blender stereo works fine under win7 without any problems so far. However, under linux (arch in my case) side-by-side stereo or similar cases will fail with "X11 glXQueryVersion() failes, verify working openGL system! initial window could not find GLX extension, exit!"
I patch intern/ghost/intern/GHOST_WindowX11.cpp anyway. It might cause other problems, but side-by-side stereo works for me so far.
PS: patch file
Only in blender-2.63: build
diff -rup blender-2.63/intern/ghost/intern/GHOST_WindowX11.cpp patched/intern/ghost/intern/GHOST_WindowX11.cpp
--- blender-2.63/intern/ghost/intern/GHOST_WindowX11.cpp 2012-04-26 16:41:12.000000000 -0400
+++ patched/intern/ghost/intern/GHOST_WindowX11.cpp 2012-05-07 16:16:50.000000000 -0400
@@ -209,8 +209,8 @@ GHOST_WindowX11(
for (samples = m_numOfAASamples; samples >= 0; samples--) {
i = 0; /* Reusing attributes array, so reset counter */
- if(m_stereoVisual)
- attributes[i++] = GLX_STEREO;
+ //if(m_stereoVisual)
+ // attributes[i++] = GLX_STEREO;
attributes[i++] = GLX_RGBA;
attributes[i++] = GLX_DOUBLEBUFFER;
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