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Job Arrays¶
A job array is a compact representation of many jobs called subjobs. Subjobs share the same job script, and have the same values for all attributes and resources, with the following exceptions:
- each subjob has a unique index, $PBS_ARRAY_INDEX
- job Identifiers of subjobs only differ by their indices
- the state of subjobs can differ (R, Q, etc.)
All subjobs within a job array have the same scheduling priority and schedule as independent jobs. An entire job array is submitted through a single qsub command and may be managed by qdel, qalter, qhold, qrls, and qsig commands as a single job.
Shared Jobscript¶
All subjobs in a job array use the very same single jobscript. Each subjob runs its own instance of the jobscript. The instances execute different work controlled by the $PBS_ARRAY_INDEX variable.
Example:
Assume we have 900 input files with the name of each beginning with "file" (e.g. file001, ..., file900). Assume we would like to use each of these input files with myprog.x program executable, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks (subjobs) - all input files in our example:
$ find . -name 'file*' > tasklist
Then we create a jobscript:
#!/bin/bash
#PBS -A OPEN-00-00
#PBS -q qprod
#PBS -l select=1,walltime=02:00:00
# change to scratch directory
SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/${PBS_JOBID}
mkdir -p $SCRDIR
cd $SCRDIR || exit
# get individual tasks from tasklist with index from PBS JOB ARRAY
TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist)
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input
cp $PBS_O_WORKDIR/myprog.x .
# execute the calculation
./myprog.x < input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
In this example, the submit directory contains the 900 input files, the myprog.x executable, and the jobscript file. As an input for each run, we take the filename of the input file from the created tasklist file. We copy the input file to the local scratch memory /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The myprog.x executable runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x is not multithreaded, then all the jobs are run as single-thread programs in a sequential manner. Due to the allocation of the whole node, the accounted time is equal to the usage of the whole node, while using only 1/16 of the node.
If running a huge number of parallel multicore (in means of multinode multithread, e.g. MPI enabled) jobs is needed, then a job array approach should be used. The main difference, as compared to the previous examples using one node, is that the local scratch memory should not be used (as it is not shared between nodes) and MPI or other techniques for parallel multinode processing has to be used properly.
Submiting Job Array¶
To submit the job array, use the qsub -J command. The 900 jobs of the example above may be submitted like this:
$ qsub -N JOBNAME -J 1-900 jobscript
506493[].isrv5
In this example, we submit a job array of 900 subjobs. Each subjob will run on one full node and is assumed to take less than 2 hours (note the #PBS directives in the beginning of the jobscript file, do not forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit a one-element only array. This is not allowed by PBSPro, but there is a workaround:
$ qsub -N JOBNAME -J 9-10:2 jobscript
This will only choose the lower index (9 in this example) for submitting/running your job.
Managing Job Array¶
Check status of the job array using the qstat command.
$ qstat -a 12345[].dm2
dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[].dm2 user2 qprod xx 13516 1 16 -- 00:50 B 00:02
When the status is B, it means that some subjobs are already running.
Check the status of the first 100 subjobs using the qstat command.
$ qstat -a 12345[1-100].dm2
dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -- |---|---| ------ --- --- ------ ----- - -----
12345[1].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
12345[2].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
12345[3].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:01
12345[4].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --
. . . . . . . . . . .
, . . . . . . . . . .
12345[100].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --
Delete the entire job array. Running subjobs will be killed, queueing subjobs will be deleted.
$ qdel 12345[].dm2
Deleting large job arrays may take a while. Display status information for all user's jobs, job arrays, and subjobs.
$ qstat -u $USER -t
Display status information for all user's subjobs.
$ qstat -u $USER -tJ
For more information on job arrays, see the PBSPro Users guide.
Examples¶
Download the examples in capacity.zip, illustrating the above listed ways to run a huge number of jobs. We recommend trying out the examples before using this for running production jobs.
Unzip the archive in an empty directory on cluster and follow the instructions in the README file-
$ unzip capacity.zip
$ cat README