Extruder motor making a knocking sound, nozzle is not clogged I've been trying to print anything for the past few days. Every time I go to print something the printer stops pushing plastic out and usually the motor makes a knocking sound.

My original thought was that my E-steps were off (because they were) but I solved that and I still have a problem. Then I noticed that I was struggling with getting the PLA filament to feed into the nozzle. I assumed it was a clogged nozzle and possibly heat creep (because I was a dummy and used my old, bowden retraction settings on my new, direct extruder). I cleared out the clog and I'm able to feed plastic through after disengaging the idler arm. Though, I do struggle getting the filament into the nozzle. Maybe it's due to the Hemera's tight tolerances or due to a misalignment in the hot end, I'm not sure yet. Once I do get the plastic in, it quickly and easily pushes through and spits out of the nozzle so I think that my nozzle isn't clogged. I did do a cold pull the other day. 

But I've noticed that my extruder is making a knocking sound, as if someone was gently rapping on my chamber door. I also see that the gears move one step back and forth. It looks to me that the motor is stuck or frozen. I'm pretty sure that it's not skipping steps. The sound happens at varying heights and not just the first layer. The first time I noticed it, it was printing the cabin of Benchy. Z > 1 mm when I finally decided to ask this question. The sound is kind of loud, but that's most likely the resonance in the machine than a symptom, stating it nonetheless. 

My setup:


Printer: Creality CR-10S 
Extruder: E3D Hemera 
Nozzle temp: 205-220&nbsp;°C
Retraction: Initially 5&nbsp;mm at 40&nbsp;mm/s, then 0.3&nbsp;mm, then most recently none 
Motor Vref: just north of 800&nbsp;mA. (I've read somewhere that the Hemera motor wants 800&nbsp;to 1000&nbsp;mA) 


I'm just not sure what could be wrong here. I feel like I checked all the steps and I'm just missing something.
A knocking or clicking sound does not imply you have a problem, it implies that you could have a problem; it can be the characteristic of the extruder. 



My own designed 2.85&nbsp;mm filament, 1:4 speed reducing belt driven extruders make clicking sounds while extruding (independent of the layer height), I have verified that no steps are lost and the printer extrudes exactly the requested amount of filament (2.85&nbsp;mm filament requires a lot more pressure for the same nozzle size, the noise is coming from inside of the metal Bulldog housing, not the stepper adjacent, it is not stepper nor filament skipping noise). 



A clicking sound in combination with gears losing position as you describe (or filament skipping back) does mean that the pressure in the nozzle is too big for the extruder to push it through. If the gears loose position, this means that the stepper is not powerful enough to push it through, this means that more current or a more powerful stepper is required (the latter option is due to the design of the extruder not possible). If the filament skips back while the gears are in place the tension/grip to the filament needs to be increased. 

In troubleshooting this problem it is best to increase the current to the stepper close to the upper side of the specifications of the stepper and see if the knocking sounds disappear. This should not be a problem for such a priced and tested extruder system, i.e. considering the reputation and quality of E3D this extruder must work out of the box unless you have received damaged components.