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Batch Jobs

A batch job is simply a set of commands grouped in a single file which are to be executed on a node or set of nodes assigned to the job by the scheduler. Below is an example batch job which contains a single command hostname. This command prints out the name of the host running the command.

tres-l1:pwolinsk:$ cat hostname.pbs 

You can use the qsub command to submit this job to the queue. Without any additional parameters to the qsub command the scheduler will select the default parameters (i.e. default queue, walltime, number of nodes and number of cores).

tres-l1:pwolinsk:$ qsub hostname.pbs

When the job finishes, the output and error messages from the job will be written to new files ending in .o<JOBID> for output and .e<JOBID> for error messages.

tres-l1:pwolinsk:$ ls -ltr |tail -3
-rw-rw-r--   1 pwolinsk pwolinsk       9 Sep 19 10:16 hostname.pbs
-rw-------   1 pwolinsk pwolinsk     266 Sep 19 10:18 hostname.pbs.o283319
-rw-------   1 pwolinsk pwolinsk       0 Sep 19 10:18 hostname.pbs.e283319
tres-l1:pwolinsk:$ cat hostname.pbs.o283319 
PBS Job Statistics:

PBS Input:

PBS Job ID: 283319.torque
Resource List: walltime=00:30:00
Resources Used: cput=00:00:00,mem=0kb,vmem=0kb,walltime=00:00:00
Queue Name: q30m32c
Program Return Code: 0
Head Node:
nnodes= 1 ncores= 1 njobs=1

The output in hostname.pbs.o283319 shows the output of the hostname command followed by the batch job scipt and accounting information from the scheduler. It shows that the job was submitted with a 30 minute walltime into queue q30m32c, and 1 core on 1 node was requested. To specify different values for these parameters we you can pass flags to the qsub command:

tres-l1:pwolinsk:$ qsub -q q06h32c -l walltime=1:00 -l nodes=1:ppn=32 hostname.pbs

The command above submitted the same job to the q06h32c queue with a walltime of 1 minute requesting all 32 cores on 1 node. Alternatively instead of passing these flags to the qusb command any line in the pbs script which starts with #PBS will be passed in as a parameter to qsub. Submitting the modified hostname.pbs script below with qsub without any flags on the command line will have the identical result

tres-l1:pwolinsk:$ cat hostname.pbs
#PBS -q q06h32c
#PBS -l walltime=1:00
#PBS -l nodes=1:ppn=32

tres-l1:pwolinsk:$ qsub hostname.pbs
batch.txt · Last modified: 2020/09/21 21:07 by root