"high CPU usage" It might very well be "high IO usage".
Try this :
Copy (using explorer, the shell, whatever) a huge file.
This will create load similar to ALTER TABLE.
Measure throughput, how much is it ?
If your server blows up just like it did on ALTER TABLE, you got a IO
system problem.
If everything is smooth, you can look into other things.
How's your fragmentation ? Did the disk ever get full ? What does the
task manager say (swap in/out, disk queue lengthn etc)
PS : try a separate tablespace on another disk.
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