CI runs slow with Nginx + PHP 7.1 + MariaDB

If someone is interested in the solution/cause of the issue:

After some more debugging I was able to identify the problem to be related to MySQL. CI and Wordpress are using InnoDB Engine while MODx and my other applications were using MyISAM. I converted one MODx installation to InnoDB and suddenly it started having exactly the same issues:


As I mentioned earlier most slowlog entries were related to sessions, so I digged in a bit deeper, and I think the problem is InnoDB clustered indexes. 

In CI the PK of the default CI session table is likely to cause those issues when used in certain setups with InnoDB. Let me sum up the following post which explains it in more detail:

From MySQL Docs:

Every InnoDB table has a special index called the clustered index where the data for the rows is stored. Typically, the clustered index is synonymous with the primary key. To get the best performance from queries, inserts, and other database operations, you must understand how InnoDB uses the clustered index to optimize the most common lookup and DML operations for each table.

From this SO answer:

According to The Queen Of Indexing - Kimberly Tripp - what she looks for in a clustered index is primarily:

• Unique
  
  
• Narrow
  
  
• Static
  

And if you can also guarantee:

• Ever-increasing pattern
  

then you're pretty close to having your ideal clustering key!

In the case of CI session table this is not really the case:

• Unique => yes
  
• Narrow => yes
  
• Static => yes
  
• Ever-increasing pattern => no
  

Here's what can happen when a non-ever-increasing clustered index is used. Source

If the clustering key is ever-increasing then new rows have a specific location where they can be placed. If that location is at the end of the table then the new row needs space allocated to it but it doesn't have to make space in the middle of the table. If a row is inserted to a location that doesn't have any room then room needs to be made (e.g. you insert based on last name then as rows come in space will need to be made where that name should be placed). If room needs to be made, it's made by SQL Server doing something called a split. Splits in SQL Server are 50/50 splits - simply put - 50% of the data stays and 50% of the data is moved. This keeps the index logically intact (the lowest level of an index - called the leaf level - is a douly-linked list) but not physically intact. When an index has a lot of splits then the index is said to be fragmented. Good examples of an index that is ever-increasing are IDENTITY columns (and they're also naturally unique, natural static and naturally narrow) or something that follows as many of these things as possible - like a datetime column (or since that's NOT very likely to be unique by itself datetime, identity).

In my case with CI and other applications this lead to the following issue:

When you are inserting a new row (the "random" hash guarantees that) it gets inserted in a random location of the index. This means that it sometimes will find no space there available to be inserted (note that InnoDB always leaves some space free in the index but when that free-available space is filled) there has to be some rearrangement of the index - and that takes time.

What the rearrangement is also causing over time is fragmentation of the index. Which will eventually make other queries and statements slower.

The solutions for me is to either use a different session driver, or switch the session table to MyISAM.