I recently aquired and IBM eServer x345, which is taking up to 12 hours to build a kernel!
sorry if it's stupod question but do you have softupdates enabled?
I've spent quite a bit of spare time trawling archives etc for any hints to the reason why. Initally I thought it was the disks causing the problem, but the general usage of the machine and disk I/O is pretty snappy just seems to be CPU intensive operations where things seem to lag.
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