I had a class last fall in which the prof used an automatic grader. He had a couple page document describe all the nit-picky formatting requirements we had to follow so that his automatic grader could run it. And, if we missed even a signle req, we got docked for it (generally in multiples of 10% of the assignment). Many people scored below-average to failing on their first couple of assignments because of this system, even though their code was flawless. So, please, please don't use automatic graders. They're more trouble than their worth, and you students will appreciate and specific comments you give. Even if it runs perfectly, comments can still sometimes be useful to make it even better.