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The problem seems to be caused because for GenOpt, the .mat file is not an input file. For GenOpt, input files are text files in which a text substitution needs to be done, while .mat is a binary file. To get your setup to work, you can specify the .mat file in the SimulationStart { Command = "..." } section. See for example example/quad/Fibonacci which uses CallParameter { Prefix="..."} to pass a file name to the command that starts the simulation.