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Another quick update. I successfully repaired the CPU Shoulder screw threading and was able to correctly reassemble the CPU boards onto the LCS. Unfortunately, when powered up CPU B is running about double the temperature as CPU A. Looking at the power consumption, CPU B is drawing significantly more power than A. Which in my opinion accounts for the excessive temperature.

I attempted thermal calibration, but the computer shut down and the CPU overheat light came on.

I know 100% the cooling system is working. In fact, the return line on CPU B is hot to the touch, again confirming the CPU is indeed running very hot. If the cooling system were not working, then the return line would be cold. The return line on CPU A is just barely warm. My leading theory is a component on CPU B might be bad. I guess my next step will be to swap A and B and see if the high temp moves with the card. Does anyone know why the power draw and idle temp can be so high? Are there known components that go bad on this card?

This is not my first experience with vintage computing. In fact at one point, I resurrected an old NeXT Computer, way back before they were collectable and expensive (should have kept it, hehe). I'll keep peeling the layers of the onion until I get to the root of the problem.

Responding to Sasho - Yes I did consider going air cooled. But that mod doesn't look trivial. I'd have to find two late '05 dual core heat sinks, and there's machining involved. Rebuilding the LCS seemed simpler, and so far I am happy with the result. I just need to find out why CPU B is drawing 25% more power than A and running hot.
 
Yeah I guess I was lucky having two g5s to thinker with.

Anyway the thing is I had the same issue with CPU B - and btw the diagnostics said similar thing about the voltage but oddly enough when I put the hefty heatsinks the issues stopped.

(Like CPU A was normal like 39 C and CPU B was 96 C)
 
My questions to the group are, do I need to consider servicing the liquid cooling system any time soon? Should I replace the thermal paste on the CPUs? I would like to upgrade the graphics card from the stock 6600. Is there anyone out there who could flash an ATI Radeon for me? Or sell me one preflashed? I don't have a PC to do this on.

Congrats! I got ATI X1900 NOS (Mac version) from eBay for about 90 bucks not too long ago, they may still have stock left.

Make sure to bump RAM and consider installing SSD (Intel 320 Series are good).
 
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Today I swapped the CPU cards and carefully reassembled my Quad. The system seems to be working and I feel like I just tamed four wild horses and got them to play nicely with each other in the same stables. I have been loading up the system, compiling binaries, compressing video, listening to music, playing YouTube, etc. but haven't been able to make the system thermally shutdown. See picture above. Temperatures on CPU B max out in the 70C range, then quickly cool down back to the low 50s when idle. Both CPUs are running cooler than on my air-cooled dual core G5. Fans are louder than I'd like, but they're not running full out either.

That being said, when I run thermal calibration, the system gives an error message that the maximum CPU temperature has been exceeded. I know this is not the case and unlike earlier attempts, the system doesn't shut down, it just gives me the error and I can either reattempt calibration or shut down. I'm not sure why calibration isn't successful. But at least now I have a 100% useable system. I'll let it cool overnight, and try calibration when the ambient temperature is cooler. But at this point, I'm inclined to say this project has been successful and I now have a reliable and useful G5 Quad. I have learned more about G5 quads and liquid cooling systems than I ever wanted to know and I can now think about upgrading the RAM, getting an SSD, better video card, etc.

I'll probably repurpose my dual core G5 as a server and play with OS X server over a network. I have a couple of older intel- iMacs that I can put Snow Leopard on and have a small vintage Mac home network.

Again: This is the best Power PC Mac ever made, and it's also the worst Power PC Mac ever made. Do not buy this computer.
 
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There are like 12 bolts you need to remove from the processor heatsinks and the whole assembly should just lift out. You NEED to change the thermal paste on the processors and the u3 chip on the back of the board or you will continually have problems with it.
The multicore G5 PowerMacs don't use the U3 northbridge, they use a new IBM designed U4 northbridge that's more reliable.

As for OP, you may reach out to Cameron Kaiser if you're still having issues: Link
 
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