Comment 12 for bug 1267507

CRC acceleration can't have any effect there, it is engaged only at replication stage. The crash happens way after.

No wonder it worked this time - galera was not loaded and the crash happens in galera. It looks like wsrep_provider was not configured in effective my.cnf

I would not worry about physical size on disk that much - 5.6 may be using different file format. What's important is the number of rows and table definition.