Grid Computing

Grid Engine & Parallel Computing

= Resources = Oracle Grid Engine Beginner's Guide to Oracle Grid Engine 6.2 Grid Info = SGE Workflow = Intro to Grid Engine Usage & Simple Workflows

= SGE Cheat Sheet = SGE Cheat Sheet qconf -mhgrp @allhosts                  edit hostgroup "@allhosts" qstat -f [-q \*@node23]                 full display info [for node23 only] 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" qmon                                     GUI qmod                                    manipulate jobs, queues qconf -rattr queue slots 0 all.q@node23 #slots -> 0 (== pbsnodes -o) qstat -s r -q all.q@node23              show all running jobs on node23 qhost -h node23,node24                  show host info for multiple nodes qhost -q -h node23,node24               ibid, plus queue info qmod -e all.q@node23                    enable node23 in queue all.q (-d == disable) qsub -j y -o `pwd` -q all.q test.sh     submit test.sh job on queue all.q qping -info node23 6445 execd 1          check status of execd on node23

qstat                                   current user jobs qstat -u "*"                            all user jobs qstat -g c                              show available nodes and load qstat -f                                detailed list of machines and job state qstat -explain c -j job-id              specific job status qdel job-id                             delete job qsub -l h_vmem=### job.sh               mem limit, see queue_conf(5) RESOURCE LIMITS

= Nested qsub = >cat job1.sge ./doCommand1 >cat job2.sge ./doCommand2 >cat job3.sge ./doCommand3
 * 1) $ -S /bin/sh
 * 2) $ -N command1
 * 1) $ -S /bin/sh
 * 2) $ -N command2
 * 3) $ -hold_jid command1
 * 1) $ -S /bin/sh
 * 2) $ -N command3
 * 3) $ -hold_jid command2