:

#!/bin/sh # Simple epilog script
JOB_EXIT_STATUS="`sed -ne 's/^exit_status=//p'\
             $SGE_JOB_SPOOL_DIR/usage | tail -1`" 
echo "--------" echo "Job exited code: $JOB_EXIT_STATUS"
echo "--------"

Trivial epilog usage - II … STARVEDETECT="`grep -c "Licensed number of users already reached” \ $SGE_O_WORKDIR/*.log `" if [ $STARVEDETECT -gt 0 ] then echo "License Error Pattern Detected in Output!" /bin/tcsh -c "cd $SGE_O_WORKDIR; \ /cl/sw/bin/restart-failed-job.pl " else echo "No problems detected" fi …

How to configure different prolog scripts for different hosts or host groups (2014-03-03)

Daniel's Blog about Grid Engine

When configuring Grid Engine a good tuning point is always to reduce the amount of queues (i.e. queue instances). When having a need for different machine type specific prolog and epilog scripts (for different heath-check for example) this does not require to configure multiple queues containing different prolog and epilog scripts. Instead you can configure them in the same queue using the bracket notation where you can define settings for queue instances (a queue setting for a host) and queue domains (a queue setting for a hostgroup).

Here is an example of how to configure different prolog scripts for different host groups

I‘ve configured two additional host groups: @centos and @suse11 for which I want to have different prolog scripts running before a job is started.

qconf -shgrpl
@allhosts
@centos
@suse11

My prolog scripts just printing out something on stdout.

cat /nfs/prolog_cent.sh 
#!/bin/sh
echo "I'm a CentOS box"
cat /nfs/prolog_suse.sh 
#!/bin/sh
echo "I'm a SUSE box"

Now we can add those two prolog scripts in the prolog configuration of one queue. Here for the host-group @centos the /nfs/prolog_cent.sh script is set. The prolog for host-group @suse11 is set respectively(of course you can also just use an host name instead of a hostgroup).

qconf -mattr queue prolog "NONE,[@centos=/nfs/prolog_cent.sh],[@suse11=/nfs/prolog_suse.sh]" all.q
daniel@mint14 modified "all.q" in cluster queue list

Now verify that the queue configuration was set in the right way.

 qconf -sq all.q | grep prolog
prolog       NONE,[@centos=/nfs prolog_cent.sh], \
                  [@suse11=/nfs/prolog_suse.sh]

Finally we submit two jobs to two different hostgroups (i.e. here queue domains since the job is required to run in all.q).

 qsub -b y -q all.q@@suse11 /bin/sleep 0
Your job 8 ("sleep") has been submitted

 qsub -b y -q all.q@@centos /bin/sleep 0
Your job 9 ("sleep") has been submitted

Now check the job output file. It must contain the prolog output.

 cat /home/daniel/sleep.o9 
I'm a CentOS box
 cat /home/daniel/sleep.o8
I'm a SUSE box

Queue associated resources

Host associated resources


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[Sep 20, 2014] How to configure different prolog scripts for different hosts or host groups

2014-03-03 | Daniel's Blog about Grid Engine

When configuring Grid Engine a good tuning point is always to reduce the amount of queues (i.e. queue instances). When having a need for different machine type specific prolog and epilog scripts (for different heath-check for example) this does not require to configure multiple queues containing different prolog and epilog scripts. Instead you can configure them in the same queue using the bracket notation where you can define settings for queue instances (a queue setting for a host) and queue domains (a queue setting for a hostgroup).

Here is an example of how to configure different prolog scripts for different host groups

I've configured two additional host groups: @centos and @suse11 for which I want to have different prolog scripts running before a job is started.

qconf -shgrpl
@allhosts
@centos
@suse11

My prolog scripts just printing out something on stdout.

cat /nfs/prolog_cent.sh 
#!/bin/sh
echo "I'm a CentOS box"
 cat /nfs/prolog_suse.sh 
#!/bin/sh
echo "I'm a SUSE box"

Now we can add those two prolog scripts in the prolog configuration of one queue. Here for the host-group @centos the /nfs/prolog_cent.sh script is set. The prolog for host-group @suse11 is set respectively (of course you can also just use an host name instead of a hostgroup).

 qconf -mattr queue prolog "NONE,[@centos=/nfs/prolog_cent.sh],[@suse11=/nfs/prolog_suse.sh]" all.q
daniel@mint14 modified "all.q" in cluster queue list

Now verify that the queue configuration was set in the right way.

 qconf -sq all.q | grep prolog
prolog                NONE,[@centos=/nfs prolog_cent.sh], \
                  [@suse11=/nfs/prolog_suse.sh]

Finally we submit two jobs to two different hostgroups (i.e. here queue domains since the job is required to run in all.q).

 qsub -b y -q all.q@@suse11 /bin/sleep 0
Your job 8 ("sleep") has been submitted

 qsub -b y -q all.q@@centos /bin/sleep 0
Your job 9 ("sleep") has been submitted

Now check the job output file. It must contain the prolog output.

 cat /home/daniel/sleep.o9 
I'm a CentOS box
 cat /home/daniel/sleep.o8
I'm a SUSE box

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