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I have two EK-XTOP REVO D5 PWM pumps, I have just filled my two loops to leak test and it seems one of them runs at full speed and the other runs at a much lower speed (10% ish).

Neither one has the PWM header plugged in, and both are powered via the same 4x Molex cable from the PSU. 

How likely is the one running full speed faulty, or am I missing something?

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Different D5's pwm controller versions. 

The new version is running 100% with no PWM signal, the older one runs at mininum RPM with no PWM signal.

To get it to the full speed you need to have constant +5v on on the PWM wire. +5 volts is a red wire on molex connector. (do not mix it with yellow it is 12volts - you will kill the pump) The PWM is the 4-th pin on 4 pin fan header.

CPU: i7 8700K OC 5.0 gHz, Motherboard: Asus Maximus VIII Hero (Z170), RAM: 32gb Corsair Vengeance RGB 3200 mHz, GPU: Asus Strix OC gtx 1080ti, Storage: Samsung 950pro 500gb, samsung 860evo 500gb, 2x2Tb + 6Tb HDD,Case: Lian Li PC O11 dynamic, Cooling: Very custom loop.

CPU: i7 8700K, Motherboard Asus z390i, RAM:32gb g.skill RGB 3200, GPU: EVGA Gtx 1080ti SC Black, Storage: samsung 960evo 500gb, samsung 860evo 1tb (M.2) Case: lian li q37. Cooling: on the way to get watercooled (EKWB, HWlabs, Noctua, Barrow)

CPU: i7 9400F, Motherboard: Z170i pro gaming, RAM: 16gb Corsair Vengeance RGB 3200 mHz, GPU: Sapphire Vega56 pulse with Bykski waterblock, Storage: wd blue 500gb (windows) Samsung 860evo 500Gb (MacOS), PSU Corsair sf600 Case: Motif Monument aluminium replica, Cooling: Custom water cooling loop

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if you have a floppy connector at the end of the molex cable just connect the 5volts with PWM cable with a paper clip

CPU: i7 8700K OC 5.0 gHz, Motherboard: Asus Maximus VIII Hero (Z170), RAM: 32gb Corsair Vengeance RGB 3200 mHz, GPU: Asus Strix OC gtx 1080ti, Storage: Samsung 950pro 500gb, samsung 860evo 500gb, 2x2Tb + 6Tb HDD,Case: Lian Li PC O11 dynamic, Cooling: Very custom loop.

CPU: i7 8700K, Motherboard Asus z390i, RAM:32gb g.skill RGB 3200, GPU: EVGA Gtx 1080ti SC Black, Storage: samsung 960evo 500gb, samsung 860evo 1tb (M.2) Case: lian li q37. Cooling: on the way to get watercooled (EKWB, HWlabs, Noctua, Barrow)

CPU: i7 9400F, Motherboard: Z170i pro gaming, RAM: 16gb Corsair Vengeance RGB 3200 mHz, GPU: Sapphire Vega56 pulse with Bykski waterblock, Storage: wd blue 500gb (windows) Samsung 860evo 500Gb (MacOS), PSU Corsair sf600 Case: Motif Monument aluminium replica, Cooling: Custom water cooling loop

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