Help with Frankenmac

[Lxixboss]

Ten years after their release and these Mac Pros are still a lot of fun to own and to work on. I have worked on a lot of original Mac Pro 1,1's and have managed to resurrect many from what was seemingly certain death. This last one, however, has me stumped.
I picked this up as a throw-in yesterday. It was reported by the seller/giver as "working sometimes". This reports itself as a Mac Pro 2.1 with two 3.0 Quad Core CPU's. The symptom is that it randomly reboots or sometimes goes into a boot loop chiming repeatedly.
I noticed that, when it reboots, the two "CPU Overheat" LED's are lit. So, I decided to take the thing apart and look at the CPU cooling situation. Right away, I noticed some differences from the 1,1's I had worked on previously... like that second screw holding the CPU fan assembly in place and the different location of one of the CPU sensor plugs (where both are along the left side of the heatsinks). Digging deeper, I noticed a type of black plastic material between the bottom of the CPU heatsinks and the motherboard. The CPU heatsinks also seemed to be glued on as they did not want to just pull off. Anyway, seeing how the thing was basically free, I got a spudger under one of the heatsinks and popped it off. I did the same with the other. Looking at the tops of the CPUs and the bottoms of the heatsinks I could see a shiny silver material on both along with a metal gasket on the bottom of the heatsinks. After some online searching, I surmised that this was the fabled "Krytox" system (although what it was doing on a 3GHz system, I don't understand since it was apparently only used on the 3.2GHz systems). I tried to get the silver stuff off but had very little success. I decided just to add some Arctic Silver and put everything back together. If did not help (nor did it seem to hurt). I can often boot the system and get a minute or two of stable operation before the mouse pointer freezes and the thing reboots itsels and the CPUs overheat and yadda yadda yadda.
Seeing that it's a ten year old system, what I think think I might have here is a Frankenmac... a Mac Pro that has had parts swapped in and out, perhaps a little willy-nilly. That might explain the system reporting the CPU's as 3.0GHz but with the Krytox system. I forgot the mention that the system is running (if that is the right word) El Capitan 10.11.6 with the 32-bit efi.boot file in the appropriate locations. Another complication is that I can't do much software sleuthing as the machine shuts after a minute or two of use and then I have to let it cool down before it will boot up again.
So, what I would like to do is replace the existing CPUs with a pair of 5150's I have lying around to see if the problem is with the CPUs. I also have to solve the heatsink situation. I thought I would simply try to wear the Krytox off the bottom of the CPUs using 2000 grit sandpaper and elbow grease. (I understand that the specialized solvents required to do this chemically are just crazy expensive.) I thought that I might then try to re-install them onto the 5150's with Arctic Silver and without the metal gaskets.
Can anyone give me some guidance with this?

Thanks in advance,

 

[Surrat]

Sounds like a genuine 2,1 to me !

The 3ghz 5365 xeons in the 2,1 were 150 watts each, so they got krytox.
You shouldnt have removed the heatsinks, that ruins the krytox and cleaning it off is pretty irritating.
The 2,1 mac pro is not a 1,1, it uses many design features of the 3,1 mac pro. The parts you describe all fit into what I know about the 2,1. I have one and did a write up about it already about the differences from it to a 1,1. It even uses a 3,1 type power supply, and not the 1,1 type.

The 2,1 mac pro has more in common with a 3,1 than it does with a 1,1.
[doublepost=1481759696][/doublepost]As to your repair question.

I would replace the heatsinks with a set from a mac pro 3,1, it should be better than trying to clean off the unique 2,1 heatsinks. Same for the cpu's, you should be able to use your 5150, or 5160, or even get a set of clean 5365 from retired servers on ebay.

My 2,1 has a failed power supply, which I havent replaced yet, its possible yours has the same problem.

I upgraded a 1,1 I have to a sudo 2,1. I used clean X5365 cpu's from ebay, clean mac pro 3,1 heatsinks (had to switch the heat sensor on one of them from the original 1,1 heatink), Radeon HD5870 from mac pro 5,1, and flashed the EFI to 2,1. It runs so well I took it to work and use it at my job as my main computer there running El Capitan.

 

[Lxixboss]

Hi Surrat,
I just read your two posts about the 2,1. Very informative and well said! While there may be some motherboard and/or PSU problems with my 2,1, I am not willing to throw in the towel yet. Perhaps you would be willing to share some of your experience with me. Here is what I did and what happened:
-I used 500 grit sandpaper to remove the Krytox from the bottoms of the heatsinks. It came off quite well and did leave some scratches on the contact patches but I figured it wasn't a big deal. (Maybe I was wrong???). I did not want to put the sandpaper to the CPUs so I put them aside at first.
-whenever I swapped out a CPU, I cleaned the thermal paste from the CPU (except, of course, the Krytox) and the heatsink and re-applied a diagonal bead of Arctic Silver 5.
-I used the existing heatsinks but did not use the metal gaskets. I also noticed that, unlike 1,1 heatsinks that have a smooth copper surface at the contact point, these 2,1 heatsinks seemed to have a grey metal (proabably aluminum or some alloy???) raised rectangular surface somehow stuck to the smooth copper surface.
-I installed a matched pair of 5160's I had lying around. Chime but no boot and a "CPU B overheat" red light on the motherboard. Thinking it might be a bad CPU, I switched the two CPU's around and got the same result.
-I then removed the 5160's and re-installed the original 5365's (Krytox covered and all). With these in place, I got about five minutes of rather sluggish performance before a spontaneous shutdown and boot loop. I was running Activity Monitor to see if the system was throttling the CPUs and it did not seem to be the case as total CPU usage was on the order of 2%. On one occasion, both CPU overheat lights were on after the bootloop. Since I was running Macs Fan Control, I noticed that CPU A was running at 47C while CPU B was running at 60C briefly before the spontaneous shutdown.

Here is what I think I will try next:
-It seems to me that I have a CPU cooling problem. I was thinking of trying a pair of heatsinks from a 1,1
What do you think of this idea?
-Could it be that the fact that I am not using the metal gaskets be a cause for this overheating? I could try re-installing them (although one was bent, I think I can straighten it out).

Anyway, if you have the time and inclination (or if anyone else want to chime in), please give me your thoughts... then there's the 5,1 I am trying to resurrect... but that's another story...

 

[Surrat]

Those gaskets dont matter, they were only there to keep the krytox in place before it hardened when the system was assembled.

47 and 60c are not overheating for those cpu's, I think the problem is elsewhere.
The 5160 are only 80 watt cpu's, and those heatsink units are made for 150 watts.
I think trying to run those 5365 cpu's with old krytox caked on top is a mistake, they will not transfer heat away properly, and you will get hot spots, maybe severely. I couldnt get the krytox off my cpu's without risking ruining the finish on top, so I stopped trying to make them work and bought a set of clean cpu's off ebay. They worked perfectly.
Did the fans go to high as soon as you powered on the mac pro? If the heatsink sensors are bad, it will cause that, or if the cpu's have bad internal heat sensors it could be part of the problem also.
I'm pretty sure you can install just one cpu for testing if need be, if you do that, use the lower socket, not the upper.
Did you make sure the cpu socket pins didnt get any lint or dust bunnies on them? they have to be super clean or problems will happen. When I first upgraded my 1,1 with the quad core cpu's, one refused to work, and it turned out it was a little dust bunny that got under the cpu, and was blocking some pins. Also make sure that none of the cpu socket pins are bent, they are fragile.

If you can get the computer to just boot up, even if its with one cpu, you could try and download the apple service diagnostic dvd images to run hardware tests. Could be really helpful.

 

[Lxixboss]

Thanks again Surrat. I have searched high and low for those Apple Service Diagnostic DVD images and have found only malware infested torrent sites. I did find the AHT for both the 1,1 and the 2,1 and will be trying them out when I get a chance. If you know of a good repository of those Apple Service Diagnostic DVD's, please share them.

 

[Lxixboss]

Well, I certainly don't want to jinx it but this problem seems to have been solved. I have had this computer running for just over five hours. I have run several applications, have installed hardware and software, have performed several (voluntary) restarts and all seems well! BADABING!!!
Over the past few days, I have been wracking my brain and Googling the hell out of another of my computers trying to find a way of taming this misbehaving cheese grater. I must have taken the whole damn thing apart half a dozen times. After a while, I started noticing that the "bad DIMM" lights were starting to light up on the risers. Always DIMM 2 on riser 1 and DIMM 1 or riser 2. I tried inversing the DIMMs and even using different DIMMs that I had lying around; all to no avail. The same two DIMM slots were always being flagged as containing bad RAM. I remembered reading something about using a pencil eraser to clean the edge contacts on the risers and on the DIMMs. So, I did that. I also cleaned the same contacts along with the RAM slots in the risers and on the backplane board with 99% Isopropyl alcohol. Boom! Bob's your uncle! Works perfectly. Right now, Mac's Fan Control is reporting nothing over 80C (and that is the RAM risers). I had been worried about the CPU heatsinks as I had sandpapered the Krytox off the heatsinks, had discarded the metal gaskets and had just applied some Arctic Silver 5. Well, that worrying seems to have been for nothing as the CPU temps are hovering in the high 40's and low 50's. So, for the time being, it seems to have been solved. We shall see if this is permanent or temporary.. I would like to thank Surrat for his advice and general hand holding. By the way, if anyone knows where to get a hold of those Apple Service Diagnostic DVD images, I would surely be beholdin' to them.