You can do this by using a nested function and variables in the containing parent workspace instead of global variables. Here's how you would apply this to your example. Note that I've made function_sum become a nested function, and it accesses a directly from the containing function workspace.
function repro
M = randi(500,100,100);
a = [1 2 3];
% Nested function
function y = function_sum(x)
y = 0;
for i = 1 : x
% Access 'a' directly from parent workspace
y = y + 1/i + 1*a(1) + 2*a(2) + 3*a(3);
end
end
tic
C = arrayfun(@function_sum,M);
CPUTime = toc
M = gpuArray(M);
tic
C = arrayfun(@function_sum,M);
GPUTime = toc;
Boost = CPUTime/GPUTime
end
