Michael: Created page with "===== Using qstat ===== qstat -f # what jobs are running qstat -f -q \*@compute-0-0 # full display info [for compute-0-0 onl..."

2013-05-13T10:03:40Z

Created page with "===== Using qstat ===== <syntaxhighlight> qstat -f # what jobs are running qstat -f -q \*@compute-0-0 # full display info [for compute-0-0 onl..."

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===== Using qstat =====
<syntaxhighlight>
qstat -f # what jobs are running
qstat -f -q \*@compute-0-0 # full display info [for compute-0-0 only
qstat -f -g c # display cluster queue summary
qstat -s r -q all.q@compute-0-0 # show all running jobs on compute-0-0
qstat -u viglen #show jobs being run by user; eg viglen; note jobid
qstat -j <jobid> #print all information with regards to jobid; numerical number
</syntaxhighlight>

===== Control jobs using qdel and qmod =====
<syntaxhighlight>
qdel <job_id> #delete job job_id
qdel -f <job_id> #delete job job_id; register job status change at sge_master without contacting sge_execd
qdel -u viglen #delete all jobs being run by user viglen
qdel 12 -u viglen #delete job with jobid 12 being run user viglen
qdel -u "*" #delete all jobs being run by all users: USE WITH LOTS OF CAUTION
qmod -sj <job_id> #suspend a running job
qmod -rj <job_id> #resume/reschedule the job
</syntaxhighlight>

===== Using qconf =====
<syntaxhighlight>
qconf -sel # show the nodes configured on sge
qconf -qpl # show parallel environments configured
qconf -sp mpi|mpich|orte # show the parallel env configuration (pre/post scripts etc)

qconf -sq all.q@compute-0-0.local # show the queue configuration per node
qconf -sq all.q # show "all.q" queue info
qconf -mq all.q # modify "all.q" queue: update hostlist, #slots
qconf -aq all.q # create queue named "all.q"

qhost -h compute-0-0,compute-0-1 # show host info for multiple nodes
</syntaxhighlight>

===== Add headnode to queue =====
<syntaxhighlight>
# on headndoe
cd /opt/gridengine
./install_execd -auto
</syntaxhighlight>

===== Submit to a specific host =====
<syntaxhighlight>
qsub -q '*@compute-0-0' script.sh
</syntaxhighlight>

===== Queue Configuration Changes =====
<syntaxhighlight>
qconf -mhgrp @allhosts # edit the lists of hosts in SGE
qconf -mq all.q # modify a queue, then you can remove nodes from the slots
</syntaxhighlight>

===== Disable/Enable a node on the queue =====
<syntaxhighlight>
qconf -rattr queue slots 0 all.q@compute-0-0 # slots -> 0 (== pbsnodes -o)
qconf -rattr queue slots 8 all.q@compute-0-0 # slots -> 8 (== pbsnodes -a)

qmod -d all.q@compute-0-0 # enable compute-0-0 in queue all.q (-d == disable)
qmod -e all.q@compute-0-0 # enable compute-0-0 in queue all.q (-d == disable)
</syntaxhighlight>

===== Check sgeexecd on nodes =====
<syntaxhighlight>
qping -info compute-0-0 537 execd 1 # check status of execd on compute-0-0
</syntaxhighlight>

===== Submission flags =====
<syntaxhighlight>
#$ -N <name-of-job> # Give your job a name; useful when using -o and -e options below in file-naming
#$ -cwd # Use the Current Working Directory
#$ -o <file-name.out> # Pipe standard output to file-name.out
#$ -e <file-name.err> # Pipe standard error ti file-name.err
##$ -j y # Join standard output and input
#$ -S /bin/bash # Interpreting Shell used is BASH
#$ -V # Export all environment variables within the qsub utility to the context of the job
#$ -pe orte 32 # 32 cores, using the openmpi PE

echo "Got $NSLOTS processors."
echo "Machines:"
cat $PE_HOSTFILE
</syntaxhighlight>

Rocks: SGE Commands - Revision history

Michael: Created page with "===== Using qstat ===== qstat -f # what jobs are running qstat -f -q \*@compute-0-0 # full display info [for compute-0-0 onl..."