Run a script that uses multiple MATLAB sessions

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First of all a way must be found to open sessions programatically.
Based on this and this it is found you can do it as follows (works on windows as well):

% Opening 3 matlab sessions
for t = 1:3
!matlab &
end

Besides simply opening them, a simple command can also be given

!matlab -r "magic(5)" &

Now, to finally combine this just a small trick remains:

for t = 1:3
   str = ['!matlab -r "magic(' num2str(t) ')" &'];
   eval(str)
end

Note that if you want to use more complicated inputs you can simply save them in a struct and call them with this index by using a wrapper script as called function.

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