It applies only on Linux :p

Clone source tree from GitHub

git clone git@github.com:mysql/mysql-server.git

Wait with coffee :)

switch branch if you want

cd mysql-server/
git checkout 5.6

Build

Prepare build directory

mkdir /path/to/mysql-server-build/
cd /path/to/mysql-server-build/

Do build

cmake -DWITH_DEBUG=1 /path/to/mysql-server/
make -j8
make test

Debug run

Prepare a test query case

cd mysql-test/
mkdir t/
echo "select 1;" > t/example.test
# initiate database
./mysql-test-run.pl --record example
# debug run (need X11 forwarding: xterm opens)
./mysql-test-run.pl --gdb example

Debugging

At the beginning of debugging, there is only one breakpoint at main() (i b).
Repeatedly run c and it terminates once, xterm resides.
Rerun the server by r in the xterm shell.
Make a breakpoint at mysql_parse by b mysql_parse.
Run c and the server starts to wait for a connection

Version: '5.6.26-debug-log'  socket: '/path/to/mysql-test/var/tmp/mysqld.1.sock'  port: 13000  Source distribution

You can connect to this instance via 13000/tcp 127.0.0.1 (not localhost).

mysql -uroot -h 127.0.0.1 --port 13000 test