Hoffman2:MATLAB:EEGLAB:Jobs - Revision history

Elau: Adding back in a portion that shouldn't have been cut out.

2014-03-21T23:20:25Z

Adding back in a portion that shouldn't have been cut out.

← Older revision		Revision as of 23:20, 21 March 2014
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	==Submit it as a Job==		==Submit it as a Job==
	Now that you have a proper M-file to run in MATLAB, go [[Hoffman2:MATLAB:Jobs \| follow the steps for how to submit this as a job to the cluster]].		Now that you have a proper M-file to run in MATLAB, go [[Hoffman2:MATLAB:Jobs \| follow the steps for how to submit this as a job to the cluster]].



			==Look at the Outputs==
			Make sure that was all worthwhile and look at the outputs. If you are still on Hoffman2, go ahead and launch MATLAB and run the following commands
			<pre>
			>> addpath(genpath('/u/home/FMRI/apps/eeglab/current/')); % Make sure EEGLAB is in the MATLAB PATH
			>> eeglab; % Launch EEGLAB
			</pre>

			And then using the GUI, load up the resulting processed file. If you followed along with our example, this output file will be in your [[Hoffman2:Introduction#scratch \| SCRATCH directory]].

Elau: Moving the common "matlab job" part to a separate page.

2014-03-21T22:54:18Z

Moving the common "matlab job" part to a separate page.

@@ Line 33: / Line 33: @@
 |}
-If you think the Pros outweigh the Cons, and they certainly do if you are processing more than one subject, then this is [[Hoffman2:MATLAB:EEGLAB:Jobs | the solution for you.]]
+If you think the Pros outweigh the Cons, and they certainly do if you are processing more than one subject, then '''this is the solution for you'''.
@@ Line 128: / Line 128: @@
-==Running the script==
+==Submit it as a Job==
-You will now need to create a BASH command script to submit as a job.  This script will setup MATLAB and tell it to run your M-file.
+Now that you have a proper M-file to run in MATLAB, go [[Hoffman2:MATLAB:Jobs | follow the steps for how to submit this as a job to the cluster]].

Elau: Added reminder about how to check on jobs.

2014-03-07T17:22:38Z

Added reminder about how to check on jobs.

← Older revision		Revision as of 17:22, 7 March 2014
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	===Identify the processing commands===		==Identify the processing commands==
	Using the EEGLAB GUI, process a data file the way your want your job to process a data file. Go from loading the file, to processing, to saving the file.		Using the EEGLAB GUI, process a data file the way your want your job to process a data file. Go from loading the file, to processing, to saving the file.

Line 47:		Line 47:


	===Make your script===		==Make your script==
	If you know the exact commands you need to run, or have the contents of an "EEG.history" from a previous analysis, then the general *.m file to create will be like the following example, found at		If you know the exact commands you need to run, or have the contents of an "EEG.history" from a previous analysis, then the general *.m file to create will be like the following example, found at
	/u/home/FMRI/apps/examples/eeglab/eeglab_example_job.m		/u/home/FMRI/apps/examples/eeglab/eeglab_example_job.m
Line 128:		Line 128:


	===Running the script===		==Running the script==
	You will now need to create a BASH command script to submit as a job. This script will setup MATLAB and tell it to run your M-file.		You will now need to create a BASH command script to submit as a job. This script will setup MATLAB and tell it to run your M-file.

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	===Submit the Job===		==Submit the Job==
	All that remains is to [[Hoffman2:Submitting_Jobs \| submit the job]] based on what you've already learned about submitting jobs.		All that remains is to [[Hoffman2:Submitting_Jobs \| submit the job]] based on what you've already learned about submitting jobs.

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	===Look at the ~~outputs=~~==		==Wait for the Job to Run==
			Remember how to [[Hoffman2:Monitoring_Jobs \| check on job status?]]



			==Look at the Outputs==
	Make sure that was all worthwhile and look at the outputs. If you are still on Hoffman2, go ahead and launch MATLAB and run the following commands		Make sure that was all worthwhile and look at the outputs. If you are still on Hoffman2, go ahead and launch MATLAB and run the following commands
	<pre>		<pre>
	>> addpath(genpath('/u/home/FMRI/apps/eeglab/current/')); % Make sure EEGLAB is in the PATH		>> addpath(genpath('/u/home/FMRI/apps/eeglab/current/')); % Make sure EEGLAB is in the MATLAB PATH
	>> eeglab; % Launch EEGLAB		>> eeglab; % Launch EEGLAB
	</pre>		</pre>

	And then using the GUI, load up the resulting processed file. If you followed along with our example, this output file will be in your [[Hoffman2:Introduction#scratch \| SCRATCH directory]].		And then using the GUI, load up the resulting processed file. If you followed along with our example, this output file will be in your [[Hoffman2:Introduction#scratch \| SCRATCH directory]].

Elau: Command style updated

2014-03-07T01:57:07Z

Command style updated

← Older revision		Revision as of 01:57, 7 March 2014
Line 4:		Line 4:

	[[Hoffman2:MATLAB:EEGLAB \| Back to all things EEGLAB]]		[[Hoffman2:MATLAB:EEGLAB \| Back to all things EEGLAB]]


	Normally, if you wanted to run something in EEGLAB, you start up MATLAB on Hoffman2, wait for a node to check out, wait for a license, and then start crunching numbers.		Normally, if you wanted to run something in EEGLAB, you start up MATLAB on Hoffman2, wait for a node to check out, wait for a license, and then start crunching numbers.
Line 166:		Line 167:
	In our example case, you would [[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line \| SSH into Hoffman2]] and execute the following commands:		In our example case, you would [[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line \| SSH into Hoffman2]] and execute the following commands:
	<pre>		<pre>
	cd /u/home/FMRI/apps/examples/eeglab		$ cd /u/home/FMRI/apps/examples/eeglab
	./q.sh ./run_eeglab_example_job.sh		$ ./q.sh ./run_eeglab_example_job.sh
	</pre>		</pre>

Elau: EEGLAB Jobs more fleshed out.

2014-03-07T01:46:07Z

EEGLAB Jobs more fleshed out.

@@ Line 34: / Line 34: @@
 If you think the Pros outweigh the Cons, and they certainly do if you are processing more than one subject, then this is [[Hoffman2:MATLAB:EEGLAB:Jobs | the solution for you.]]
-If you know the exact commands you need to run, or have the contents of an "EEG.history" from a previous analysis, then the general *.m file to create will be the the following example, found at
   /u/home/FMRI/apps/examples/eeglab/eeglab_example_job.m
 <pre>
@@ Line 111: / Line 124: @@
 EEG = eeg_checkset( EEG );
 </pre>

Elau: Starting the EEGLAB Jobs page.

2014-03-07T01:02:44Z

Starting the EEGLAB Jobs page.

New page

[[Hoffman2 | Back to all things Hoffman2]]

[[Hoffman2:MATLAB | Back to all things MATLAB]]

[[Hoffman2:MATLAB:EEGLAB | Back to all things EEGLAB]]

Normally, if you wanted to run something in EEGLAB, you start up MATLAB on Hoffman2, wait for a node to check out, wait for a license, and then start crunching numbers.

But what if your analysis in EEGLAB is going to take 10 hours, and you need to shut your computer down and leave in five hours? Or you don't want your MATLAB job to crash just because your flaky WiFi decides to die in hour nine of the analysis?

Well, if you have run this analysis before and have the "EEG.history" contents, you should be able to create a MATLAB script (*.m file) from said history and run it as a headless job on Hoffman2.

{| class="wikitable"
|+ Pros and Cons of Running your EEGLAB analysis as a job
! Pros
! Cons
|- class="ccn-table-odd ccn-table-left"
| style="width:30em;" | Learn how to submit command line scripts and feel powerful controlling lots of computers
| style="width:30em;" | Have to learn command line scripts and how to submit jobs correctly
|- class="ccn-table-even ccn-table-left"
| style="width:30em;" | Be able to have your analysis run without tying up your computer for hours or days at a time
| style="width:30em;" | Have to run the analysis through at least once partially to create your script
|- class="ccn-table-odd ccn-table-left"
| style="width:30em;" | Be able to run MATLAB jobs longer than 24 hours
| style="width:30em;" | Have to be comfortable editing MATLAB code to create your *.m file
|- class="ccn-table-even ccn-table-left"
| style="width:30em;" | Be able to run MATLAB jobs that use way more memory than your laptop can.
| style="width:30em;" |
|- class="ccn-table-odd ccn-table-left"
| style="width:30em;" | Possibly be able to run multiple analyses at once if you make the extra step and compile your code (so it doesn't need a MATLAB license)
| style="width:30em;" |
|}

If you think the Pros outweigh the Cons, and they certainly do if you are processing more than one subject, then this is [[Hoffman2:MATLAB:EEGLAB:Jobs | the solution for you.]]

If you know the exact commands you need to run, or have the contents of an "EEG.history" from a previous analysis, then the general *.m file to create will be the the following example, found at
/u/home/FMRI/apps/examples/eeglab/eeglab_example_job.m
<pre>
% eeglab_example_job.m
%
% Edward Lau
% eplau[at]ucla[dot]edu
% 2014.03.06
% Example EEGLAB script that can be submitted as a job on Hoffman2.
%
% This M-file will:
% 0. Set the paths for the input and output files.
% 1. Load the EEGLAB "set" file
% 2. Bandpass filter it to 1-45Hz
% 3. Average re-reference the data
% 4. Save the new data file with "preproc" appended to the old name (e.g. worked on "Subj1.set" resulting in "Subj1_preproc.set)
%
%
% WARNING:
% This example does not necessarily reflect the best practices for how EEG should be pre-processed and
% should only be viewed as an example of how to script basic EEGLAB steps.

%% 0. Variables to set
% The directory where the data to be processed lives.
INPUT_DIR = '/u/home/FMRI/apps/eeglab/current/sample_data/';

% The EEGLAB ".set" file that should be processed
INPUT_FILE = 'eeglab_data.set';

% The directory where the processed data should be saved
OUTPUT_DIR = getenv('SCRATCH');

% The EEGLAB ".set" filename that should be saved after processing
OUTPUT_FILE = sprintf('%s_%s.%s', INPUT_FILE(1:end-4), 'preproc', 'set');

%% Make sure EEGLAB is in your PATH, change "current" to whichever version of EEGLAB you prefer
addpath(genpath('/u/home/FMRI/apps/eeglab/current'));

%% Load up EEGLAB in headless mode
eeglab('nogui');

%% 1. Load up your data
EEG = pop_loadset('filename', INPUT_FILE, 'filepath', INPUT_DIR);

% Set EEG variables appropriately
EEG = eeg_checkset( EEG );
ALLEEG = EEG;
CURRENTSET = 1;

%% Do your analyses
% This could be built from the contents of an EEG.history array from a previous analysis

% 2. Bandpass filter 1-45Hz
EEG = pop_eegfiltnew(EEG, 1, 45, 424, 0, [], 0);
EEG = eeg_checkset( EEG );

% 3. Average re-reference the data
EEG = pop_reref( EEG, []);
EEG = eeg_checkset( EEG );

%% 4. Don't forget to save your data afterward
OUTDIR = getenv('SCRATCH');
EEG = pop_saveset( EEG, 'filename', OUTPUT_FILE, 'filepath', OUTPUT_DIR);
EEG = eeg_checkset( EEG );
</pre>