Something got fixed on my machine (Probably by the gcc and glibc update)
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Running the PyOpenGL GLUT demo "gears.py", which is basically identical to the standard glxgears program, today I get 1430fps on my workstation, (compared to about 1600 for glxgears today). This same machine was getting around 150fps last week (with either program). I'm guessing the complete system rebuild with gcc 4.x and glibc 2.4.x (which was supposed to have quite a few performance fixes for amd64) is the source of the yay.
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