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Top Forums Shell Programming and Scripting Creating script with multiple job arrays Post 303026243 by idbemad on Thursday 22nd of November 2018 08:39:22 AM
Old 11-22-2018
Creating script with multiple job arrays

Hello everyone,

First of all this is my first post and im fairly new to working with Unix and creating scripts etc. so there will probably be wrong phrases used.

Lets get to my questions.

I have multiple scripts that submit Slurms/Jobs to the cluster starting like this and doing certain tasks:

Code:
#!/bin/bash
#SBATCH --partition=
#SBATCH --ntasks=
#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=1-14

...


I have to run multiple of those scripts AFTER all the Slurms from the preceeding job are finished. Now I want to write a script that does exactly that. I already tried something like this:

Code:
#!/bin/bash

sbatch ~/testscript1.sh

wait

sbatch ~/testscript2.sh


the problem seems to be that the skript thinks that testscript1.sh is done as soon as it submitted all the slurms in the array to the server and then it starts testscript2.sh. This leads to problems because testscript2.sh works with some files that are only created when the submitted slurms from testscript1.sh are done.

Thank you for your help

Last edited by Scrutinizer; 11-22-2018 at 09:53 AM.. Reason: code tags
 

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SERVICE(8)						    BSD System Manager's Manual 						SERVICE(8)

NAME
service -- control (start/stop/etc.) or list system services SYNOPSIS
service -e service -R service [-v] -l | -r service [-v] <rc.d script> start|stop|etc. DESCRIPTION
The service command is an easy interface to the rc.d system. Its primary purpose is to start and stop services provided by the rc.d scripts. When used for this purpose it will set the same restricted environment that is in use at boot time (see below). It can also be used to list the scripts using various criteria. The options are as follows: -e List services that are enabled. The list of scripts to check is compiled using rcorder(8) the same way that it is done in rc(8), then that list of scripts is checked for an "rcvar" assignment. If present the script is checked to see if it is enabled. -R Restart all enabled local services. -l List all files in /etc/rc.d and the local startup directories. As described in rc.conf(5) this is usually /usr/local/etc/rc.d. All files will be listed whether they are an actual rc.d script or not. -r Generate the rcorder(8) as in -e above, but list all of the files, not just what is enabled. -v Be slightly more verbose ENVIRONMENT
When used to run rc.d scripts the service command sets HOME to / and PATH to /sbin:/bin:/usr/sbin:/usr/bin which is how they are set in /etc/rc at boot time. EXIT STATUS
The service utility exits 0 on success, and >0 if an error occurs. EXAMPLES
The following are examples of typical usage of the service command: service named status service -rv The following programmable completion entry can be use in bash(1) for the names of the rc.d scripts: _service () { local cur cur=${COMP_WORDS[COMP_CWORD]} COMPREPLY=( $( compgen -W '$( service -l )' -- $cur ) ) return 0 } complete -F _service service SEE ALSO
bash(1) (ports/shells/bash), rc.conf(5), rc(8), rcorder(8) HISTORY
The service utility first appeared in FreeBSD 7.3. AUTHORS
This manual page was written by Douglas Barton <dougb@FreeBSD.org>. BSD
December 11, 2012 BSD
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