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I'm running Dapper. I've got a P4-3Ghz machine with 1GB Ram. It's dual booted with XP. All GTK based apps seem to launch really slowly (Gedit takes 12 seconds, GCalctool takes 10 seconds, Gnometris takes 12 seconds etc..). I'm not 100% sure what apps are and are not GTK based. But Xmms launches fast, and the python IDLE editor launches fast too. The hard drive light is NOT on during the delay.
I initially fixed this problem by upgrading the kernel with the linux-686-smp package and running prelink. But after installing a few other things (like F-spot, Ipodder etc.) prelinking and rebooting, the apps all started launching slowly again.
I've watched the strace output on launching Gedit from a terminal. Everything flies by until I reach the chunks of read() statements that appear to involve fonts. These statements go by significantly more slowly than the rest. The same behaviour was seen watching an strace of Gcalctool.
I think my system's got about 1200+ fonts on it. I have no idea if that's a lot or not. I've deleted the font-cache files in my /usr/share/X11/fonts/100dpi and 75dpi folders and forced a recache with fc-cache -v -f. It seemed to recache everything, but these apps still launch slowly.
Again, it only *appears* to be a problem for GTK based apps.
Also, once the app is open, launching a second instance of it is much much quicker. And the apps work fine once they are opened.
During the launching delay, the CPU usage is a steady 100% for those 10 or 15 seconds.
Not really sure if I can be of some help. If you are running GNOME, then most apps will be GTK2. IDLE is not GTK2 (I think its built using TK) and XMMS is GTK1 so thats why they are probably starting quite fast. From what you mention, it does seem like it could be a problem with having so many fonts. Did the problem start before or after you added the fonts?