^ i think it has something to do with having everything on one HDD. best try it with multiple HDD's and see if there is a diff. btw, prepare takes me max 10 minutes here and rebuild similar using a P4 3.2 HT with multiple HDD's. maybe something to do with Vista?
Using the external drive is probably a bad idea. An SATA drive is much, much faster than USB-2... Not sure what it could be, but both of those two phases are disc-bound while ENCODE is processor-bound, so it is almost assuredly disc related. I usually complete a PREPARE in 6 minutes (12-13 if I'm doing REDISTRIBUTION). REBUILD usually takes 10-15 minutes (with burn-time included). This is with a standard 250GB ATA drive (with 8MB cache).
Connect the IDE drive and try running on it alone... I'm sure you have a drive throughput problem. It could be anything, maybe caching, I don't know... but your system is running incredibly slow on the part of the process that depends on disc.
@downloada: Make sure if the caching is supported by ur drive, turn caching on. Secondly u can try increasing the buffer size by increasing the buffer size for your IDE size. I am not sure in Vista hw u would tht, but here is general concept of it: edit system settings and increase buffer size for device on IRQ line 14 or 15 depending on whether your IDE drive is plugged onto primary or secondary channel.
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