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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 Jake,<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'>Sorry I seem to have missed this question (the word AMICA at the end was hidden in the short subject listing).<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'>On the Mac, it seems to be finding the data file okay, but there is a discrepancy between the actual file size and the number of time points you are giving it. Are you sure the data size is 128 x 459165? The error you are getting arises when you specify more frames / time points than are actually in the file and it tries to read past the end of file.<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 assume it’s not a floating point precision vs. double issue (data should be in float by default) as it looks like you are using floatwrite in the scripts to create tmpdata…fdt.<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'>Have you tried it and gotten the same error with the sample datafiles, or another (smaller) dataset?<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 data size is correct, the only other possibilities I can think of are:<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span dir=LTR></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>The “byte_size” or word size is different on that mac from most macs. The default on mac and win is 4, but on linux clusters it is 1. Actually I think amica actually tries to set this automatically now by writing and reading a word, so this is unlikely to be the cause. Also I think the automatic procedure supercedes any attempt to manually set byte_size.<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span dir=LTR></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>There is an issue with RAM or stack size, or a hardware issue with the disk … also unlikely I would think.<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'>Hopefully the problem will be more apparent to you when you consider that the data length is not being set correctly …<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 you are still unable to resolve it.<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><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"'> eeglablist-bounces@sccn.ucsd.edu [mailto:eeglablist-bounces@sccn.ucsd.edu] <b>On Behalf Of </b>Jacob Anderson<br><b>Sent:</b> Wednesday, July 03, 2013 2:45 PM<br><b>To:</b> eeglablist@sccn.ucsd.edu<br><b>Subject:</b> Re: [Eeglablist] Troubleshooting with AMICA<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Dear List,<o:p></o:p></p><div><p class=MsoNormal>I found success in running AMICA within MATLAB and at the prompt after loading the scripts and binary onto a linux machine. Initially, I got a similar error message to the one in my initial list email. Going off of a friend's suggestion that there might be something up with permissions (thanks Scott Burwell!!!), I gave the 'amica12' binary file full -rwx permissions. After a MATLAB restart, I tried running runamica12.m again and it worked! <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I went back to the original Mac computer, and modified the permissions for the mac64 binary. However, I'm still not able to run the scripts, and I get the same error. I'm going to experiment more at another time, but perhaps there's an additional permission setting I could change to make it work. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>That's what I know at this point.<o:p></o:p></p></div><div><p class=MsoNormal>Cheers,<o:p></o:p></p></div><div><p class=MsoNormal>Jake<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Thu, Jun 27, 2013 at 12:00 PM, Jacob Anderson <<a href="mailto:jea@umn.edu" target="_blank">jea@umn.edu</a>> wrote:<o:p></o:p></p><div><p class=MsoNormal>Dear List,<o:p></o:p></p><div><p class=MsoNormal>I'm trying AMICA out for the first time, and I'm running into some problems. After downloading the mac64 binary and MATLAB functions from Jason's website, I tried passing a continuous, 128-channel dataset through the algorithm and got the error below. It looks like there is a Fortran error message that pops up from a failure to run the 'amica12mac64' binary. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I'm currently using EEGLAB 12.0.2.1b within Matlab 2013a on OSX (10.8.4). I've tried using both the GUI and command line methods to see if they work, both fail. The GUI just hangs, but I do get an error at the command line referencing that it can't access the "<span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>libiomp5.dylib" library. Perhaps this library changed in the recent releases of OSX. I did a quick google search, and it looks like this library has something to do with Fortran and Intel, which corroborates the error message below. The </span><span style='font-family:"Arial","sans-serif";color:black'><a href="http://sccn.ucsd.edu/wiki/Amica_Download" target="_blank">http://sccn.ucsd.edu/wiki/Amica_Download</a> page mentions moving this library into the directory the binary is run from, but I can't find the library for some reason.</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>I'm going to find a Win7 machine to try these scripts on this afternoon, but I wanted to drop a note here to see if anyone else may have run into this same issue. </span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>Thanks,</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-family:"Arial","sans-serif";color:black'>Jake</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>/bin/sh: qconf: command not found<o:p></o:p></p></div><div><p class=MsoNormal>/bin/sh: qconf: command not found<o:p></o:p></p></div><div><p class=MsoNormal>/bin/sh: qconf: command not found<o:p></o:p></p></div><div><p class=MsoNormal>No recognized parallel environment found. Run qconf -spl to get a list of available environments and use keyword use_pe.<o:p></o:p></p></div><div><p class=MsoNormal>Running locally with maximum of 4 threads.<o:p></o:p></p></div><div><p class=MsoNormal>Writing data file: /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt<o:p></o:p></p></div><div><p class=MsoNormal>mkdir: /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/: File exists<o:p></o:p></p></div><div><p class=MsoNormal> 1 processor name = <o:p></o:p></p></div><div><p class=MsoNormal> 1 host_num = 1917549169<o:p></o:p></p></div><div><p class=MsoNormal> This is MPI process 1 of 1 ; I am process 1 of<o:p></o:p></p></div><div><p class=MsoNormal> 1 on node: xxxxx<o:p></o:p></p></div><div><p class=MsoNormal> 1 : node root process 1 of 1<o:p></o:p></p></div><div><p class=MsoNormal>Processing arguments ...<o:p></o:p></p></div><div><p class=MsoNormal> num_files = 1<o:p></o:p></p></div><div><p class=MsoNormal> FILES: <o:p></o:p></p></div><div><p class=MsoNormal> /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt<o:p></o:p></p></div><div><p class=MsoNormal> num_dir_files = 1<o:p></o:p></p></div><div><p class=MsoNormal> matrix block_size = 256<o:p></o:p></p></div><div><p class=MsoNormal> number of models = 1<o:p></o:p></p></div><div><p class=MsoNormal> number of density mixture components = 3<o:p></o:p></p></div><div><p class=MsoNormal> pdf type = 0<o:p></o:p></p></div><div><p class=MsoNormal> max_iter = 2000<o:p></o:p></p></div><div><p class=MsoNormal> num_samples = 1<o:p></o:p></p></div><div><p class=MsoNormal> data_dim = 128<o:p></o:p></p></div><div><p class=MsoNormal> field_dim = 459165<o:p></o:p></p></div><div><p class=MsoNormal> do_history = 0<o:p></o:p></p></div><div><p class=MsoNormal> histstep = 10<o:p></o:p></p></div><div><p class=MsoNormal> share_comps = 0<o:p></o:p></p></div><div><p class=MsoNormal> share_start = 100<o:p></o:p></p></div><div><p class=MsoNormal> comp_thresh = 0.990000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> share_int = 100<o:p></o:p></p></div><div><p class=MsoNormal> initial lrate = 5.000000000000000E-002<o:p></o:p></p></div><div><p class=MsoNormal> minimum lrate = 1.000000000000000E-008<o:p></o:p></p></div><div><p class=MsoNormal> lrate factor = 0.500000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> initial rholrate = 5.000000000000000E-002<o:p></o:p></p></div><div><p class=MsoNormal> rho0 = 1.50000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> min rho = 1.00000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> max rho = 2.00000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> rho lrate factor = 0.500000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> kurt_start = 3<o:p></o:p></p></div><div><p class=MsoNormal> num kurt = 5<o:p></o:p></p></div><div><p class=MsoNormal> kurt interval = 1<o:p></o:p></p></div><div><p class=MsoNormal> do_newton = 1<o:p></o:p></p></div><div><p class=MsoNormal> newt_start = 50<o:p></o:p></p></div><div><p class=MsoNormal> newt_ramp = 10<o:p></o:p></p></div><div><p class=MsoNormal> initial newton lrate = 1.00000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> do_reject = 0<o:p></o:p></p></div><div><p class=MsoNormal> num reject = 3<o:p></o:p></p></div><div><p class=MsoNormal> reject sigma = 3.00000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> reject start = 2<o:p></o:p></p></div><div><p class=MsoNormal> reject interval = 3<o:p></o:p></p></div><div><p class=MsoNormal> max_thrds = 2<o:p></o:p></p></div><div><p class=MsoNormal> write step = 10<o:p></o:p></p></div><div><p class=MsoNormal> write_nd = 0<o:p></o:p></p></div><div><p class=MsoNormal> write_LLt = 1<o:p></o:p></p></div><div><p class=MsoNormal> dec window = 1<o:p></o:p></p></div><div><p class=MsoNormal> max_decs = 3<o:p></o:p></p></div><div><p class=MsoNormal> fix_init = 0<o:p></o:p></p></div><div><p class=MsoNormal> update_A = 1<o:p></o:p></p></div><div><p class=MsoNormal> update_c = 1<o:p></o:p></p></div><div><p class=MsoNormal> update_gm = 1<o:p></o:p></p></div><div><p class=MsoNormal> update_alpha = 1<o:p></o:p></p></div><div><p class=MsoNormal> update_mu = 1<o:p></o:p></p></div><div><p class=MsoNormal> update_beta = 1<o:p></o:p></p></div><div><p class=MsoNormal> invsigmax = 100.000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> invsigmin = 0.000000000000000E+000<o:p></o:p></p></div><div><p class=MsoNormal> do_rho = 1<o:p></o:p></p></div><div><p class=MsoNormal> load_rej = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_c = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_gm = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_alpha = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_mu = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_beta = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_rho = 0<o:p></o:p></p></div><div><p class=MsoNormal> load_comp_list = 0<o:p></o:p></p></div><div><p class=MsoNormal> do_mean = 1<o:p></o:p></p></div><div><p class=MsoNormal> do_sphere = 1<o:p></o:p></p></div><div><p class=MsoNormal> doPCA = 1<o:p></o:p></p></div><div><p class=MsoNormal> pcakeep = 128<o:p></o:p></p></div><div><p class=MsoNormal> pcadb = 30.0000000000000 <o:p></o:p></p></div><div><p class=MsoNormal> byte_size = 4<o:p></o:p></p></div><div><p class=MsoNormal> doscaling = 1<o:p></o:p></p></div><div><p class=MsoNormal> scalestep = 1<o:p></o:p></p></div><div><p class=MsoNormal>mkdir: /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/: File exists<o:p></o:p></p></div><div><p class=MsoNormal> output directory = /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/<o:p></o:p></p></div><div><p class=MsoNormal> 1 : setting num_thrds to 2 ...<o:p></o:p></p></div><div><p class=MsoNormal> 1 : using 2 threads.<o:p></o:p></p></div><div><p class=MsoNormal> 1 : node_thrds = 2<o:p></o:p></p></div><div><p class=MsoNormal> getting segment list ...<o:p></o:p></p></div><div><p class=MsoNormal> blocks in sample = 459165<o:p></o:p></p></div><div><p class=MsoNormal> total blocks = 459165<o:p></o:p></p></div><div><p class=MsoNormal> node blocks = 459165<o:p></o:p></p></div><div><p class=MsoNormal> node 1 start: file 1 sample 1 index <o:p></o:p></p></div><div><p class=MsoNormal> 1<o:p></o:p></p></div><div><p class=MsoNormal> node 1 stop : file 1 sample 1 index <o:p></o:p></p></div><div><p class=MsoNormal> 459165<o:p></o:p></p></div><div><p class=MsoNormal>forrtl: severe (36): attempt to access non-existent record, unit 8, file /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt<o:p></o:p></p></div><div><p class=MsoNormal>Image PC Routine Line Source <o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 0039A6C8 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 003990A9 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 0037099F Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 00336294 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 00335967 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 0034CB44 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 0034B413 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 00229E34 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 001FC4D2 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 0000218D Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>amica12mac64 00002145 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>Unknown 00000002 Unknown Unknown Unknown<o:p></o:p></p></div><div><p class=MsoNormal>No gm present, setting num_models to 1<o:p></o:p></p></div><div><p class=MsoNormal>No W present, exiting<o:p></o:p></p></div><div><p class=MsoNormal>Reference to non-existent field 'W'.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Error in runamica12 (line 854)<o:p></o:p></p></div><div><p class=MsoNormal> weights = mods.W(:,:,1);<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Error in amica_test (line 3)<o:p></o:p></p></div><div><p class=MsoNormal>[ EEG.icaweights, EEG.icasphere, mods ] = runamica12(EEG.data(:,:));<o:p></o:p></p></div></div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:#888888'><o:p> </o:p></span></p></div><p class=MsoNormal><span style='color:#888888'>-- <o:p></o:p></span></p><div><p class=MsoNormal><span style='color:#888888'>*************************************************<br>Jacob E. Anderson, MA<br>Doctoral Student<br>Institute of Child Development<br>51 East River Rd.<br>Minneapolis, MN 55455<br><br>E-mail: <a href="mailto:jea@umn.edu" target="_blank">jea@umn.edu</a><br>Web: <a href="http://www.cehd.umn.edu/icd/people/gradstudents/andersonJ.html" target="_blank">Click Here</a><o:p></o:p></span></p></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></body></html>