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COOLING AND QUIETING, REVISITED
I ran with this setup for about four months, and was fairly
happy with it. However, when I opened up the system to do some
maintenance, I noticed that the CPU and motherboard
temperatures dropped 12°C and 3°C respectively with the side cover off. This
caused me to rethink my approach.
As had long been evident, the hardest thing to do in
this system is cool the motherboard quietly. When I took a closer look
at the board with this in mind, it was clear that the motherboard
heatsinks are designed to catch the downwash from the stock CPU cooler.
This is especially true of the VRM and the MCH, highlighted in this
photo from Newegg:

Hot spots on the P5LD2 motherboard that need airflow: Vcore and MCH heatsinks.
This caused me to question the choice of the Ninja, which has
all its airflow parallel to and well above the motherboard. I reread the
recently updated SPCR
heatsink summary (which coincidentally warns about
overheated VRMs), and saw that the Thermalright
XP-120 rated nearly as high as the Ninja, so I tried one. I was surprised when I
unpacked it by how much smaller the fins are than the Ninja. This
turned out to be significant, because when I mounted its fan blowing
down, the air leaving the fins was so hot it actually increased
the motherboard temperature. I also tried blowing up through the fins,
hoping this would suck air through the motherboard heatsinks, but that
only worked when the fan was run at an unacceptably loud speed. Oh
well, back to the Ninja.
While remounting the Ninja on the motherboard, I noticed that
the fan could be mounted closer to the motherboard and provide some
turbulence around the VRM and northbridge heatsinks if the retaining wires are
stretched around the Ninja mounting clips, like this:

The fan can sit right on top of the northbridge heatsink if the retainers are bent around the clips.
It occurred to me that the temperatures were so much lower
with the side cover off that I might be able to slow down the fans
enough to make the overall system both cooler and quieter.
This turned out to be the case. When I set all four fans to 5V, the
system was cooler and significantly quieter than my prior setup, and was by now much too quiet to measure with the tools at hand. I did have to seal
the gap in the lower chamber between the disk cage and the fan bulkhead so that the HDDs would get some air
flow. A bit of packing tape did the job – duct tape would not be removable.
At this point, the back fan was the loudest thing in the case. Its sound was a low thrumming combined with a 400-Hz tone. The
center of the fan was resonating just like the top fan had earlier. I removed the silicone gasket, and it was quieter, but still
resonated. Then I tried cramming some folded tinfoil between the fan hub and the case grill to damp the ringing, but this was only partly effective.
This all-5V setup ran quite well, but over time the motherboard
would overheat, causing erroneous fan sensor readings or other errors. In an attempt to increase the turbulance around the
motherboard heatsinks, I turned up the CPU fan to 985 RPM, but that didn't help. What worked better was increasing the top case fan to 1010 RPM
while leaving the other three fans at 5V. I ran the system this way for a week or so.
While revisiting how much I could overclock (discussed
below), I continued to encounter motherboard heat issues. Clearly it
was time to take direct action, and mount an additional fan blowing
directly at the motherboard heatsinks. By happy coincidence an
AcoustiFan can be nestled snugly on top of the front pair of DIMMs, which is
where I mounted it. I also moved the CPU fan to the front of the Ninja
so these two fans would blow back across the various heatsinks. I put
a bit of foam on the motherboard fan hub where it bumps against the
graphics card, and secured the fan with a couple of cable ties and some
elastic, as shown in this photo.

Directly cooling the motherboard
with a fan set on top of the DIMMs.
This arrangement not only cooled the motherboard heatsinks, it significantly improved the graphics and PCI card cooling, and let me increase the graphics overclocking. However, it doesn't cool the northbridge chip optimally because its heatsink fins are perpendicular to the air flow. The geometry of the mounting clips
doesn't allow for rotation of the heatsink. Rather than do radical surgery, I decided to insert a simple air deflector. This dropped the MCH heatsink temperature a couple of degrees. Here's a photo:

An old business card used as an air deflector for the MCH heatsink.
The back case fan remained the loudest part of the system even at 5V, and it still had that annoying ringing. So I tried turning it off altogether to see if it was really needed. It wasn't: the temperatures barely budged with it off. This
resulted in my next configuration: case open, top case fan 5V (695 RPM), CPU fan 5V (685 RPM), power supply/hard disk fan 5V (675 RPM), motherboard fan at 995 RPM, and rear panel case fan off.
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