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After I updated Magento, it starts to use more CPU than usual as you can see below. After 05-07, CPU system time increases, just at the day I updated Magento to 1.9.3.3.

After 05-07 cpu system time increase, the day i deploy Magento 1.9.3.3 update

In this second image you can see CPU usage closer. After clearing cache, CPU system usage drops (between 21:00 and 22:00):

cpu system drop after cache clear

Is there any explanation for this high CPU system usage after Magento update?

I guess cache is more used in this new Magento version, so that it uses more system to read the cache.

Is this ok? Should I care?

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iowait time is what you want to watch out for. Other than that its hard to give you good advice other than at first glance it looks fine.

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