In the objective function, you can put a large penalty or result to make it like a bad result, so pattern search won't consider it and move to next step. For example:
function fval = objective(x)
program_output = function_to_call_your_program(x);
if iszero(program_output) | isempty(program_output)
fval = 1000; % large value
else
fval = program_output;
end
end
