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Contents Bulletin Scripting in shell and Perl Network troubleshooting History Humor

Starting and Killing SGE Daemons

News Grid Engine Recommended Links sge_qmaster Excluding SGE execution host from scheduling sge_execd - Sun Grid Engine job execution agent SGE shepherd
Getting information about hosts Administration Hosts Execution hosts  ulimit problem with infiniband in SGE MPI startup(): RLIMIT_MEMLOCK too small problem with SGE and Infiniband Prolog and epilog scripts Gridengine diag tool
qping qstat qacct qalter -- Change Job Priority qmod qsub -- Submitting Jobs To Queue Instance qconf
SGE cheat sheet Creating and modifying SGE Queues Monitoring Queues and Jobs  Monitoring and Controlling Jobs Grid Engine Config Tips Humor Etc

Introduction

That are two main daemons in SGE:

Both are controlled via init scripts.

Sometime minor problems can often be fixed by restarting iether execution daemon on the affected node(s) or both master and execution daemon.

Note: execution daemon can be stopped using option softstop instead of traditional stop.  That is an important, but rarely mentioned in official documentation opportunity, which allow to preserves running jobs

# This script can be called with the following arguments:
#
#       start       start execution daemon
#       stop        Terminates the execution daemon
#                   and the shepherd. This only works if the execution daemon
#                   spool directory is in the default location.
#       softstop    do not kill the shepherd process
#
# Unix commands which may be used in this script:
#    cat cut tr ls grep awk sed basename
#
# This script requires the script $SGE_ROOT/util/arch
#

PATH=/bin:/usr/bin:/sbin:/usr/sbin

To check, if daemons are running

On execution node:

[0]root@mysite54: # ps -ef | grep sge_
root     14508     1  0 May16 ?        00:00:17 /sge/bin/lx24-amd64/sge_execd
root     18547 14508  0 15:03 ?        00:00:00 sge_shepherd-4461 -bg
root     19060 19038  0 15:47 pts/1    00:00:00 grep sge_
on SGE master node
# ps -ef | grep sge
root      4463     1  0 Nov01 ?        00:00:07 /sge/bin/lx24-amd64/sge_execd
root      4597     1  0 Nov01 ?        00:29:01 /sge/bin/lx24-amd64/sge_qmaster

Stopping daemons

In linux you can use command service. For example

service sgeexecd.p6444 stop

You can also stop daemons directly from /etc/init.d directory:

cd /etc/init.d

./sgeexecd.p6444 stop
   Shutting down Grid Engine execution daemon
./sgemaster.p6444 stop
   shutting down Grid Engine qmaster

For execution daemon two options exist:

Restarting Daemons From the Command Line

Log in as root on the machine on which you want to restart Grid Engine system daemons. In linux you can use service command:

service sgeexec.p6444 stop && sgeexec.p6444 start

The init script for sgeeexecd  also allow softstop option for execution daemon. Which preserves running processes.

First check is daemon is running. If NFS was not available, then daemon was unable to start and thus is not running. So remount of NFS partition is not enough. You need also to restart sge_execd daemon on the node

[0]root@mysite16: # ps -ef | grep sge
root      8187     1  0 16:08 ?        00:00:00 /sge/bin/lx24-amd64/sge_execd
root     10043  9972  0 16:17 pts/1    00:00:00 grep sge

The startup script is at /etc/init.d

Killing daemons using qconf

To kill Grid Engine system daemons from the command line, use one of the following commands:

% qconf -ke[j] {<hostname>[,...] | all}
% qconf -ks
% qconf -km

You must have manager or operator privileges to use these commands. See Managing Users Access for more information about manager and operator privileges.

Feeing hosts for maintenance or other tasks

If you want to wait for any active jobs to finish before you run the shutdown procedure, use the qmod -dq command for each cluster queue, queue instance, or queue domain before you run the qconf sequence described above. For information about cluster queues, queue instances, and queue domains, see About Configuring Queues.

% qmod -dq {<cluster-queue> | <queue-instance> | <queue-domain>}

The qmod -dq command prevents new jobs from being scheduled to the disabled queue instances. You should then wait until no jobs are running in the queue instances before you kill the daemons. You can use asterisk to denote all queues. For example

qmod -dq *@b11

See Excluding SGE execution host from scheduling for more information.


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Rebooting execution hosts

To reboot execution hosts, you need to ensure they’re empty and avoid races with job submission. Thus, submit a job which requires exclusive access to the host and then does a reboot. Since you want to avoid root being able to run jobs for security reasons, use sudo(1) with appropriate settings to allow password-less executions of the commands by the appropriate users. You want to comment out Defaults requiretty from /etc/sudoers, add !requiretty to the relevant policy line, or use -pty y on the job submission. It is cleanest to shut down the execd before the reboot.

The job submission parameters will depend on what is allowed to run on the hosts in question, but assuming you can run SMP jobs on all hosts (some might not be allowed serial jobs), a suitable job might be

qsub -pe smp 1 -R y -N boot-$1 -l h=$node,exclusive -p 1024 -l h_rt=60 -j y <<EOF
/usr/bin/sudo /sbin/service sgeexecd.ulgbc5 softstop
/usr/bin/sudo /sbin/reboot
EOF
where $node is the host in question, and we try to ensure the job runs early by using a resource reservation and a high priority.

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