Difference between revisions of "Job submission"

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(Created page with "__NOTOC__ == Command line == bsub -n 4 -W 4:00 -R "rusage[mem=4096]" echo hello Command line advisor == Job script == #!/bin/bash #BSUB -n 24 # 24 c...")
 
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__NOTOC__
 
__NOTOC__
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== Basic job submission ==
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A basic BSUB job submission command consists of three parts:
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{| style="color: black;"
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|-
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| style="width: 50px; background: #BFE5D9; text-align: center;"| bsub
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| style="width: 100px; background: #B2D9EA;text-align: center; "| LSF options
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| style="width: 50px; background: #FFBDAF; text-align: center"| job
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|}
  
== Command line ==
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# The BSUB executable command
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# LSF options requesting resources and defining job-related options
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# A job to be submitted
  
bsub -n 4 -W 4:00 -R "rusage[mem=4096]" echo hello
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Here is an example:
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{| style="color: black;"
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|-
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| style="width: 50px; background: #BFE5D9; text-align: center;"| bsub  
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| style="width: 250px; background: #B2D9EA;text-align: center; "| -n 4 -W 4:00 -R "rusage[mem=4096]"
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| style="width: 150px; background: #FFBDAF; text-align: center"| "python myscript.py"
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|}
  
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Let's start from the third part, a job can be either
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{| class="wikitable"
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|-
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| a single Linux command || cmd
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|-
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| a program with its path || /path/to/myprogram
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|-
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| a command or program with its arguments || cmd arg1 arg2
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|-
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| multiple commands || "cmd1 ; cmd2"
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|-
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| piped command || "cmd1 | cmd2"
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|}
 
Command line advisor
 
Command line advisor
  

Revision as of 15:43, 20 January 2021

Basic job submission

A basic BSUB job submission command consists of three parts:

bsub LSF options job
  1. The BSUB executable command
  2. LSF options requesting resources and defining job-related options
  3. A job to be submitted

Here is an example:

bsub -n 4 -W 4:00 -R "rusage[mem=4096]" "python myscript.py"

Let's start from the third part, a job can be either

a single Linux command cmd
a program with its path /path/to/myprogram
a command or program with its arguments cmd arg1 arg2
multiple commands "cmd1 ; cmd2"
piped command cmd2"

Command line advisor

Job script

#!/bin/bash
#BSUB -n 24                     # 24 cores
#BSUB -W 8:00                   # 8-hour run-time
#BSUB -R "rusage[mem=4000]"     # 4000 MB per core
cd /path/to/execution/folder
command arg1 arg2
bsub < job_script.bsub

Interactive session

bsub -n 4 -W 4:00 -R "rusage[mem=4096]" -Is bash