Here read this
Mr. Tom Popper (Jim Carrey) is a driven businessman who is clueless when it comes to the important things in life—until he inherits six penguins. Popper's penguins turn his swank New York apartment into a snowy winter wonderland—and the rest of his life upside-down. Filmed on a refrigerated soundstage with real Gentoo penguins, Mr. Popper's Penguins is a contemporary, loose adaptation of the classic book.
Of course they are real, that is why this production needed 29 animators and 149 effects crew.
Seriously, do you really think anyone would even attempt to train penguins? Yes six of them were real, with their refridgerated soundstage, and their extensive CGI EMBELLISHMENT!
In reality, it was a combination of real live penguins and penguin animation.
Watch https://www.youtube.com/watch?v=lItQbuLBFpg starting at about 0:55 to learn about the real live penguins that were used.
Also watch https://www.youtube.com/watch?v=3vT3tFSXZjI from the beginning to see a sample of the animated penguins created by one of the animators who worked on this film.