Make the cake: Preheat the oven to 350 degrees F. Butter three 9-inch-round cake pans and line the bottoms with parchment paper; butter the parchment and dust with flour.
Sift the flour, cocoa, baking soda and salt into a large bowl. Whisk the granulated sugar and eggs in a separate large bowl until combined. Gradually stir in the vegetable oil. Add the flour mixture, alternating with the buttermilk, beginning and ending with the flour mixture, stirring well after each addition. Stir in the vanilla and red food coloring.
Divide the batter evenly among the pans and bake until a toothpick inserted into the center comes out clean, about 40 minutes. Cool the cakes in the pans for 10 minutes, then turn out onto racks to finish cooling; peel off the parchment.
Make the frosting: Beat the cream cheese and butter in a large bowl with a mixer until creamy. Beat in the confectioners' sugar until the mixture is smooth. Beat in the vanilla and nuts, reserving 2 tablespoons nuts for garnish. (You can make the cakes and/or frosting up to 2 days ahead; wrap the cakes in plastic wrap and refrigerate the frosting.)
Spread the frosting between the layers, on the side and on top of the cake. Garnish with the reserved pecans.