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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Graham,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>As stated in the tutorial the distributed computing functions are intended to distribute workload over different computers running a Torque or SGE batch system: <i>“</i></span><i><span style='font-size:11.5pt;font-family:"Calibri","sans-serif";color:black;background:white'>This tutorial covered how to distribute your computations/workload over multiple computers in a cluster that uses the Torque or SGE batch queue system”. </span></i><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>However, what you could do is make use of Matlab’s parallel processing tools. Matlab allows you to open a pool of so-called ‘workers’ to distribute processing jobs to allowing you to run multiple processes in parallel. Please see </span><a href="http://www.mathworks.nl/help/distcomp/matlabpool.html">http://www.mathworks.nl/help/distcomp/matlabpool.html</a> and <a href="http://www.mathworks.nl/help/matlab/ref/parfor.html">http://www.mathworks.nl/help/matlab/ref/parfor.html</a>.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Once you’ve opened a pool of workers using ‘matlabpool’, you can use ‘parfor’ in the same way as you would use ‘for’ to create a loop that runs all processes in parallel over all four cores. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jim<o:p></o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>Graham Peyton<br><b>Sent:</b> woensdag 26 juni 2013 12:14<br><b>To:</b> fieldtrip@science.ru.nl<br><b>Subject:</b> [FieldTrip] QSUB toolbox on a multi-core computer<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Dear FieldTrip community,<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'>I am trying to carry out an MEG analysis using the qsub distributed computing toolbox. I'm using a quad-core i7 computer, and was hoping that I'd be able to distribute the workload over all four cores. <br><br>I have followed the tutorial below exactly:<br><a href="http://fieldtrip.fcdonders.nl/tutorial/distributedcomputing">http://fieldtrip.fcdonders.nl/tutorial/distributedcomputing</a><o:p></o:p></p></div><div><p class=MsoNormal>The problem I am having is this: I managed to run example 1 (with my own dataset), but I am finding that when I use <span style='font-family:"Courier New"'>qsubcellfun</span>, the function <span style='font-family:"Courier New"'>ft_definetrial</span> is executed <b>sequentially</b> (for each condition), <i>not</i> in <b>parallel</b>. Is there a way I can correct this, so as to parallelize the analysis? Or is the toolbox not designed for multi-core machines? <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>Many thanks,<br><br>Graham Peyton<o:p></o:p></p></div></div></div></div></body></html>