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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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DH_INSTALLINIT(1)						     Debhelper							 DH_INSTALLINIT(1)

NAME
dh_installinit - install init scripts and/or upstart jobs into package build directories SYNOPSIS
dh_installinit [debhelperoptions] [--name=name] [-n] [-R] [-r] [-d] [--params] DESCRIPTION
dh_installinit is a debhelper program that is responsible for installing init scripts with associated defaults files, as well as upstart job files into package build directories. It also automatically generates the postinst and postrm and prerm commands needed to set up the symlinks in /etc/rc*.d/ to start and stop the init scripts. FILES
debian/package.init If this exists, it is installed into etc/init.d/package in the package build directory. debian/package.default If this exists, it is installed into etc/default/package in the package build directory. debian/package.upstart If this exists, it is installed into etc/init/package.conf in the package build directory. OPTIONS
-n, --noscripts Do not modify postinst/postrm/prerm scripts. -o, --onlyscripts Only modify postinst/postrm/prerm scripts, do not actually install any init script, default files, or upstart job. May be useful if the init script or upstart job is shipped and/or installed by upstream in a way that doesn't make it easy to let dh_installinit find it. -R, --restart-after-upgrade Do not stop the init script until after the package upgrade has been completed. This is different than the default behavior, which stops the script in the prerm, and starts it again in the postinst. This can be useful for daemons that should not have a possibly long downtime during upgrade. But you should make sure that the daemon will not get confused by the package being upgraded while it's running before using this option. -r, --no-restart-on-upgrade Do not stop init script on upgrade. --no-start Do not start the init script on install or upgrade, or stop it on removal. Only call update-rc.d. Useful for rcS scripts. -d, --remove-d Remove trailing d from the name of the package, and use the result for the filename the upstart job file is installed as in etc/init/ , and for the filename the init script is installed as in etc/init.d and the default file is installed as in etc/default/ . This may be useful for daemons with names ending in d. (Note: this takes precedence over the --init-script parameter described below.) -uparams --update-rcd-params=params -- params Pass params to update-rc.d(8). If not specified, defaults will be passed to update-rc.d(8). --name=name Install the init script (and default file) as well as upstart job file using the filename name instead of the default filename, which is the package name. When this parameter is used, dh_installinit looks for and installs files named debian/package.name.init, debian/package.name.default and debian/package.name.upstart instead of the usual debian/package.init, debian/package.default and debian/package.upstart. --init-script=scriptname Use scriptname as the filename the init script is installed as in etc/init.d/ (and also use it as the filename for the defaults file, if it is installed). If you use this parameter, dh_installinit will look to see if a file in the debian/ directory exists that looks like package.scriptname and if so will install it as the init script in preference to the files it normally installs. This parameter is deprecated, use the --name parameter instead. This parameter is incompatible with the use of upstart jobs. --error-handler=function Call the named shell function if running the init script fails. The function should be provided in the prerm and postinst scripts, before the #DEBHELPER# token. NOTES
Note that this command is not idempotent. dh_prep(1) should be called between invocations of this command. Otherwise, it may cause multiple instances of the same text to be added to maintainer scripts. SEE ALSO
debhelper(7) This program is a part of debhelper. AUTHORS
Joey Hess <joeyh@debian.org> Steve Langasek <steve.langasek@canonical.com> 9.20120909 2012-04-10 DH_INSTALLINIT(1)
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