[Eeglablist] AMICA throws a bus error

孙亚楠 sunyanan2008 at gmail.com
Wed Sep 30 01:29:36 PDT 2015


Hi all,

Just to update, AMICA worked on my MEG data after set the 'numprocs' to 1
or 0. I am not sure how that happened as my computer has 4 physical
processors.

Hi Jason,
Could explain how the argument 'numprocs' influences AMICA processing?

Thanks,
Yanan

On 29 September 2015 at 16:59, 孙亚楠 <sunyanan2008 at gmail.com> wrote:

> Hi eeglablist members,
>
> I get the same bus error like what Michael got before. Has anyone solved
> this?
>
> I can run amica successfully on the sample data (Memorized.fdt) and on my
> EEG data (64 channels) but not on my MEG data (160 channels Yokogawa) where
> showed "forrtl: severe (180): SIGBUS, bus error occurred".
>
> The MEG data has standardized and it can be run successfully using the
> AMICA app but bus error happened when calling runamica12.m in MATLAB.
>
> P.S. I am running runamica12 on R2014b, iMac 10.10.5.
>
> Thanks,
> Yanan
>
> On 17 June 2015 at 14:20, Michael Spezio <mspezio at scrippscollege.edu>
> wrote:
>
>> Dear Jason, Makoto, and other AMICA users,
>>
>> I am able to successfully run AMICA in Matlab with runamica12 (R2014b,
>> iMac 10.9.5) on the sample data Memorize.fdt.
>>
>> However, I get a bus error when I try to run AMICA on my own data. I've
>> posted the error below.
>>
>> I've verified that the data rank is equal to the number of channels
>> (202). I've also verified that the cnt is correct, 118 epochs, 900 points
>> per epoch. The epochs are 4 nonoverlapping types, each having the -1 to 2
>> second default bounds.
>>
>> Can you provide any insight into what is going wrong? I'm following
>> Makoto's pipeline.
>>
>> Are there additional checks I need to do on my data prior to AMICA?
>>
>> Thanks.
>>
>> Best,
>>
>> Michael
>>
>> [ EEG.icaweights, EEG.icasphere, mods ] = runamica12(EEG.data(:,:));
>>
>> Processing arguments ...
>>  num_files =            1
>>  FILES:
>>
>>  /Users/mlspezio/Matlab/scripts/Projects/HLCC_EEG/HLCC_EEG_Preprocessing/tmpdata
>>  92389.fdt
>>  num_dir_files =            1
>>  initial matrix block_size =          256
>>  do_opt_block =            0
>>  number of models =            1
>>  number of density mixture components =            3
>>  pdf type =            0
>>  max_iter =         2000
>>  num_samples =            1
>>  data_dim =          202
>>  field_dim =       106200
>>  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 =          202
>>  pcadb =    30.0000000000000
>>  byte_size =            4
>>  doscaling =            1
>>  scalestep =            1
>> mkdir:
>> /Users/mlspezio/Matlab/scripts/Projects/HLCC_EEG/HLCC_EEG_Preprocessing/amicaouttmp/:
>> File exists
>>  output directory =
>>
>>  /Users/mlspezio/Matlab/scripts/Projects/HLCC_EEG/HLCC_EEG_Preprocessing/amicaou
>>  ttmp/
>>            1 : setting num_thrds to            2  ...
>>            1 : using           2 threads.
>>            1 : node_thrds =            2
>>  i =            1  real ierr =            0
>>  bytes in real =            1
>>            1 : REAL nbyte =            1
>>  getting segment list ...
>>  blocks in sample =       106200
>>  total blocks =       106200
>>  node blocks =       106200
>>  node            1  start: file            1  sample            1  index
>>            1
>>  node            1  stop : file            1  sample            1  index
>>       106200
>>            1 : data =   -7.69530153274536       -17.7782669067383
>>  getting the mean ...
>>   mean =  -0.427972755604667      -0.451065303007086
>>  -0.407206153567977
>>  subtracting the mean ...
>>  getting the sphering matrix ...
>>  cnt =       106200
>>  doing eig nx =          202  lwork =       408040
>>  minimum eigenvalues =   9.293485032426282E-002  0.123639438673911
>>   0.145761886209716
>>  maximum eigenvalues =    76318.4901712733        22041.6054108954
>>    4928.60680527982
>>  num eigs kept =          202
>>  numeigs =          202
>>  sphering the data ...
>>            1 Allocating variables ...
>>            1 : Initializing variables ...
>>            1 : block size =          256
>>            1 : entering the main loop ...
>> forrtl: severe (180): SIGBUS, bus error occurred
>> /Users/mlspezio/Matlab/toolboxes/UseAMICA/amica12mac64
>> /Users/mlspezio/Matlab/scripts/Projects/HLCC_EEG/HLCC_EEG_Preprocessing/amicaouttmp/input.param:
>> Signal 52
>> No gm present, setting num_models to 1
>> No W present, exiting
>>
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>
>
>
> --
> Yanan Sun
> PHD Student
> ARC Centre of Excellence in Cognition and its Disorders
> & Department of Cognitive Science,
> Faculty of Human Sciences,
> Macquarie University,
> NSW, 2109, Australia
>



-- 
Yanan Sun
PHD Student
ARC Centre of Excellence in Cognition and its Disorders
& Department of Cognitive Science,
Faculty of Human Sciences,
Macquarie University,
NSW, 2109, Australia
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