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Top Forums Shell Programming and Scripting Writing single script with mutiple sbatch parts Post 303026357 by idbemad on Monday 26th of November 2018 07:08:12 AM
Old 11-26-2018
Writing single script with mutiple sbatch parts

Hello,

I wrote several scripts that work with job arrays (sbatch) that look like this:


Code:
#!/bin/bash
#SBATCH --partition=carl.p
#SBATCH --ntasks=4
#SBATCH --time=0-10:00
#SBATCH --mem-per-cpu=48G
#SBATCH --job-name=basic_test
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=
#SBATCH --array=1-48



These scripts all do different things and some need to be finished before other scripts can start.

I already figured out how to write a jobdependency script that times which scripts need to be started and which need to wait until specific scripts are finished. Now I want to know if it is possible to combine all those different scripts into one big script. I want to do this because I dont want to copy all the different scripts everytime i want to use them and I also want to use the same variables in the different scripts so that I only have to define them once. This is just to make everything more user friendly.

I wanted to do something like this



Code:
#!/bin/bash
#SBATCH --partition=carl.p
#SBATCH --ntasks=4
#SBATCH --time=0-10:00
#SBATCH --mem-per-cpu=48G
#SBATCH --job-name=basic_test
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=
#SBATCH --array=1-12      



Here would be the first script that submits 12 jobs only containing the code up to the next SBATCH input...

CODE
CODE 
CODE
...




           #!/bin/bash
           #SBATCH --partition=carl.p
           #SBATCH --ntasks=4
           #SBATCH --time=0-10:00
           #SBATCH --mem-per-cpu=48G
           #SBATCH --job-name=basic_test
           #SBATCH --mail-type=END,FAIL
           #SBATCH --mail-user=
           #SBATCH --array=1-48           
           #SBATCH --dependency:afterok Job_id_of_first_script
  
            Here would be the second script which needs to run the 48 jobs from the second SBATCH input only once

            CODE
            CODE
            CODE
            ...

and so on.

These scripts should all work seperately so I dont want the first SBATCH to start a new SBATCH for the second job everytime. I have not tried anything to do this and I just wanted to know if this is at all possible.

Thanks in advance
 

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SHUNIT2(1)																SHUNIT2(1)

NAME
shunit2 - A unit test framework for shell scripts SYNOPSIS
shunit2 unitfile DESCRIPTION
shUnit2 is a xUnit unit test framework for Bourne based shell scripts, and it is designed to work in a similar manner to JUnit, PyUnit, etc.. If you have ever had the desire to write a unit test for a shell script, shUnit2 can do the job. You can either run shunit2 directly from the commandline and specify the unit file or directly source the shunit2 executable. If you directly execute shunit2 and don't specify a unitfile shunit2 assumes a empty testfile and will return without an error message. EXAMPLE
Simple script to test if 1 equals 1 #! /bin/sh testEquality() { assertEquals 1 1 } # load shunit2 . shunit2 Execute shUnit2 unit tests directly from the commandline shunit2 /path/to/unit/file OPTIONS
shunit2 does not support any commandline options at all. You can either source shunit2 to execute your unit tests or directly run shunit2 as a commandline script. SEE ALSO
For more information see http://code.google.com/p/shunit2/ or have a look at the installed documentation in /usr/share/doc/shunit2/ AUTHOR
shunit2 was written by Kate Ward <kate.ward@forestent.com>. This manpage was written by Ulrich Dangel <mru@spamt.net>. 2.1.6 03/25/2012 SHUNIT2(1)
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