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en:services:application_services:high_performance_computing:running_jobs_slurm:dependencies [2022/03/09 13:07] – created mbodenen:services:application_services:high_performance_computing:running_jobs_slurm:dependencies [2022/03/09 13:40] (current) – [Job Dependencies] mboden
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 +====== Job Dependencies ======
 +Slurm supports dependencies between jobs, allowing users to define simple workflows and pipelines. To create a depenency, you can use the following sbatch flag: 
 +<code>-d, --dependency=<dependency_list></code>
 +where ''dependency_list'' specifies which jobs to depend on and what kind of dependency it is. This is an example of a simple dependency:
 +<code bash>sbatch --dependency=afterok:11536887</code>
 +This will submit a job, which can only start once the job with the ID 11536887 finished successfully.
  
 +A list of possible dependency types can be found in the following table and in the [[https://slurm.schedmd.com/sbatch.html#OPT_dependency|sbatch man-page]].
 +
 +^type^Job runs after...^
 +| after:job_id | job starts or is cancelled |
 +| afterany:job_id | Terminated in any way  |
 +| afternotok:job_id | Terminated non-zero |
 +| afterok:job_id | finished normally |
 +| aftercorr:job_id | After corresponding task in array |
 +| singleton | Only one of a kind may run at a time |
 +
 +Multiple jobs can be specified by appending with a colon as delimiter, e.g. ''-d after:123:124:125''.
 +
 +===== Scripting with Job Dependencies =====
 +Manually creating complex job dependencies on the command line can be cumbersome and error-prone. It is advised to set up scripts to do this task for you. ''sbatch'' has the ''<nowiki>--parsable</nowiki>'' flag to make this task easier: When using this flag, only the job ID will be returned and it can be used to capture the job ID into a variable.
 +
 +===== Examples =====
 +
 +Capture ''sbatch'' output into variable and use it in the next job:
 +<code bash>
 +# submit a first job, extract job id
 +jobid=$(sbatch --parsable job1.sbatch)
 + 
 +# submit a second job with dependency: starts only if the previous job terminates successfully)
 +jobid=$(sbatch --parsable --dependency=afterok:$jobid job2.sbatch)
 + 
 +# submit a third job with dependency: starts only if the previous job terminates successfully)
 +jobid=$(sbatch --parsable --dependency=afterok:$jobid job3.sbatch)</code>
 +
 +----
 +
 +Submit scripts, each with a with dependency on the previous one:
 +<file bash sub_dep.sh>#!/bin/bash
 +
 +ID=$(sbatch --parsable $1)
 +shift
 +for script in "$@"; do
 +  ID=$(sbatch --parsable --dependency=afterany:${ID} $script)
 +done</file>
 +Usage: ''./sub_dep.sh scriptA.sh scriptB.sh scriptC.sh scriptD.sh''