TORQUE options#

TORQUE Submission Flags: common and useful directives#

Below is a list of the most common and useful directives.

Option	System type	Description	Jobscript comment
-k	All	Send "stdout" and/or "stderr" to your home directory when the job runs	#PBS -k o or #PBS -k e or #PBS -koe
-l	All	Precedes a resource request, e.g., processors, wallclock
-M	All	Send an e-mail message to an alternative e-mail address	#PBS -M me@mymail.be
-m	All	Send an e-mail when a job begins execution, ends, or aborts	#PBS -m b or #PBS -m be or #PBS -m ba
mem	Shared Memory	Memory & Specifies the amount of memory you need for a job.	#PBS -I mem=90gb
mpiproces	Clusters	Number of processes per node on a cluster. This usually equals the number of processors on a node.	#PBS -l mpiprocs=4
-N	All	Give your job a unique name	#PBS -N galaxies1234
-ncpus	Shared Memory	The number of processors to use for a shared memory job.	#PBS ncpus=4
-r	All	Control whether or not jobs should automatically re-run from the start if the system crashes or reboots.	#PBS -r n or #PBS -r y
select	Clusters	Number of compute nodes to use. Usually combined with the mpiprocs directive	#PBS -l select=2
-V	All	Ensure that the environment in which the job runs is the same as the one in which it was submitted	#PBS -V
Walltime	All	Maximum time a job can run before being stopped. Format is HH:MM:SS	#PBS -l walltime=12:00:00

Environment Variables in Batch Job Scripts#

TORQUE-related environment variables in batch job scripts.

# Using PBS - Environment Variables:
# When a batch job starts execution, a number of environment variables are
# predefined, which include:
#
#      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.

IMPORTANT!! All PBS directives MUST come before the first line of executable code in your script, otherwise they will be ignored.

When a batch job is started, a number of environment variables are created that can be used in the batch job script. A few of the most commonly used variables are described here.

Variable	Description
PBS_ENVIRONMENT	set to PBS_BATCH to indicate that the job is a batch job; otherwise, set to PBS_INTERACTIVE to indicate that the job is a PBS interactive job.
PBS_JOBID	the job identifier assigned to the job by the batch system. This is the same number you see when you do qstat.
PBS_JOBNAME	the job name supplied by the user
PBS_NODEFILE	the name of the file that contains the list of the nodes assigned to the job . Useful for Parallel jobs if you want to refer the node, count the node etc.
PBS_QUEUE	the name of the queue from which the job is executed
PBS_O_HOME	value of the HOME variable in the environment in which qsub was executed
PBS_O_LANG	value of the LANG variable in the environment in which qsub was executed
PBS_O_LOGNAME	value of the LOGNAME variable in the environment in which qsub was executed
PBS_O_PATH	value of the PATH variable in the environment in which qsub was executed
PBS_O_MAIL	value of the MAIL variable in the environment in which qsub was executed
PBS_O_SHELL	value of the SHELL variable in the environment in which qsub was executed
PBS_O_TZ	value of the TZ variable in the environment in which qsub was executed
PBS_O_HOST	the name of the host upon which the qsub command is running
PBS_O_QUEUE	the name of the original queue to which the job was submitted
PBS_O_WORKDIR	the absolute path of the current working directory of the qsub command. This is the most useful. Use it in every job script. The first thing you do is, cd $PBS_O_WORKDIR after defining the resource list. This is because, pbs throw you to your $HOME directory.
PBS_VERSION	Version Number of TORQUE, e.g., TORQUE-2.5.1
PBS_MOMPORT	active port for mom daemon
PBS_TASKNUM	number of tasks requested
PBS_JOBCOOKIE	job cookie
PBS_SERVER	Server Running TORQUE