MATLAB: Do I get ‘Error using online_concatenator/concat’ after a worker aborted during execution of a PARFOR loop

Parallel Computing Toolbox

I am using a PARFOR loop to perform some computations in parallel. At some point, I receive the following warning:

Warning: A worker aborted during execution of the parfor loop. The parfor loop will now run again on the remaining workers. 
> In parallel_function (line 599)

However, shortly after the PARFOR loop has been restarted, the execution errors out with one of the following errors:

Error using online_concatenator/concat (line 46) 
Assertion failed. 
Error using online_concatenator/concat (line 54)
Subscript indices must either be real positive integers or logicals.

Best Answer

This is a bug that has originated in R2013b and prevents the PARFOR loop to re-run successfully after a worker aborted. There are no workarounds.

Please contact Technical Support to get assistance with finding out why the worker aborted in the first place.

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Try this:

inputFolder = '/home/user/PycharmProjects/2.5dataconversion/images/patient_1';
outputFolder = '/home/user/PycharmProjects/2.5dataconversion/images/patient_2';
filePattern = fullfile(inputFolder, '*.png'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles) - 2
	% Read in image 1
	baseFileName = theFiles(k).name;
	fullFileName = fullfile(inputFolder, baseFileName);
	image1 = imread(fullFileName);
	% Read in image 2
	baseFileName = theFiles(k+1).name;
	fullFileName = fullfile(inputFolder, baseFileName);
	image2 = imread(fullFileName);
	% Read in image 3
	baseFileName = theFiles(k+2).name;
	fullFileName = fullfile(inputFolder, baseFileName);
	image3 = imread(fullFileName);
	% Now create an RGB image from those 3 gray scale images.
	rgbImage = cat(3, image1, image2, image3);
	% Write to disk
	baseFileName = sprintf('image %2.2d.png', k);
	outputFullFileName = fullfile(outputFolder, baseFileName);
	imwrite(rgbImage, outputFullFileName);
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Best Answer

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