Lost connection to MySQL server during query (no replies)

I am new to relatively new to MySQL. I am using workbench and the server is on the local PC.

I've being struggling with a problem where for more intensive queries I get the following error: 'Error Code 2013: Lost connection to MySQL server during query'. This always seems to happen after exactly 30 seconds duration.

I therefore thought that there must be some time out limit at 30 seconds. I changed all of the variables that looked like they might be appropriate/were set to 30 seconds, but this didn't help.

SET GLOBAL connect_timeout=1000;
SET GLOBAL max_execution_time=10000;
SET GLOBAL net_read_timeout=600;
SET GLOBAL net_write_timeout=600;
SET GLOBAL innodb_flushing_avg_loops=40;
SET GLOBAL innodb_sync_spin_loops=40;

Any advice would be greatly appreciated.