are you using 7-branch?
in my 7.1 system there is same problem. top shows often nonsense in CPU
usage of a process, but totals are OK.
you even gave an example - bzip2 can't use 0% CPU running - more close to
100% :)
as long as everything goes fine 100% CPU load is OK. if it's mostly mysql
then optimize your database, if you can't change hardware
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