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Search index 4.8 gig, reputation index 1.1 gig - too big?

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No, it's normal for those tables to grow in size according to the size of your community. They're not logging tables, they contain actual data.

Your search index will grow according to how much content you have on your site, not much you can do about that other than move to Elasticsearch and have all your search data stored there. But you'll still end up needing to store about the same amount of data in memory when going that route.

Reputation index is just records of who has given reputation on your site. That is rather large, but that likely just means the reputation system is very heavily used in your community.

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