...
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qcat jobID
qcat -e jobID
qtail jobID
qtail -e jobID |
Job submitting
There are several ways jobs can be submitted:
...
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# print file hello.sh
[korisnik@x3000c0s25b0n0:~] $ cat hello.sh
#!/bin/bash
#PBS -N hello
echo "Hello world"
# submit job script
[korisnik@x3000c0s25b0n0:~] $ qsub hello.sh
14572.x3000c0s25b0n0.hsn.hpc.srce.hr
# print directory content
[korisnik@x3000c0s25b0n0:~] $ ls -l
total 5140721
-rw------- 1 korisnik hpc 0 Jun 1 07:44 STDIN.e14571
-rw------- 1 korisnik hpc 12 Jun 1 07:44 STDIN.o14571
-rw------- 1 korisnik hpc 0 Jun 1 08:02 hello.e14572
-rw------- 1 korisnik hpc 12 Jun 1 08:02 hello.o14572
-rw-r--r-- 1 korisnik hpc 46 Jun 1 07:55 hello.sh
# print output file content
[korisnik@x3000c0s25b0n0:~] $ cat hello.o14572
Hello world |
In the case of an interactive session, using the qsub -I option without an input script will open a terminal on the main working node within which we can run commands:
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# hostname on access node
[korisnik@x3000c0s25b0n0:~] $ hostname
x3000c0s25b0n0
# interactive session
[korisnik@x3000c0s25b0n0:~] $ qsub -I -N hello-interactive
qsub: waiting for job 14574.x3000c0s25b0n0.hsn.hpc.srce.hr to start
qsub: job 14574.x3000c0s25b0n0.hsn.hpc.srce.hr ready
# hostname on working node
[korisnik@x8000c0s3b0n0:~] $ hostname
x8000c0s3b0n0 |
In the case of an array of jobs, using the qsub -J X-Y[:Z] option we can submit a given number of identical jobs in the range X to Y with step Z:
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# submit job array
[korisnik@x3000c0s25b0n0:~] $ qsub -J 1-10:2 hello.sh
14575[].x3000c0s25b0n0.hsn.hpc.srce.hr
# print directory content
[korisnik@x3000c0s25b0n0:~] $ ls -l
total 5140744
-rw------- 1 korisnik hpc 0 Jun 1 07:44 STDIN.e14571
-rw------- 1 korisnik hpc 12 Jun 1 07:44 STDIN.o14571
-rw------- 1 korisnik hpc 0 Jun 1 08:02 hello.e14572
-rw------- 1 korisnik hpc 0 Jun 1 08:21 hello.e14575.1
-rw------- 1 korisnik hpc 0 Jun 1 08:21 hello.e14575.3
-rw------- 1 korisnik hpc 0 Jun 1 08:21 hello.e14575.5
-rw------- 1 korisnik hpc 0 Jun 1 08:21 hello.e14575.7
-rw------- 1 korisnik hpc 0 Jun 1 08:21 hello.e14575.9
-rw------- 1 korisnik hpc 12 Jun 1 08:02 hello.o14572
-rw------- 1 korisnik hpc 12 Jun 1 08:21 hello.o14575.1
-rw------- 1 korisnik hpc 12 Jun 1 08:21 hello.o14575.3
-rw------- 1 korisnik hpc 12 Jun 1 08:21 hello.o14575.5
-rw------- 1 korisnik hpc 12 Jun 1 08:21 hello.o14575.7
-rw------- 1 korisnik hpc 12 Jun 1 08:21 hello.o14575.9
-rw-r--r-- 1 korisnik hpc 46 Jun 1 07:55 hello.sh |
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This method is preferred over multiple submissions (e.g. with a for loop) because: - reduces job queue load - each job will compete for resources simultaneously with everyone else in the queue, instead of one after the other
- easier management - modification of all jobs is possible by calling the main (e.g. 14575[]) or individual (e.g. 14575[3]) job identifier
The environment variables defined by PBS during their execution are: - PBS_ARRAY_INDEX - ordinal number of sub-jobs in the job field (e.g. one to nine in the example above)
- PBS_ARRAY_ID - identifier of the main job field
- PBS_JOBID - subjob identifier in the job field
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