Jeremy Cole has an excellent article on why a mysqld instance will swap despite proper memory settings on modern hardware here. A quick hand-wave of a summary goes: in modern architecture, every process is, by default, limited to a 1/Nth of the available memory on a machine, where N is the number of cores, and will start to swap on disk when all the available memory in that 1/Nth is consumed.

The eventual solution for a large, single-instance mysqld-running machine is to enable numa_interleave in the mysqld_safe section of the config:

Implicitly, when that flag is set, mysqld is being started by mysqld_safe with a numactl flag that will spread the memory …