Running Arrays on PBS Professional


If you are intending to run the same program with the different input files, it is best you use Jobs Array instead of creating separate programs for the input files which is tedious. It is very easy

Amending the Submission Scripts (Part 1)

To create an arrays jobs, you have to use the -J option on the PBS Scripts. For 10 sub-jobs, you do the following

#PBS -J 1-10

Amending the Submission Scripts (Part 2)

If your input files are concatenated with a running number. For example, if your input file is data1.gjf, data2.gjf, data3.gjf, data4.gjf, data5.gjf ….. data10.gjf

inputfile=data$PBS_ARRAY_INDEX.gjf

Submitting the Jobs

a. To submit the jobs, just

% qsub yoursubmissionscript.pbs

Checking Jobs

b. You will notice that after you qstat, you will notice that your jobs bas a “B”

% qstat -u user1
544198[].node1 Gaussian-09e user1 0 B q32

You have to do a “-t” or “-Jt”

% qstat -t 544198[]

% qstat -t 544198[]
Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
544198[].node1 Gaussian-09e user1 0 B q32
544198[54].node1 Gaussian-09e user1 00:40:21 R q32
544198[55].node1 Gaussian-09e user1 00:15:25 R q32

To delete the Sub Jobs

% qdel "544198[5]"

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