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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:black'>Hi Tyler,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Are you running this on the SCCN cluster or your own cluster? Could you tell me what command you are using to run amica in matlab, and if it is your own cluster setup, what mpirun or mpiexec command is running, whether it is sge or torque and what if any qsub script is being run?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Also the first lines of the stdout generated by Amica where it identifies the processes and their respective nodes …<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>I wonder if you are actually running multiple (overlapping) copies of the same run on several nodes, as can happen with the mpirun commands in some environment setups, instead of having the processes run in concert and communicating.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Jason<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><div><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"'> eeglablist [mailto:eeglablist-bounces@sccn.ucsd.edu] <b>On Behalf Of </b>Tyler Grummett<br><b>Sent:</b> Monday, July 24, 2017 9:00 AM<br><b>To:</b> EEGLABLIST<br><b>Subject:</b> [Eeglablist] Running AMICA in a super-computer<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div id=divtagdefaultwrapper><p><span style='font-family:"Calibri","sans-serif";color:black'>Dear eeglab,<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>Recently Im facing a problem when running multiple AMICAs in a super-computer at once, where I get the following error:<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:red'>...</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'> iter 258 lrate = 1.0000000000 LL = -0.0238247322 nd = 0.0001777274, D = 0.89129E-01 0.89129E-01 ( 33.34 s, 182.8 h)</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'> iter 259 lrate = 1.0000000000 LL = -0.0238213053 nd = 0.0001768634, D = 0.89103E-01 0.89103E-01 ( 34.18 s, 187.4 h)</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'> iter 260 lrate = 1.0000000000 LL = -0.0238178712 nd = 0.0001762253, D = 0.89076E-01 0.89076E-01 ( 33.08 s, 181.4 h)</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>forrtl: Permission denied</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>forrtl: severe (28): CLOSE error, unit 19, file "Unknown"</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>Image PC Routine Line Source </span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 00000000010D4003 Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 00000000010D1A6D Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 0000000000441780 Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 0000000000419E08 Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 00000000004021DE Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 000000000118C1A4 Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:red'>amica15ub 00000000004020C1 Unknown Unknown Unknown</span><span style='font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>However, this error doesn the error doesnt generate an error in matlab so it tries to proceed forward and uses the ICA weights from the most recent iteration. Obviously this isnt ideal, as AMICA requires a lot of iterations to get good ICs.<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>Does anyone have any idea how to fix this or find a work around? I can confirm that there are no jobs using the same temporary file, temporary output folder, or any of the functions that are run in AMICA. They are all copied to their own folder and run independently. At least thats what I hope is happening.<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>Im running out of things to try.<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>Regards,<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'>Tyler<o:p></o:p></span></p><p><span style='font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><div id=Signature><div name=divtagdefaultwrapper><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>************************* <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Tyler Grummett ( BBSc, BSc(Hons I))</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>PhD Candidate</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Brain Signals Laboratory</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Flinders University</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Rm 5A301</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Ext 66125</span></i><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></body></html>