japalmer29
commented
3 years ago Are you sure you're using pop_loadset correctly? I think you need keywords, like EEG=pop_loadset('filename',filename,'filepath',filepath);
On Sun, Oct 25, 2020, 6:44 PM moo-n notifications@github.com wrote:
Hello, I've been trying to run AMICA on NSG server but it doesn't work. Attached the code I used to run it and the outputs I got. the dataset I'm using is epoched. I tried both running it using one node and using multiple nodes by setting numprocs=4 and both failed. the input file:
%% test_script_amica_nsg.m
% add eeglab to path
eeglab; close;
% load dataset
filepath = [ pwd filesep ];
filename = '23456.set';
EEG = pop_loadset(filename, filepath);
% define parameters
numprocs = 1; % # of nodes (1-4: default 1)
max_threads = 24; % # of threads (1-24: default = 24)
num_models = 1; % # of models of mixture ICA
max_iter = 3000; % max number of learning steps
% run amica on NSG
outdir = [ pwd filesep 'amicaouttmp' filesep ];
runamica15_nsg(EEG, 'num_models',num_models, 'outdir',outdir, 'max_iter',max_iter);
output files STDOUT
< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) November 27, 2019To get started, type doc.
For product information, visit www.mathworks.com.
[�Warning: Adding folders named 'resources' to the path is not supported:
/projects/ps-nsg/home/nsguser/applications_centos7/eeglab_new/functions/resources]�
[�> In path (line 109)
In addpath (line 86)
In eeglab>addpathifnotinlist (line 2053)
In eeglab>myaddpath (line 2082)
In eeglab (line 287)
In runAmica (line 3)]�
eeglab: options file is ~/eeg_options.m
EEGLAB: adding "ANTeepimport" v1.13 (see >> help eegplugin_eepimport)
EEGLAB: adding "BCI2000import" v0.36 (see >> help eegplugin_BCI2000import)
EEGLAB: adding "BDFimport" v1.10 (see >> help eegplugin_bdfimport)
EEGLAB: adding "Biosig" to the path; subfolders (if any) might be missing from the path
EEGLAB: adding "Fieldtrip-lite" to the path; subfolders (if any) might be missing from the path
EEGLAB: adding "Fileio" to the path; subfolders (if any) might be missing from the path
EEGLAB: adding "MEF_import" v1.10 (see >> help eegplugin_mefimport)
EEGLAB: adding "NEUROPRAXimport" v1.00 (see >> help eegplugin_NEUROPRAXimport)
EEGLAB: adding "WearableSensing" v1.09 (see >> help eegplugin_pop_WearableSensing)
EEGLAB: adding "amica" v1.5.1 (see >> help eegplugin_amica)
EEGLAB: adding "bci2000legacy" v1.0 (see >> help eegplugin_bci2000legacy)
EEGLAB: adding "bdfimport" v1.1 (see >> help eegplugin_bdfimport)
EEGLAB: adding "biopac" v1.00 (see >> help eegplugin_biopac)
EEGLAB: adding "bva-io-" v1.5.13 (see >> help eegplugin_bva_io)
EEGLAB: adding "bva-io" v1.5.13 (see >> help eegplugin_bva_io)
EEGLAB: adding "cogniscan" v1.1 (see >> help eegplugin_cogniscan)
EEGLAB: adding "corrmap" v2.02.1 (see >> help eegplugin_corrmap)
EEGLAB: adding "ctfimport" v1.04 (see >> help eegplugin_ctfimport)
EEGLAB: adding "dipfit" v2.3 (see >> help eegplugin_dipfit)
EEGLAB: adding "egilegacy" v1.0 (see >> help eegplugin_egilegacy)
EEGLAB: adding "erpssimport" v1.01 (see >> help eegplugin_erpssimport)
EEGLAB: adding "firfilt" v1.6.2 (see >> help eegplugin_firfilt)
EEGLAB: adding "gtecimport" v3.15.01 (see >> help eegplugin_gtecimport)
EEGLAB: adding "import_NihonKodenM00files" v1.11 (see >> help eegplugin_importNihonKodenM00)
EEGLAB: adding "instepascimport" v1.00 (see >> help eegplugin_ascinstep)
EEGLAB: adding "loadcurry" v2.0 (see >> help eegplugin_loadcurry)
EEGLAB: adding "loadhdf5v" v1.1 (see >> help eegplugin_loadhdf5)
EEGLAB: error while adding plugin "eegplugin_mffimport"
Error using error
Function is not defined for 'cell' inputs.
EEGLAB: adding "mffmatlabio" v2.01 (see >> help eegplugin_mffmatlabio)
EEGLAB: adding "musemonitor" v3.1 (see >> help eegplugin_musemonitor)
EEGLAB: adding "neuroimaging4d" v1.00 (see >> help eegplugin_4dneuroimaging)
EEGLAB: adding "neuroneimport" v1.0.3.4 (see >> help eegplugin_neurone)
EEGLAB: adding "neuroscanio" v1.1 (see >> help eegplugin_neuroscanio)
EEGLAB: adding "procominfinity" v1.00 (see >> help eegplugin_procom)
EEGLAB: adding "snapmaster" v1.0 (see >> help eegplugin_snapmaster)
EEGLAB: adding "xdf-EEGLAB" v1.14 (see >> help eegplugin_xdfimport)
[�Warning: Adding folders named 'resources' to the path is not supported:
/projects/ps-nsg/home/nsguser/applications_centos7/eeglab_new/functions/resources]�
[�> In path (line 109)
In addpath (line 86)
In eeglab>addpathifnotinlist (line 2053)
In eeglab>myaddpath (line 2082)
In eeglab (line 287)
In eeglab (line 1084)
In runAmica (line 3)]�
pop_loadset(): loading file /projects/ps-nsg/home/nsguser/ngbw/workspace/NGBW-JOB-EEGLAB_TG-985C5F6F32174E75A1931EDA1AD2E76B/12456/12456.set ...
Running AMICA on single node ...
INTERNAL ERROR: invalid error code ffffffff (Ring Index out of range) in rdma_cm_get_hostnames:1267
Warning: RDMA CM Initialization failed. Continuing without RDMA CM support. Please set MV2_USE_RDMA_CM=0 to disable RDMA CM.
1 processor name = comet-18-44.sdsc.edu 1 host_num = 1457401042This is MPI process 1 of 1 ; I am process 1 of
1 on node: comet-18-44.sdsc.edu 1 : node root process 1 of 1Processing arguments ...
forrtl: severe (66): output statement overflows record, unit -5, file Internal Formatted Write
Image PC Routine Line Source
amica15c 0000000000E88B8B Unknown Unknown Unknown
amica15c 0000000000E86B97 Unknown Unknown Unknown
amica15c 000000000044D799 Unknown Unknown Unknown
amica15c 000000000040CD6C Unknown Unknown Unknown
amica15c 000000000040A6B6 Unknown Unknown Unknown
libc.so.6 00002B5285D823D5 Unknown Unknown Unknown
amica15c 000000000040A529 Unknown Unknown Unknown
Oops! AMICA did not run succesfully...
`
STDERR `
{�Unrecognized function or variable 'filename'.
Error in runamica15_nsg (line 922)
if exist(filename,'file')
Error in runAmica (line 18)
runamica15_nsg(EEG, 'num_models',num_models, 'outdir',outdir,
'max_iter',max_iter);
}�
`
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moo-n
Hello, I've been trying to run AMICA on NSG server but it doesn't work. Attached the code I used to run it and the outputs I got. the dataset I'm using is epoched. I tried both running it using one node and using multiple nodes by setting numprocs=4 and both failed. the input file:
output files STDOUT
STDERR `
`