Faculty for Chemistry and Pharmacy - Group of Prof. Zipse

Commands for the PBS Queueing System

The PBS queueing system integrates all computers in the CIP-F room into one compute cluster. PBS schedules and executes jobs across all of the cluster nodes. Jobs can be submitted into the queueing systems from any node of the cluster. Important PBS commands are:

gives an overview over jobs running on the cluster in a simple output format:

Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
1201.cicum81     Diani-Kat_Isobu  c1165            126:46:0 R long            
1227.cicum81     Didma-Kat_SiMe3  c1165            80:42:06 R long            
1242.cicum81     Benzh_AllylTMS_  c1165            61:18:29 R long            
1250.cicum81     py50ax           zipse            01:34:42 R long            
1251.cicum81     py51a            zipse            01:25:50 R long            
1252.cicum81     py51b            zipse            01:19:16 R long            

The first column designated with Job id displays a unique identification number for each of the jobs such as "1201.cicum81". This job carries the identification number "1201" and was submitted from node "cicum81". An additional name provided by the user on submit time is displayed in the second column designated Name. Only the first 15 characters of the name are shown. The third column lists the job's owner. The fourth column Time Use lists the elapsed CPU time for each of the jobs in the format hh:mm:ss. The fifth column S describes the status of a particular job using "R" for running jobs and "Q" for jobs that are queued and waiting. The last column Queue describes the type of queue the jobs are running in. Currently, there is a "long" queue available for jobs exceeding 30 min CPU time and a "short" queue for shorter jobs. In case no queue is selected explicitly, the "long" queue is chosen by default.

qstat -n
provides the same basic information as before and adds the requested memory and requested CPU time (if set by the user on submit time) as well as the name of the node allocated to a particular job.

                                                            Req'd  Req'd   Elap
Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
1201.cicum81.cu c1165    long     Diani-Kat_  16420  --  --    --  336:0 R 127:0

In this particular example the job 1201 is running on cluster node "cicum86".

qstat -f
provides the full information for each job. The wealth of information provided by this option is rarely necessary (or even helpful).

qsub file-name
submits a command file named file-name for execution into the PBS queueing system. A command file can contain both commmands for the queueing systems as well as an input file for a computational chemistry package. An example for running a HF/6-31G(d) single point calculation with Gaussian 03 (g03) can be found here.

qsub -l nodes=node-name file-name
submits a command file named file-name for execution on a particular cluster node named node-name. This can be particularly helpful for queueing a sequence of jobs that have to execute one after the other.

qsub -q long file-name
submits the command file file-name into the "long" queue. This only makes sense if the queue has not been specified explicitly already in the command file itself.

qdel job-id
deletes the job with job id job-id from execution/the waiting list.

pbsnodes -a
gives an overview over the status of all nodes of the compute cluster.

Additional information is available in the PBS manual pages.