Hi Quentin,

I cannot really run the code because as you say it is incomplete. One observation is that you use procedural style, like in C or Fortran or so. My guess is that you "speak" one of those. The thing is that in Mathematica there are other styles, such as functional or rule based.

It turns out that functional style is quite optimised and usually faster than procedural. Given your description of the problem, I suspect that the speed gain that you might achieve like that would be substantial. You have three nested loops and getting rid of some/all of them should help.

Cheers,

Marco

Hi Quentin,

this does not answer you question but have you tried optimising that within Mathematica, i.e. without compilation first? Using the Table command is actually quite slow:

Table[0, {40000}, {40000}]; // AbsoluteTiming

takes 43.5 seconds on my computer.

ConstantArray[0, {40000, 40000}]; // AbsoluteTiming

and

Normal[SparseArray[{}, {40000, 40000}]]; // AbsoluteTiming

run about 7.95 seconds. If you can use a SparseArray only it becomes really fast:

SparseArray[{}, {40000, 40000}]; // AbsoluteTiming

Also further calculations on SparseArray are quite fast: 0.000203 seconds.

Cheers,

Marco