Multiple job submission
Sometimes users will want to submit large numbers of jobs based on the same job script. Rather than using a script to repeatedly call qsub, a feature known as job arrays now exists to allow the creation of multiple jobs with one qsub command. Additionally, this feature includes a new job naming convention that allows users to reference the entire set of jobs as a unit, or to reference one particular job from the set.
Job arrays are submitted through the -t option to qsub, or by using #PBS -t in your batch script. This option takes a comma-separated list consisting of either a single job ID number, or a pair of numbers separated by a dash. Each of these jobs created will use the same script and will be running in a nearly identical environment.
> qsub -t 0-4 job_script
1098[].hostname
> qstat -t
1098[0].hostname ...
1098[1].hostname ...
1098[2].hostname ...
1098[3].hostname ...
1098[4].hostname ...
Versions of TORQUE earlier than 2.3 had different semantics for the -t argument. In these versions, -t took a single integer number—a count of the number of jobs to be created.
Each 1098[x] job has an environment variable called PBS_ARRAYID, which is set to the value of the array index of the job, so 1098[0].hostname would have PBS_ARRAYID set to 0. This allows you to create job arrays where each job in the array performs slightly different actions based on the value of this variable, such as performing the same tasks on different input files. One other difference in the environment between jobs in the same array is the value of the PBS_JOBNAME variable.
# These two examples are equivalent in TORQUE 2.2
> qsub -t 0-99
> qsub -t 100
# You can also pass comma delimited lists of ids and ranges:
> qsub -t 0,10,20,30,40
> qsub -t 0-50,60,70,80
Running qstat displays a job summary, which provides an overview of the array's state. To see each job in the array, run qstat -t.
The qalter, qdel, qhold, and qrls commands can operate on arrays—either the entire array or a range of that array. Additionally, any job in the array may be accessed normally by using that job's ID, just as you would with any other job. For example, running the following command would run only the specified job:
qrun 1098[0].hostname
The slot limit is a way for administrators to limit the number of jobs from a job array that can be eligible for scheduling at the same time. When a slot limit is used, TORQUE puts a hold on all jobs in the array that exceed the slot limit. When an eligible job in the array completes, TORQUE removes the hold flag from the next job in the array. Slot limits can be declared globally with the max_slot_limit parameter, or on a per-job basis with qsub -t.
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