Disk write in iotop when doing mysql "Copy to tmp table"
If your new instance of MySQL is creating temporary tables with the InnoDB storage engine, the innodb_io_capacity could be throttling the rate at which it writes pages to disk.

However, even throttled, I would expect a mere 400MB to be pretty quick to write to disk. Have you considered the possibility that the disk drives on your new server are simply faulty?

I would recommend running some benchmarks with sysbench or iozone to see if you can reproduce the slow I/O speed without MySQL.



Re your comment:

The best figures to look at for a database server are random read, random write, and mixed workload. Run a similar benchmark on your old database server, and compare them. If your new database server has significantly lower numbers, that would explain the difference you're seeing.