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parallel_matlab [2011/08/09 5:09 pm PDT]
John Colby created
parallel_matlab [2011/08/09 5:16 pm PDT] (current)
John Colby
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   * SGE environment variables [[https://​wiki.duke.edu/​display/​SCSC/​SGE+Env+Vars|www]]   * SGE environment variables [[https://​wiki.duke.edu/​display/​SCSC/​SGE+Env+Vars|www]]
  
-At the UNIX command prompt, MATLAB can be run in a batch mode by piping in a script like <wrap box>​matlab -nodisplay < myscript.m</​wrap>​.+At the UNIX command prompt, MATLAB can be run in a batch mode by piping in a script like ''​<wrap box>​matlab -nodisplay < myscript.m</​wrap>​''​.
  
 However, to run a set of parallel jobs, we need some way to pass in the current job index. MATLAB doesn'​t provide a way of doing this, itself, but we //can// get access to unix environment variables. The SGE cluster manager already stores the job array task ID as ''​SGE_TASK_ID'',​ so we are all set. However, to run a set of parallel jobs, we need some way to pass in the current job index. MATLAB doesn'​t provide a way of doing this, itself, but we //can// get access to unix environment variables. The SGE cluster manager already stores the job array task ID as ''​SGE_TASK_ID'',​ so we are all set.
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 </​file>​ </​file>​
  
-Submit the job array with ''​fsl_sub''​ or a similar ''​qsub''​ wrapper: <wrap box>​fsl_sub -t jobarray.txt</​wrap>​+Submit the job array with ''​fsl_sub''​ or a similar ''​qsub''​ wrapper: ​''​<wrap box>​fsl_sub -t jobarray.txt</​wrap>​''​
  
 Check the output logs to make sure everything is working: Check the output logs to make sure everything is working:
parallel_matlab.txt ยท Last modified: 2011/08/09 5:16 pm PDT by John Colby
 
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