Jpdiaz: remove reference to amica to provide separate details about running amica via openmpi on hoffman

2021-04-01T09:16:16Z

remove reference to amica to provide separate details about running amica via openmpi on hoffman

← Older revision		Revision as of 09:16, 1 April 2021
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	% This script uses the Fieldtrip qsub toolbox to submit a job array		% This script uses the Fieldtrip qsub toolbox to submit a job array
	% that runs the function 'step2_preprocessUpToDipfit' on each individual .set file.		% that runs the function 'step2_preprocessUpToDipfit' on each individual .set file.
	~~% The function performs ASR, AMICA, DIPFIT, and ICLabel which can take about~~
	~~% 3000-14000 seconds to run on a single subject.~~
	%		%

Jpdiaz: fieldtrip qsub example

2021-03-30T00:40:46Z

fieldtrip qsub example

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%% qsubjobarray.m
%
% This script uses the Fieldtrip qsub toolbox to submit a job array
% that runs the function 'step2_preprocessUpToDipfit' on each individual .set file.
% The function performs ASR, AMICA, DIPFIT, and ICLabel which can take about
% 3000-14000 seconds to run on a single subject.
%

% add paths, which will be passed to qsub
addpath /u/project/CCN/apps/matlab/fieldtrip/qsub/ % qsub toolbox
addpath /u/project/CCN/apps/matlab/eeglab/14.1.0b/ % eeglab

% generate list of all .set files within specific folder
FILELIST=dir('/u/project/labgroup/EEG/allsubjs/reprocessed/step1/*.set');

% commands to setup env
qmem = 2024*2024*2024; % in bytes (~8GB)
qtim = 14400; % in seconds (4HR)
qopt = '-j y -pe shared 4 '; % options (note trailing space)

% usual commands to initiate matlab
matlabcmd='. /u/local/Modules/default/init/modules.sh; module load matlab/9.1; matlab';

%% Submit Job Array
jobidarray={};

% Enter the main loop
for i = 1:size(FILELIST,1) % 500 per user job limit

% call to qsubfeval command
jobidarray{i}= qsubfeval(@step2_preprocessUpToDipfit, FILELIST(i), ...
'memreq', qmem, ... % bytes
'timreq', qtim, ... % seconds
'backend', 'sge', ... % SGE
'diary', 'always', ... % log level
'options', qopt, ...
'matlabcmd', matlabcmd);

pause(10) % 10 seconds (to avoid overload)

end

% save array to load output at later time
save jobarray.mat jobidarray

Hoffman2:MATLAB:qsubjobarray.m - Revision history

Jpdiaz: remove reference to amica to provide separate details about running amica via openmpi on hoffman

Jpdiaz: fieldtrip qsub example