Is the PWM header that you are having trouble with the one located closest to the IO shield? Or is it the one located on the side of the motherboard where the SATA connections are?

I am on an X99 Classified and have a closed loop system with dual fans on a passive Y splitter (came with the closed loop) working off that back PWM connection. They work fine under temperature control, ramp up, ramp down and the RPM is returned.
 
You might want to check the temperature profile under the SMART control for the CPU2 header to see at what temperatures the fan kicks in at what speed.

gtxjackbauer
I have my self powered pumps (MCP-35X2) connected via Y-Splitter to the main PWM CPU Fan header and they are working great controlled via BIOS.  My fans on the other hand, x9 Swiftech Helix120 PWM fans on a self powered Swiftech 8-way PWM fan splitter, are connected to the second PWM CPU Fan header.  When I change settings on the first header for my pumps, they respond accordingly.  When I do the same for my fans, they do not.  They have been running at full load.  If my fans or pumps aren't getting a PWM signal which is needed since they are spec'd for that, they will run @ 100% speed.  I am guessing, even though its advertised that the second PWM Fan header isn't really PWM OR my PWM signal isn't strong enough to transfer to all the fans, including the countless Y-splitters used to bunch up the fans from different locations of the rig.
 
Anyone have anything similar that can give their insight on what might be happening here?
 
-Thanks

I have the same swiftect power block i could only get it to work on the cpu1 fan header.

Any update on this issue?  I just recently started having issues with my EVGA X99 Classified "CPU Fan 2" connector while using the Cooler Master 280L cooling kit.  I can't seem to get the fans on the radiator spinning properly.  It appears only 1 out of the 2 fans are spinning at approximately 10% speed. I also noticed in the BIOS the "CPU Fan 2" RPM speed is showing "N/A".  Any thoughts?  This seemed to work properly for the first few months  - radiator fans seemed adaptive and could be set to "MAX" via bios for extreme cooling.  I'm running the latest BIOS update v1.16 (released 3/5/2015).
 
 

Andrey_T

siliconcpuI just recently started having issues with my EVGA X99 Classified "CPU Fan 2" connector while using the Cooler Master 280L cooling kit.

 
How exactly are you connecting the fans? Are you connecting each Cooler Master fan to a separate MB fan header? Or are you using the Y-harness from the Cooler Master kit and connect both fans to a single MB fan header?
 

The fans on the Cooler Master radiator are connected via 4-pin Y-cable to the "CPU Fan 2" motherboard connector.  I recall being able to see the RPM in the bios and having control over the speed of these fans via the Y-cable but can't seem to get a reading anymore.  It only shows "N/A" in the bios.  One fan is running super slow and the other is not moving at all.  Despite having these fans not operating properly I'm running at stock i7-5930k speeds (3.5Ghz) with idles at 32C.  Not too worried but I'm trying to find a solution.  In the mean time I've purchased a 4-pin PWM adapter to molex connector to give me 100% juice on these fans.  It should be arriving tomorrow but I'm trying to figure out why this stopped working on it's own?

The other really weird part is if I take the Cooler Master 4-pin pump cable and move it from CPU Fan 1 to 2 the pump BARELY works.  It doesn't seem like this CPU Fan 2 is providing enough power.  Using the radiator fans on "CPU Fan 1" gets both fans spinning at 100% and quite nicely :)  I can't explain what is happening to this CPU Fan 2 connection on the board but it doesn't seem to be producing the same amount of power it did the last couple months.... thoughts?

siliconcpu
The fans on the Cooler Master radiator are connected via 4-pin Y-cable to the "CPU Fan 2" motherboard connector.  I recall being able to see the RPM in the bios and having control over the speed of these fans via the Y-cable but can't seem to get a reading anymore.  It only shows "N/A" in the bios.  One fan is running super slow and the other is not moving at all.

 
What is your current BIOS fan profile setting for "CPU Fan 2"?
 
If in X99 "CPU Fan 2" is not a true PWM header (which is apparently the case), then it controls the fan speed by adjusting the DC voltage, just like other 3-pin fan headers do. The problem with this method is that if the DC voltage is too low, the fan might not even be able to start (or will rotate slowly and inconsistently). The behavior might vary from one fan to another even if both fans are from the same batch. This looks exactly like what you observe: one fan is stalled, while the other is barely spinning.
 
Also, when you use Y-harness, the RPM feedback is taken from only one of the two fans ("master" fan), which is indicated by the label on the Y-harness. If in your case the "master" fan happened to be the one that does not spin at all, then it is perfectly expected that you see "N/A" in BIOS as RPM value from your fans. The "master" fan is standing still, which is why BIOS shows "N/A". If you swap the fan ends of the Y-harness, you might be able to see the RPM value from the fan that is spinning slowly instead of "N/A". (Try this.)
 
Anyway, have you tried setting "CPU Fan 2" to max speed mode in BIOS? Does it make both fans spin at full speed?
 

Any update on that issue? I'm having the same problem...

sputnik7913
Any update on that issue? I'm having the same problem...

The x99 Classified only has 1 PWM controlled fan header, cpu1.
 
The FTW K has 5 PWM fan controllers.

bdary

whitrzac

sputnik7913
Any update on that issue? I'm having the same problem...

The x99 Classified only has 1 PWM controlled fan header, cpu1.
 
The FTW K has 5 PWM fan controllers.

Minor correction here.  The Classified has two PWM CPU fan headers.

No it does not. The only true PWM header is the CPU1 header. CPU2 does not offer PWM control.

The descriptions in the BIOS confirms this, as does my experience trying to use a PWM spliter on CPU2.

bdary
So the manual is wrong?  Interesting.  What BIOS descriptions are you referring to?

On the right side when adjusting fan speed. It lists pwm control for the cpu1 and voltage for all the others.
A powered pwm spliter only works on the cpu1 header too

blue box on the right, it lists pwm mode or voltage mode

I've tried bdary.  It doesn't work unfortunately. 

Hi guys
 
The Last update to the BIOS addressed PWM fan header so 
please make sure you update to the latest BIOS


I run a total of 4 fans and a Pump on my X99
2 fans on "CPU" (Y splitter)
2 FANS on "CPU 2" (Y splitter)
and the pump an "AUX"

 
Click on the blue bar to reveal hidden menu
 

 

 
Hope this helps

Regards, Rick
 
 
 

Its not........... it's a micro 2 X99
 But it does have FIVE 4 pin headers two of which are CPU and CPU 2
 
after I updated to the new BIOS I noticed some extra functions and settings about PWM controll

Just trying to help

Regards Rick

the new bios didn´t fix anything, still the same issue