View source for PBS Queue

==Basic PBS commands==

* qsub <script> - will submit your script to the queue
* qstat - will display a list of jobs running
* qdel <jobid> - remove the job from the queue

==Sample qsub script==
 #PBS -l nodes=1:ppn=2
 #PBS -l walltime=24:00:00 
 
 cd /nfs/user03/sudipto
 ls
 echo "Hello World"
 echo "My first seawulf job"

 Job id                    Name             User            Time Use S Queue
 ------------------------- ---------------- --------------- -------- - -----
 514722.nagling            STDIN            liuxt12         1657:13: R batch
 514723.nagling            STDIN            liuxt12         3366:45: R batch
 514724.nagling            jet3dKn0.002PR20 wli             874:42:4 R batch
 514725.nagling            ...dKn0.002PR100 wli             855:59:2 R batch
 514803.nagling            jet3dKn0.002PR10 wli             596:48:0 R batch
 514809.nagling            SAM              mriessen        542:37:3 R batch
 514811.nagling            STDIN            justin          00:00:32 R batch
 514815.nagling            latency_test     penzhang               0 Q batch
 514822.nagling            flex_1.dock.csh  xinyu           34:26:46 R batch
 514839.nagling            flex_2.dock.csh  xinyu           31:22:33 R batch
 514856.nagling            flex_5.dock.csh  xinyu           26:33:35 R batch
 514859.nagling            ....1_2.dock.csh xinyu           06:13:43 R batch
 514862.nagling            p0.10            hjli            326:10:5 R batch
 514863.nagling            p0.4             hjli            325:49:5 R batch
 514864.nagling            p0.7             hjli            332:11:4 R batch
 514884.nagling            ...1_p0.0_11.csh xinyu           17:16:57 R batch
 514920.nagling            STDIN            lli             00:34:43 R batch

On seawulf the 'nodes' command shows a list of free nodes

        avail   alloc   down
 nodes:  35      165     25
 wulfie: 35      165     25

Use the man or info command in Unix to get more details of usage for these commands.
You can use PBS commands inside your script. These are usually optional, but can be useful.
There is an example script see [[NAMD on Seawulf]]

 #PBS -l nodes=8:ppn=2
 #PBS -l walltime=08:00:00
 #PBS -N my_job_name
 #PBS -M user@ic.sunysb.edu
 #PBS -o namd.md01.out
 #PBS -e namd.md01.err
 #PBS -V

Using these PBS directives will name the job, the output files etc.
 #PBS -j oe
 #PBS -o pbs.out    
This will join the output and error streams into the output file. 
$PBS_O_WORKDIR is an environment variable that contains the path the script was submitted in. Usually you want to define a specific workdir and use that instead of relying on this variable.

==Advanced Tricks==
Delete all your jobs
 qstat -u sudipto | awk -F. '/sudipto/{print $1}' | xargs qdel
Delete all your queued jobs only. Leaves all runnings jobs alone. 
 qstat -u sudipto | awk -F. '/00 Q /{printf $1" "}' | xargs qdel
 qstat -u sudipto | awk -F. '/ Q   --/{printf $1" " }' | xargs qdel
List all working nodes in the queue
 pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node

 set NODELIST=`pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node`
 foreach node ($NODELIST) 
/usr/local/torque-2.1.6/bin/qsub -l nodes=${NODE} ${HOME}/get.nodes.stats.csh
done