my swap gets crazy large and the loop takes 600 seconds. Can someone let me know why this happens?

Everything you need to know is evident from these 3 lines:

$U = $S = 100000;
...
for($u = 0;  $u < $U;  $u++ ) {   
   ...
   for($s = 0;  $s < $S;  $s++ ) {
    
       $distance[ $u ][ $s ] = 0;
[download]

You are creating an Array of Arrays with 100,000 x 100,000 elements.

Each sub array will require 3.2MB. 100,000 of those and you'll need 300 Gigabytes of virtual ram. Since you probably only have somewhere between 4GB and say 32GB of physical ram, the rest will need to be swapped to disk.

If your system is doing that in 10 minutes you must have a pretty fast disk set-up. Rather than complaining, you should be impressed.