Is there a reason for wanting to compile100,000 functions that are essentially the same?

CompliationOptions needs to be part of the call to Complie[], not do. Try something like this:

Do[
  Compile[
   {
    {aFile[[i, 1]], _Real},
    {aFile[[i, 2]], _Real},
    {aFile[[i, 3]], _Real}
    },
   col1 = aFile[[i, 1]];
   col2 = aFile[[i, 2]];
   col3 = aFile[[i, 3]];
   g1 = col1 col3;
   g2 = col2 col3;
   g3 = g1 g2^2;
   , CompilationOptions -> {InlineExternalDefinitions -> True}, 
   RuntimeOptions -> "Speed"
   ]
  , {i, 100000}
  ];

Hi Mike, Your code worked in Mathematica. I tried the same code using the IkernelLink(MathLinkFactory) and MathKernel in C#.Net 2019, but it did not work.

I created a string "codeString" equal to the code and used mathlink.EvaluateToOutputForm(codeString,0); This worked for all other code expect the one above. Any thoughts?