Found that it is impossible after asking the question:
Coder support for LargeArrayDims
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It seems that by default, MATLAB Coder generates MEX files that are compiled without support for the LargeArrayDims option. Thus arrays in the generated MEX are limited to 2^32 elements. This results in errors like:
"Cannot grow a matrix with greater than intmax() elements."
I cannot see an option to enable LargeArrayDims either within the MATLAB Coder UI, or within the options to the coder.config object.
Is it possible to build a MEX Coder project with support for LargeArrayDims?
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