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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
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
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:
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
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.
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 EOFwhere $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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