How to Run a PBS Batch Job
The following information is available regarding using PBS
on the Particle Physics PC farm:
General Information and Examples
To run a batch job through PBS, you first create a PBS script. The script
specifies, among other things, the number of cpus,
the amount of memory,
and the length of time you're requesting. Each system has additional resources
that you can request.
When a batch job starts execution, a number of environment variables are predefined,
Variables defined on the execution host.
Variables exported from the submission host with
-v (selected variables) and -V (all variables).
Variables defined by PBS.
The following reflect the environment where the user ran qsub:
PBS_O_HOST The host where you ran the qsub command.
PBS_O_LOGNAME Your user ID where you ran qsub.
PBS_O_HOME Your home directory where you ran qsub.
PBS_O_WORKDIR The working directory where you ran qsub.
These reflect the environment where the job is executing:
PBS_ENVIRONMENT Set to PBS_BATCH to indicate the job is a batch job, or
to PBS_INTERACTIVE to indicate the job is a PBS interactive job.
PBS_O_QUEUE The original queue you submitted to.
PBS_QUEUE The queue the job is executing from.
PBS_JOBID The job's PBS identifier.
PBS_JOBNAME The job's name.
PBS Resources Resource_List.mem = 256mb
Resource_List.cput = 08:00:00
Resource_List.ncpus = 1
Resource_List.neednodes = 1:ppn=1
Resource_List.nice = 10
Resource_List.walltime = 72:00:00
PBS directives are specified as comments in the script. In particular,
all lines beginning with #PBS are PBS directives. After the PBS
directives is the body of the script -- commands which are executed when
the script runs. Here are samples PBS script.
To submit the above script to PBS, you use the qsub
command. For instance, if the script were called myscript you'd
submit it using
physdsk2 560> qsub myscript
The second line is the job identifier returned by PBS, and indicates that
the script has been accepted.
PBS is configured at the PC farm so that you are not required to be logged into
the system you want to submit a job to. For example, you could submit a
job from physdsk1 or physdsk2 .
You can submit a job to a specific PBS server by specifying the server host name
for that system. For example:
physdsk2 561> qsub -q M@eio09 myscript
This command submitted a job from physdsk2 to eio33 .
You can specify the number of CPUs your job needs (-l ncpus=),
memory (-l mem=), and the maximum wall clock time (-l walltime=).
These numbers should not exceed the queue limits. If you do not specify
any values, the default values associated with the queue are used (currently,
1 CPU, 8 hours and nice=10).
- By default, PBS executes your job from your home directory. However, you
can use the environment variable PBS_O_WORKDIR to change to the
directory where you submitted your job, since PBS sets this variable to
the directory from which you issued the 'qsub' command.
The "-V" option can be used to export all environment variables from the
submitting shell to your PBS job.