[Eeglablist] Troubleshooting with AMICA
Jacob Anderson
jea at umn.edu
Wed Jul 3 14:45:29 PDT 2013
Dear List,
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!
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.
That's what I know at this point.
Cheers,
Jake
On Thu, Jun 27, 2013 at 12:00 PM, Jacob Anderson <jea at umn.edu> wrote:
> Dear List,
> 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.
>
>
> 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 "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
> http://sccn.ucsd.edu/wiki/Amica_Download page mentions moving this
> library into the directory the binary is run from, but I can't find the
> library for some reason.
>
> 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.
>
> Thanks,
> Jake
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> /bin/sh: qconf: command not found
> /bin/sh: qconf: command not found
> /bin/sh: qconf: command not found
> No recognized parallel environment found. Run qconf -spl to get a list of
> available environments and use keyword use_pe.
> Running locally with maximum of 4 threads.
> Writing data file: /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt
> mkdir: /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/: File exists
> 1 processor name =
> 1 host_num = 1917549169
> This is MPI process 1 of 1 ; I am process 1
> of
> 1 on node: xxxxx
> 1 : node root process 1 of 1
> Processing arguments ...
> num_files = 1
> FILES:
> /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt
> num_dir_files = 1
> matrix block_size = 256
> number of models = 1
> number of density mixture components = 3
> pdf type = 0
> max_iter = 2000
> num_samples = 1
> data_dim = 128
> field_dim = 459165
> do_history = 0
> histstep = 10
> share_comps = 0
> share_start = 100
> comp_thresh = 0.990000000000000
> share_int = 100
> initial lrate = 5.000000000000000E-002
> minimum lrate = 1.000000000000000E-008
> lrate factor = 0.500000000000000
> initial rholrate = 5.000000000000000E-002
> rho0 = 1.50000000000000
> min rho = 1.00000000000000
> max rho = 2.00000000000000
> rho lrate factor = 0.500000000000000
> kurt_start = 3
> num kurt = 5
> kurt interval = 1
> do_newton = 1
> newt_start = 50
> newt_ramp = 10
> initial newton lrate = 1.00000000000000
> do_reject = 0
> num reject = 3
> reject sigma = 3.00000000000000
> reject start = 2
> reject interval = 3
> max_thrds = 2
> write step = 10
> write_nd = 0
> write_LLt = 1
> dec window = 1
> max_decs = 3
> fix_init = 0
> update_A = 1
> update_c = 1
> update_gm = 1
> update_alpha = 1
> update_mu = 1
> update_beta = 1
> invsigmax = 100.000000000000
> invsigmin = 0.000000000000000E+000
> do_rho = 1
> load_rej = 0
> load_c = 0
> load_gm = 0
> load_alpha = 0
> load_mu = 0
> load_beta = 0
> load_rho = 0
> load_comp_list = 0
> do_mean = 1
> do_sphere = 1
> doPCA = 1
> pcakeep = 128
> pcadb = 30.0000000000000
> byte_size = 4
> doscaling = 1
> scalestep = 1
> mkdir: /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/: File exists
> output directory = /Users/ande2523/Documents/MATLAB/amica/amicaouttmp/
> 1 : setting num_thrds to 2 ...
> 1 : using 2 threads.
> 1 : node_thrds = 2
> getting segment list ...
> blocks in sample = 459165
> total blocks = 459165
> node blocks = 459165
> node 1 start: file 1 sample 1 index
> 1
> node 1 stop : file 1 sample 1 index
> 459165
> forrtl: severe (36): attempt to access non-existent record, unit 8, file
> /Users/ande2523/Documents/MATLAB/amica/tmpdata12699.fdt
> Image PC Routine Line Source
>
> amica12mac64 0039A6C8 Unknown Unknown Unknown
> amica12mac64 003990A9 Unknown Unknown Unknown
> amica12mac64 0037099F Unknown Unknown Unknown
> amica12mac64 00336294 Unknown Unknown Unknown
> amica12mac64 00335967 Unknown Unknown Unknown
> amica12mac64 0034CB44 Unknown Unknown Unknown
> amica12mac64 0034B413 Unknown Unknown Unknown
> amica12mac64 00229E34 Unknown Unknown Unknown
> amica12mac64 001FC4D2 Unknown Unknown Unknown
> amica12mac64 0000218D Unknown Unknown Unknown
> amica12mac64 00002145 Unknown Unknown Unknown
> Unknown 00000002 Unknown Unknown Unknown
> No gm present, setting num_models to 1
> No W present, exiting
> Reference to non-existent field 'W'.
>
> Error in runamica12 (line 854)
> weights = mods.W(:,:,1);
>
> Error in amica_test (line 3)
> [ EEG.icaweights, EEG.icasphere, mods ] = runamica12(EEG.data(:,:));
>
>
>
>
>
>
> --
> *************************************************
> Jacob E. Anderson, MA
> Doctoral Student
> Institute of Child Development
> 51 East River Rd.
> Minneapolis, MN 55455
>
> E-mail: jea at umn.edu
> Web: Click Here<http://www.cehd.umn.edu/icd/people/gradstudents/andersonJ.html>
>
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