Difference between revisions of "Jobscript"

Latest revision as of 08:23, 4 September 2019

General

A jobscript can be used to submit the job you wish to execute to a Batch-Scheduler. It is very similar to a sh-file and generally uses the same format, but is more powerful. Besides shell commands, you can use so-called magic cookies, e.g. #BSUB for LSF systems. This allows you to specify a lot of parameters, e.g. the time and memory your application requires or - if your code runs in parallel - the number of compute slots to employ.

Structure

Like a regular sh-file, your jobscript should start with a shebang (#!), e. g. in case you are using zsh:

#!/usr/bin/env zsh

Usually, this first line is followed by several directives using magic cookies, that are explained in more depth in the next section. The third part of a jobscript consists of shell commands, for example, to change to your working directory, to load the needed Modules and to execute your application.

Magic Cookies

The magic cookie differs from Batch-Scheduler to Batch-Scheduler. Click here to figure out which one you are going to need. Depending on your batch system, these pages provide more information on how to use magic cookies in your jobscript: LSF, SLURM, Torque.

One advantage of jobscripts is that the parameters that are prefixed with magic cookies are treated like comments. So you can run your jobscript as an sh-file without the Batch-Scheduler and if that works, still adjust and correct the lines with magic cookies destined for the Batch-Scheduler.

Job Submission

Depending on your Batch-Scheduler, proceed to one of the links below to find out how to submit your job to a batch system that controls the resources for computation: LSF, SLURM, Torque.

Note that all incoming jobs (defined in a jobscript) are added to a queue. The Batch-Scheduler decides at what time a certain job is executed. The waiting time depends on various factors, e. g. the time and memory you asked for in your jobscript. The rule of thumb is: the more resources your job needs, the longer it will be queued.

You can always check the current status of your submitted jobs and their ids with shell commands that are also explained on the pages linked above.

References

Jobscript examples

@@ Line 1: / Line 1: @@
+[[Category:Basics]]
 == General ==
-A jobscript can be used to submit the job you wish to execute to a batch system. It is very similar to a [[sh-file]] and generally uses the same format, but is more powerful. Besides shell commands, you can put the so called magic cookie #BSUB. This allows you to specify a lot of parameters, e. g. the time and memory your application requires or - if your code runs in parallel - the number of compute slots to employ.
+A jobscript can be used to submit the job you wish to execute to a [[Batch-Scheduler]]. It is very similar to a [[sh-file]] and generally uses the same format, but is more powerful. Besides shell commands, you can use so-called magic cookies, e.g. #BSUB for [[LSF]] systems. This allows you to specify a lot of parameters, e.g. the time and memory your application requires or - if your code runs in parallel - the number of compute slots to employ.
-== #BSUB Usage ==
+__TOC__
-To use the magic cookie, start a new line in your script with "#BSUB". Following that, you can put one of the parameters shown below, where the word written in <...> should be replaced with a value.
-Basic settings:
+== Structure ==
-{| class="wikitable" style="width: 40%;"
-| Parameter || Function
-|-
-| -J <name> || job name
-|-
-| -o <path> || path to the file where the job output is written
-|-
-| -e <path> || path to the file for the job error output
-|}
-Requesting resources:
+Like a regular [[sh-file]], your jobscript should start with a shebang (#!), e. g. in case you are using [[Shell|zsh]]:
-{| class="wikitable" style="width: 60%;"
+<syntaxhighlight lang="zsh">
-| Parameter || Function || Default
+#!/usr/bin/env zsh
-|-
+</syntaxhighlight>
-| -W <runlimit> || runtime limit in the format [hour:]minute; once the time specified is up, the job will be killed by the [[scheduler]] || 00:15
-|-
-| -M <memlimit> || memory limit per process in MB || 512
-|-
-| -S <stacklimit> || limit of stack size per process in MB || 10
-|}
-Parallel programming (read more [[Parallel programming|here]]):
+Usually, this first line is followed by several directives using magic cookies, that are explained in more depth in the next section.
-{| class="wikitable" style="width: 60%;"
+The third part of a jobscript consists of shell commands, for example, to change to your working directory, to load the needed [[Modules]] and to execute your application.
-| Parameter || Function
-|-
-| -a openmp || start a parallel job for a shared-memory system
-|-
-| -n <num_threads> || number of threads to execute OpenMP application with
-|-
-| -a openmpi || start a parallel job for a distributed-memory system
-|-
-| -np <num_procs> || number of processes to execute MPI application with
-|}
-The big advantage of jobscripts is that the parameters that are prefixed with "#BSUB" are treated just like command line arguments. By setting them inside your jobscript already, it's easier to adjust them or look them up later.
+== Magic Cookies ==
+The magic cookie differs from [[Batch-Scheduler]] to Batch-Scheduler. Click [[Schedulers|here]] to figure out which one you are going to need.
+Depending on your batch system, these pages provide more information on how to use magic cookies in your jobscript: [[LSF#.23BSUB_Usage|LSF]], [[SLURM#.23SBATCH_Usage|SLURM]], [[Torque]].
+One advantage of jobscripts is that the parameters that are prefixed with magic cookies are treated like comments. So you can run your jobscript as an [[sh-file]] without the [[Batch-Scheduler]] and if that works, still adjust and correct the lines with magic cookies destined for the [[Batch-Scheduler]].
 == Job Submission ==
-This command submits your job to a batch system that controls the resources for computation.
+Depending on your [[Schedulers|Batch-Scheduler]], proceed to one of the links below to find out how to submit your job to a batch system that controls the resources for computation:
+[[LSF#Job_Submission|LSF]], [[SLURM#Job_Submission|SLURM]], [[Torque#Job_Submission|Torque]].
- $ bsub < jobscript.sh
-Note that all incoming jobs (defined in a jobscript) are added to a queue. When to run a job is decided by the [[scheduler]]. The waiting time depends on various factors, e. g. the time and memory you asked for in your jobscript. The rule of thumb is: the more resources your job needs, the longer it will be queued.
-You can always check the current status (pend or run) of your submitted jobs and their ids. with the following shell command. Once your jobs have finished, the command will print "No unfinished jobs found".
+Note that all incoming jobs (defined in a jobscript) are added to a queue. The [[Batch-Scheduler]] decides at what time a certain job is executed. The waiting time depends on various factors, e. g. the time and memory you asked for in your jobscript. The rule of thumb is: the more resources your job needs, the longer it will be queued.
- $ bjobs
+You can always check the current status of your submitted jobs and their ids with shell commands that are also explained on the pages linked above.
-In order to remove a job that you submitted, you can type this command:
+== References ==
- $ bkill <job_id>
+[[jobscript-examples|Jobscript examples]]