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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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CHECKBASHISMS(1)					      General Commands Manual						  CHECKBASHISMS(1)

NAME
checkbashisms - check for bashisms in /bin/sh scripts SYNOPSIS
checkbashisms script ... checkbashisms --help|--version DESCRIPTION
checkbashisms, based on one of the checks from the lintian system, performs basic checks on /bin/sh shell scripts for the possible presence of bashisms. It takes the names of the shell scripts on the command line, and outputs warnings if possible bashisms are detected. Note that the definition of a bashism in this context roughly equates to "a shell feature that is not required to be supported by POSIX"; this means that some issues flagged may be permitted under optional sections of POSIX, such as XSI or User Portability. In cases where POSIX and Debian Policy disagree, checkbashisms by default allows extensions permitted by Policy but may also provide options for stricter checking. OPTIONS
--help, -h Show a summary of options. --newline, -n Check for "echo -n" usage (non POSIX but required by Debian Policy 10.4.) --posix, -p Check for issues which are non POSIX but required to be supported by Debian Policy 10.4 (implies -n). --force, -f Force each script to be checked, even if it would normally not be (for instance, it has a bash or non POSIX shell shebang or appears to be a shell wrapper). --extra, -x Highlight lines which, whilst they do not contain bashisms, may be useful in determining whether a particular issue is a false posi- tive which may be ignored. For example, the use of "$BASH_ENV" may be preceded by checking whether "$BASH" is set. --version, -v Show version and copyright information. EXIT VALUES
The exit value will be 0 if no possible bashisms or other problems were detected. Otherwise it will be the sum of the following error val- ues: 1 A possible bashism was detected. 2 A file was skipped for some reason, for example, because it was unreadable or not found. The warning message will give details. SEE ALSO
lintian(1). AUTHOR
checkbashisms was originally written as a shell script by Yann Dirson <dirson@debian.org> and rewritten in Perl with many more features by Julian Gilbey <jdg@debian.org>. DEBIAN
Debian Utilities CHECKBASHISMS(1)
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