The CPUs I ordered on ebay from Germany (I'm living in Belgium) where sold with IHS. (Integrated Heat Spreader) I read some articles and checked some videos on Youtube where people mentioned that CPU with IHS could be installed but the Heatsink mustn't be screwed @ (over?) 80%. I did not want to detach the mac pro heatsinks, so I carefully screwed them down, tried to boot, checked the RAM, the temp sensors and the fans. (By the way, heatsink fans were full of compact dust! I do clean the "accessible" fans every 6 months, but never feel the skills to remove the heatsinks since last week)
(While you have the CPU tray out, check if the Northbridge heatsink (plastic) retainers are still intact. Ref: Mac Pro Northbridge High Temperatures due to Broken Heatsink Retainer.)

So, I could get everything to work fine!

I made some stress render with some Blender benchmark scenes. CPU's working blazingly fast! But they go really hot too without fan triggering! I read some articles about fan management and OS X since Mavericks, I wish I read them before. I've always used iStat widget (not menu and never used MacFanControl before), and the only temp sensor I've read for the past 7 years since I bought the Mac Pro was called "CPU A" and "CPU B". But with Mac Fan Controls, those names are referring to the Heatsinks temp sensors (yeah, I discovered some new sensors last week installing mac fan control ^^) CPU A Diode is going way hotter than the Heatsink! And I never checked that before.

(Did you flash your (2009) Mac Pro 4,1 bootrom to (2010) 5,1? (He later said yes.) The Mac Pro 5,1 rom has microcode changes for Xeon 56xx series CPUs, (as well as enabling faster memory and audio via Mini Displayport). Back in 2010 when testing (X5550) 2009 Mac Pro CPU temperatures (before audio/FW IO bug fixed), there was some confusion over readings/accuracy, max temps of cores/how they were determined, etc.) Temperature Monitor/Hardware monitor back then was the best/most complete/accurate utility, but I've not used any since. (2009 Mac Pro in storage for years now.) IIRC, 3rd party kernel extensions for reading internal CPU (Core) temperatures are no longer allowed in later OS X versions, but maybe developers have other ways now.)

I never had any shutdown or strange behavior with it so it was "normal". The only thing I was used to check was the Fan RPM. When spinning faster than usual, I clean the accessible ones, and used air spray to remove what I could from the heatsinks without removing them.

- When Idle, CPU A diode Temp is about 48°C (with default fan management). CPU B is always 7-10°C cooler than CPU A. It was like this before, it's a normal behavior, so I'm only concerned about CPU A. (It's normal for CPU A to have more load/usage.)
- When rendering and letting OS X to manage the fan, CPU A Diode goes up to 85°C, INTAKE and EXHAUST are running at the minimum (600 - 700RPM), Heatsinks are running at 1400-1800RPM. When at 85°C, it still goes a bit hotter, and the fan is still not making very much noise.
(When you see those temps, do you have a utility to report CPU speed to see if it's throttling back due to overtemp? (The CPU should throttle back or shut down/kernel panic if overheating.) And I'd keep a good backup - two, rotated just in case of corruption. Does Apple Diagnostics show any errors? Apple calls them 'reference codes', and they only list a general processor related code - PPR001.)
- When controlling with Mac Fan Control, I can get CPU A diode to 68 - 72 °C, but the noise is becoming quite loud and more than noticeable. Did some test all the day long, and then I shut the computer down for the night.

The next day, when booting the Mac Pro, a fan was going crazy. I checked Mac Fan Controls, and there was a temp sensor missing. It was working well before, but it seems that the Heatsink connection to the CPU board was too loose. (Cooling/system fans typically have a failsafe mode - if no reading (or open ckt) is detected, they default to max speed.)

The good thing: the cpus I bought are working right, the bad thing, this is not the reliable way of upgrading the (2009) Mac Pro. You can upgrade with a lidded CPU, but it is definitely not a safe operation. The best thing to do would have been to buy a de-lidded CPU from DNcomputers for example. But it was too late. I've got some tech background working at an apple official reseller at the technical service, and I do not like having heatsink not properly screwed down. Even if still working fine with MacFanControl. I clearly do not want the cpu board the be crushed too, and a lidded CPU not correctly placed can damage the cpu board by long term!

So, I started reading about IHS removal process. Found a bit of everything, even a hammer and a vice XD ! Finally found someone on YouTube who did it correctly with a dedicated video for the Mac Pro: www.youtube.com/watch?v=aPhDfUkll-ol. I did the same thing, but the part when he scrubs the chip with water and sandpaper! I found it a bit too crazy. I scraped it carefully with a plastic sprudge tool.
I do not recommend anybody without some tech skills to try the same process!

It was a very stressful moment. So stressful that I prefer to do it only one at the time. I did a first one, and then started the macpro with only CPU A. If CPU A is dead, 350€ lost. But I've got a second MacPro 4,1, single core and this one requires a lidded CPU so the left one would fit. If CPU A is working, let's do the other one.

CPU A is working! So, I did the other one, and, it went a bit harder than the first one. Some of the paste melt on a small metallic chip, even got some of the soldered past (thermal paste?) on a side of the removed IHS. My god! Please tell me that this will not damage it! I carefully removed the paste and the small covered chip seemed to be OK. So, I put the CPU B, heatsink well screwed down. Everything's working! Great I did not break anything.

Temperatures are quite the same as with the IHS. CPU A Diode goes up to 85 - 90°C without fan spinning very fast (1600 - 1800 rpm for the BOOST A and B) letting OS X managing everything. (I remember seeing that with my 2009 Mac Pro, fans didn't seem to ramp up much with higher temps.)

As I mentioned, I've never really been concerned about temperature, but about fan noise. To me, when they were making noise, that means that I had to clean them. Now everything is clean, the CPU's are way faster so they become way hotter but is it safe to let OS X manage everything? I couldn't find any reliable infos about CPU heat inside MacPros 4,1-5,1. I've never encountered any overheat problem so far, neither with the new ones, everything is working fine, no unexcpected shutdown or anything. I'm just concerned about the "normal" temp for a X5690 on heavy load (all threads to 100% for a long period of time, rendering process can take many many many hours to achieve, sometimes a week long)

Thanks a lot for your time and have a nice day!
-Nicolas T.
3D Animator & Designer
www.garcia-nicolas.com

Cooler is always better, but understand about the fan noise at higher rpm. Is it possible to move the mac pro farther away from your work area? (I've not looked into trying to reduce fan noise with the OEM fans. Bearing type and even blade pitch can affect that. Don't know of any low-noise direct replacements. Not sure if there's any way of isolating them/padding any contact areas, if that would even matter.)
Our previous page on 2009 Mac Pro 12-core CPU Upgrades has some past reports on dual X5690's but they didn't list temps seen in use. (One report mentioned reducing the number of turns on the Heatsink screws when using an IHS CPU.) I'd mentioned there that Intel's X5690 specs lists 130W TDP and Apple's fastest config for this Mac Pro was dual X5670's (95W TDP). The linked X5690 page lists Tcase as 78.5°C (see Tcase notes below from Intel), but doesn't list Tjunction max (which they now do only for mobile CPUs that don't have an IHS. (Tcase refers to the IHS sensor/temp, Tjunction is the internal junction temperature.) Here's a related clip from Intel's Temperature-Related Frequently Asked Questions for Desktop and Mobile Intel CPUs - underline/emphasis/italics mine.
(Also the microcode changes in Mac Pro 5,1 firmware for X5600 series CPUs may affect some features/functions when using it on a 4,1 rom system. Update: He later said he *had* updated the bootrom/EFI to Mac Pro 5,1.)

What is Tcase vs. Tjunction?
These terms are related to processor temperature for desktop and mobile systems based on Intel® Processors. To allow optimal system operation and long-term reliability, the processor must not exceed the maximum case temperature specifications as defined by the applicable thermal profile.

Tcase is the temperature measurement using a thermocouple embedded in the center of the heat spreader. (By removing the IHS from the CPU, you no longer have the "case".) This initial measurement is done at the factory. Post-manufacturing, Tcase is calibrated by the BIOS, through a reading delivered by a diode between and below the cores.

Tjunction is synonymous with core temperatures, and calculated based on the output from the Digital Thermal Sensor (DTS) using the formula Tjunction = (Tjunction Max - DTS output). Tjunction Max (Tj Max) is also referred to as TCC Activation Temperature in certain processor datasheets.

Why does Intel provide the Tcase specification for desktop processors and the Tjunction specification for mobile processors?
Mobile processors do not have an integrated heat spreader like desktop processors. This is the reason why the mobile thermal specification refers to Tjunction Max instead of Tcase Max. What does Tcase Max and Tjunction Max mean?

Tcase Max is the maximum temperature that the Tcase sensor should reach. Both Tcase and the thermal specification information can be found on the Intel web site.

Tjunction Max is the maximum temperature the cores can reach before thermal throttling is activated. Thermal throttling happens when the processor exceeds the maximum temperature. The processor shuts itself off in order to prevent permanent damage. Tjunction Max (Tj Max) is also referred to as TCC Activation Temperature in certain processor datasheets.

What should I do if my desktop board BIOS is reporting a high temperature for my processor?
Intel provides a diode between and below the cores with a reading calibrated by the BIOS. This reading can vary greatly between BIOS versions and BIOS vendors. Contact your point of purchase if you purchased your computer from a computer manufacturer.

Does my third-party application report accurate temperatures for my processor?
Most third-party applications are reporting the processor temperature fairly accurately. Because reports can sometimes show erroneous data, download Intel® Processor Diagnostic Tool to test if your processor is working correctly.
(Diagnostics Tool is for Linux and Windows. And valid for products (CPUs) list doesn't include X5xxx Xeons.)

Does Intel provide temperature ranges for each processor?
Intel does not provide temperature ranges for each processor, as it varies by processor. You can find the thermal specifications for a processor... follow these steps:

1. Go to the ark.intel.com product information page.
2. Select Desktop Products or Mobile Products.
3. Select the processor family from the list provided.
4. Click the processor name located in the Product Name column.
5. Under Quick Links, click Download Datasheet.