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If I activate Layout Cache on a live page, after 4-5 hours the checkout gets significally slower. After some hours more it is up to 20 seconds load time.

It's gone, as soon as I deactivate the layout cache.

What could be the reason for that? What point I should start diggin'?

I have a CE 1.9.9.3 running.

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There is no 1.9.9.3 - I assume you mean 1.9.2.3. And you want to profile, I recommend blackfire.io but you can use xdebug too

The Magento extension Aoe_Profiler is also a good start to find bottlenecks. (Thanks @fschmengler)

There is NO way for us to solve this, and I never heard about such an issue.

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The solution is quite simple. The cache folder never got flushed and there was a lot of files piling up. This post helped me with a solution:

    #!/bin/sh
MAGENTOROOT="htdocs"
### Delete Frontpage Cache that is older than one day. ###
find $MAGENTOROOT/var/cache/fpc* -type f -mmin +3600 -exec rm {} \;
### Delete Magento Caches that are older than 120min ###
find $MAGENTOROOT/var/cache/mage* -type f -mmin +120 -exec rm {} \;
#### Delete repotrts older than 7 days ###
find $MAGENTOROOT/var/report/ -mtime +7 -exec rm -f {} \;
#### Delete session data (should be the same time as session cookie time) ###
find $MAGENTOROOT/var/report/ -mmin +120 -exec rm -f {} \;

https://webmasterei-prange.de/magento-checkout-cart-sehr-langsam-im-live-betrieb/

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