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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 Joseph,<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'>It seems to be getting confused in trying to automatically set up the binary filename (full path) and the MPI bin directory location … referencing “dreamio4 …” when it tries to run the run the binary, seeming missing a beginning “/”. First off, have you verified that the binary runs on the command line with one of the sample input.param and datafiles?<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'>If the binary runs standalone (see amica webpage), then you might try bypassing the beginning section of runamica12.m and setting:<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'> MPI_BIN = <full path of your mpich2 bin directory><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> AMBIN = <amica binary file name with full path><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'>And for running on the cluster, it’s best use a filename, and specify the number of channels with ‘num_chans’, and output directory with ‘outdir’.<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'>It also seems to be finding a “make” parallel environment and trying to use openmpi. Make is not really a supported parallel environment—it was added as a workaround for a cluster at UCLA and I thought it was unique to that cluster. You should be able to query sge to tell you the available parallel environments with:<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'> $ qconf –spl<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'>Ideally you would have mpich2 installed, and a parallel environment called “mpich”, or <pe_name> set up to use it. You can check the pe setup with “qconf –sp <pe_name>”. If you have a valid parallel environment set up and named, you can add the matlab command line keyword:<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'> >> runamica12( ‘/home/me/mydata.fdt’, ‘num_chans’, EEG.nbchan, ‘outdir’, ‘/home/me/myoutput/’…, ‘use_pe’, ‘<pe_name>’, …);<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'>It has also worked on openmpi installations (orte, as opposed to mpich), but may not work on all openmpi.<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'>Besides the parallel environment, and the path names being set up correctly, you need to have a queue set up. You should be able to see a list of queues (and available slots) with:<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'> $ qstat –g c<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'>Or just a list of queues with “qconf –sql”. Then with a queue name, you can add the matlab command line keyword,<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'> >> runamica12( ‘/home/me/mydata.fdt’, ‘num_chans’, EEG.nbchan, ‘outdir’, ‘/home/me/myoutput/’ …, ‘use_queue’, ‘<queue_name>’, …);<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'>To set the number of processors to use (your queue must have this number of slots available to run the job), use the keyword,<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'> >> runamica12( …., ‘numprocs’, 16, …);<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'>To get 16 slots/cores for example.<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'>If it successfully submits a job, it will give you a job id number in the immediate matlab output. You can use “qstat” to check the job status, either “qw” for queue wait, or “r” for running. It should put a file in your home directory called qsub.sh.o<jobid>, which contains all the output, and a similar file containing any error output, in addition to the output saved in the output directory specified by the ‘outdir’ keyword.<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'>Let me know if none of that helps.<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><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><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"'> Makoto Miyakoshi [mailto:mmiyakoshi@ucsd.edu] <br><b>Sent:</b> Tuesday, December 04, 2012 7:40 PM<br><b>To:</b> Joseph Orr; Jason Palmer<br><b>Cc:</b> eeglablist@sccn.ucsd.edu<br><b>Subject:</b> Re: [Eeglablist] getting started with AMICA<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Dear Jason,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Could you help him please?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Makoto<o:p></o:p></p><div><p class=MsoNormal>---------- Forwarded message ----------<br>From: <b>Joseph Orr</b> <<a href="mailto:oricon@umich.edu">oricon@umich.edu</a>><br>Date: 2012/12/4<br>Subject: [Eeglablist] getting started with AMICA<br>To: <a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br><br><br><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I am trying to run AMICA for the first time and am running in to some trouble. I am using a cluster running Kubuntu 64-bit with SGE installed.</span><o:p></o:p></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I downloaded the amica12lnx64 binary and have runamica12.m in my path. I loaded a .set file and executed "</span><span style='font-size:13.5pt'>[ EEG.icaweights, EEG.icasphere, mods ] = runamica12( EEG.data(:,:) )"</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I received the following on the command line:<br><br>mpich is not a parallel environment<br>orte is not a parallel environment<br>Using make parallel environment.<br>Writing data file: /dreamio2/banichlab/studies/VTS/eeg/VTS_ERP2/tmpdata91338.fdt<br>bash: dreamio4: command not found<br>Please disregard any Warnings about X11 forwarding.<br>qsub id = <br>You can watch the last 25 lines of the output with:<br> $ watch tail -n 25 qsub.sh.o<br>or in Matlab:<br> >> system('watch tail -n 25 qsub.sh.o')<br>You can load the output as it's running by typing:<br> >> mods = loadmodout12('/dreamio2/banichlab/studies/VTS/eeg/VTS_ERP2/amicaouttmp/')<br>Error in ==> runamica12 at 101<br>binfile = 'amica12lnx64';<br><br>??? Output argument "weights" (and maybe others) not assigned during<br>call to<br>"/dreamio2/banichlab/studies/VTS/eeg/toolboxes/runamica12.m>runamica12".<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> <br>Do I need to set up additional files to get AMICA to run?<br><br>Thanks in advance,<br>Joe<o:p></o:p></span></p></div><p class=MsoNormal><br>_______________________________________________<br>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><o:p></o:p></p></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>-- <br>Makoto Miyakoshi<br>JSPS Postdoctral Fellow for Research Abroad<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<o:p></o:p></p></div></div></body></html>