Repeating the above comment to provide an "answer" for this question:
The config file /etc/percona-server.conf.d/mysqld.cnf was not being included in the standard "global config" file, commonly known at /etc/my.cnf. @OP added !includedir /etc/percona-server.conf.d to the end of the global config and then the changes were visible upon restart of MySQL.
numactl --interleave=all. Or: innodb_numa_interleave=1, available as a MySQL VARIABLE as of 5.6.27. More discussion : http://mysql.rjweb.org/doc.php/memory#numa
I may be that the OS has decided to take residence in the 'first' core, and ran out of space in the memory hanging off that core. By using "interleave" you declare that RAM is really spread around ...