Pulsing rendering under X11 Opengl Ubuntu

I am writing a game engine in C. I am having pulsing lag in my rendering.  About ever 1 second there is a lag hiccup.  I experienced a very similar problem when I used to play DOOM II.  It would pulse lag 4 times in a row , about 1 second  apart.  The solution was to terminate the window manager explorer.exe .  I am now on Ubuntu Linux using an OpenGL context with the X11 window manager.  I think the window manager here may be doing the same thing.  I do not think I can terminate the windon manager here though …