It ran ok for me, my rom is in the directory (in RetroPie 2.4)
/home/pi/RetroPie/roms/atari2600-libretro/
Both my keyboard and joypad worked fine with up,down,left,right and the fire button.
By default the retroarch keys are:
input_player1_a = x
input_player1_b = z
input_player1_y = a
input_player1_x = s
input_player1_start = enter
input_player1_select = rshift
input_player1_l = q
input_player1_r = w
input_player1_left = left
input_player1_right = right
input_player1_up = up
input_player1_down = down