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doku:job_arrays [2014/05/28 11:15] – irdoku:job_arrays [2014/06/12 14:48] – ir
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 ====== Job arrays ====== ====== Job arrays ======
  
-Job arrays are sets of similar but **independent** jobs.  Submit sets of similar and independent “tasks”: +Job arrays are sets of similar but **independent** jobs that are submitted. 
-     *''qsub -t 1-500:1 example_3.sge'' submits 500 instances of the same script+ 
 +=== Example: BLAST === 
 +**B**asic **L**ocal **A**lignment **S**earch **T**ool (BLAST; an algorithm for comparing biological sequence information) 
 + 
 +     *submit 500 instances of the same script
      *each instance (“task”) is executed independently      *each instance (“task”) is executed independently
      *all instances subsumed with a single job ID      *all instances subsumed with a single job ID
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      *task numbering scheme: ''-t <first>-<last>:<stepsize>''      *task numbering scheme: ''-t <first>-<last>:<stepsize>''
      *related: ''$SGE_TASK_FIRST,$SGE_TASK_LAST,$SGE_TASK_STEPSIZE''      *related: ''$SGE_TASK_FIRST,$SGE_TASK_LAST,$SGE_TASK_STEPSIZE''
 +
 +''qsub example_3.sge'' 
      
-Example: 
 <code> <code>
 #$ -cwd #$ -cwd
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 ### #$ -pe mpich 12 ### #$ -pe mpich 12
 ### ###
-### set first and last task_id and stepwidth of array tasks. stepwidth should be identical with the+### set first and last task_id and stepwidth of array tasks.  
 +### stepwidth should be identical with the
 ### number of jobs per node  ### number of jobs per node 
 #$ -t 1-18:3 #$ -t 1-18:3
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 #$ -N job_array_with_multilple single tasks on one node #$ -N job_array_with_multilple single tasks on one node
 #$ -pe mpich <N> #$ -pe mpich <N>
-### set first and last task_id and stepwidth of array tasks. stepwidth should be identical with the+### set first and last task_id and stepwidth of array tasks.  
 +### stepwidth should be identical with the
 ### number of jobs per node  ### number of jobs per node 
 #$ -t 1-18:3 #$ -t 1-18:3