Rav Avraham Reznikov, the rav of Ichilov Medical Center in Tel Aviv, has issued an interesting psak regarding the smoking of medical marijuana on Shabbos.

To start, Rav Reznikov clarifies that his discussion only deals with medical marijuana that has been authorized for the patient and is legal to take. Regular marijuana, non-medical, is illegal to consume in any fashion, and is also prohibited from a halachic perspective,  and is not under discussion.

So, Rabbi Reznikov says, on Shabbos, it would be preferable to consume medical marijuana in one's food - hash brownies, for example - and that would be allowed as it would be considered food. THC pills, containing the active ingredient, and using a vaporizer to steam the marijuana into you if prepared in advance, would also be allowed.

However, sometimes ingesting the marijuana via alternative methods is not possible. So, base don the Biur Halacha that says that when a sick person might deteriorate and his illness might get worse, we are even machalel shabbos for him.

What about separating trumos and maasros from the marijuana on Shabbos? Rav Reznikov says that medical herbs are exempt from trumos and maasros and shmitts is also not an issue. Marijuana is not considered a food fit for humans.
sources: Srugim and Kipa