Pretty sure you have a clogged burner or maybe more. Open the front panel and inspect the burner tubes for something that might have clogged them up. Here in FL we have mud daubers that love to make their home inside the older Haywards. When the burners get clogged up it causes the unit to burn bad. The job to clean the unit is a very messy job.
You will need to clean the unit. Shut off gas, turn off power to unit if it is electronic, remove burner tray, clean out clogged burners. Now with the tray removed, get a hose with a nozzle on it. Remove the top of the heater and spray down thru the top to get the soot off of the heat exchanger. Once you start spraying you will see tons of black powder substance, soot. Be careful, the soot is nasty and if you get it on your clothes you will not be happy. Spray from the top for a decent amount of time. Then set the top back on the heater and take the hose and put it up in where the burners go and spray up into the heat exchanger. Be careful as more black soot will spray out the top. I suggest you put a towel over your head or you could get a bath on black water. Again spray for a decent amount of time. Then remove the top and spray from the top down one more time.
Now that it's all clean you can put the burners back in, hook it all up, put the top on, and fir it up. hopefully you have the problem solved. Now if it knocks and bangs or sounds like gravel when it heats up, then the bypass is broken and that's another story.
Good luck.