Remove liquid metal thermal paste on 2008 3.2ghz?

Discussion in 'Mac Pro' started by DIY_glenn, Sep 10, 2015.

  1. DIY_glenn, Sep 10, 2015
    Last edited: Sep 10, 2015

    DIY_glenn macrumors member

    Sep 7, 2015
    I'm in the process of moving the contents of a 2008 chassis to a 2006 one. This involves some modification, but it seems doable.

    I'm now ready to remove the Logic board from the 2008 machine, but the heatsinks for the two CPUs needs to be removed first.
    I unscrewed them, and got surprised by the silver liquid-ish goo underneath (liquid metal?), and a square gasket of some sort (with grease to avoid shorts?). I read through some manuals, and found that this is special for the 3.2Ghz, and that the heatsinks shouldn't be apart from the CPU in more than 30 minutes, so I just mounted them straight back on, without removing the board yet. No manuals stated anything about removing it, reapplying etc.

    What do I do from here? Is it reusable? Not supposed to be replaced with my normal "Noctua NT-H1" thermal paste?
    What about the gasket etc?

    I didn't expect any problems with this, but I guess this Mac is a bit more complex than typical machines.
  2. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    So I've read up on liquid metal thermal paste, and seems like a big hassle! On most setup it seems like it gives only 1-2 degrees (C) lower temperature. Is it really any point in using it at all?

    I'm thinking of removing it with isopropanol, but I'm not sure if it will get it all? It seems to oxidize quickly of what I can see from experiences from other people. I would rather not have to sand down my CPU and heatsink before reapplying a "normal" thermal paste. And I don't quite understand why you would have to remove it completely either, if it's liquid metal, it should help filling any uneven flats.

    I guess without conductive liquid metal thermal paste, you won't need the Krytox grease on the gasket to keep it sealed either?

    But should the gasket be used with normal thermal paste?
  3. pastrychef macrumors 601


    Sep 15, 2006
    New York City, NY
    Just clean off the old thermal compound and re-apply fresh thermal compound. Thermal compound is about as easy to find as any computer related product. Nothing to panic about.

    Aside from that, if you don't even have any experience with thermal compound, you probably shouldn't rip apart your Mac Pro...
  4. Gav2k macrumors G3


    Jul 24, 2009
    Regardless of the manual I would never remove a heat sink and reseat using the same thermal material that's very bad practice.

    As above get it all off. Use a razor blade to get it off then alcohol to get the remainder. Reapply a paste of your choosing as5 is my favourite.
  5. flehman macrumors 6502


    Feb 21, 2015
    I upgraded a 3,1 with dual 2.8 processors to the dual 3.2 processors using MX-4 and experienced no problems. Others have used Arctic Silver successfully. In all likelihood any fresh application of a modern aftermarket thermal compound will outperform a factory-applied compound that has been inside your Mac Pro for 7 years. If anything you will probably see lower temps.
  6. DIY_glenn, Sep 11, 2015
    Last edited: Sep 11, 2015

    DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Excellent, thanks for your feedback! It's nice to know that the Noctua thermal paste I have probably will be more than enough

    But still, this is liquid metal, not a typical thermal paste, meaning that it will not be removed 100% with just alcohol.
    What I'm worried about is that there will be some left that has to be sanded/polished off, or if you can leave the traces that remain (typically filling any indents) and still apply new "normal" thermal paste.

    I have replaced the thermal paste on a 2009 Mac Pro after the plastic retainer of the HS broke, and I had to reseat it - no problem, has been running constantly on for two years, but that was normal thermal paste which easily cleaned off with alcohol, not liquid metal...

    Btw, what about the gasket? Did you use it when upgrading from 2.8ghz? Is it only to be used with liquid metal, or should it be used with normal thermal paste as well?
  7. DIY_glenn, Sep 11, 2015
    Last edited: Sep 11, 2015

    DIY_glenn thread starter macrumors member

    Sep 7, 2015
    I have a lot of experience with typical thermal compound, as I'm more than capable of disassembling a typical server/computer, but I've never dealt with liquid metal thermal paste, and I'm afraid of the oxidation that might happen after trying to remove it.
    It looks like this after removing the HS, it's still liquid:

    I left it for 10 minutes before I put the heatsink back in, as I read that it could oxidize when in direct contact with air. At first I thought I had ripped the heat spread off the CPU, because of the gasket around it (the gasket for my CPU was stuck on the heatsink), that's when I googled and realized that the 3.2ghz has a special liquid metal compound and a gasket with Krytox to contain it.

    There's a thread on it here: Liquid Metal Thermal Interface material but it doesn't answer how to actually remove it and reuse the heatsink, rather than replacing it.
  8. flehman macrumors 6502


    Feb 21, 2015
    Razor should get a lot of it and any thermal compound remover and q-tips can get the rest. Key is to work slowly and be patient, if you get impatient and try to remove too much at once you risk slopping it all over. Arctic Silver makes a pretty good 2-step system for removing thermal paste; there are probably other good ones out there.

    You are kind of locked into this path now anyway because as a previous commenter correctly observed, it is not advisable to keep using the old paste once you have detached the heat sink from the CPU.
  9. DIY_glenn, Sep 11, 2015
    Last edited: Sep 11, 2015

    DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Of course! I want to remove it, and I'm not planning on reusing it. The reason why I put the HS back is because I didn't have any solvents ready to handle the liquid metal immediately, and as you only have approximately 15 minutes before oxidation can damage the HS or CPU, I put it back until I knew more about how to remove it.

    The process you're describing is what you'd typically do with normal thermal paste, but it will not work with liquid metal thermal paste. Removal is almost impossible, so I wanted some feedback from someone who has actually removed the OEM thermal paste on a 3.2ghz Mac Pro V3.1.

    Using a metal brush or sandpaper is a bit frightening because of the possibility of scratching the surface, or making it uneven.

    Just to be clear, this is what we are talking about, it is not normal thermal paste:

    It eats away aluminium in no time, and oxidizes copper +++ if exposed to air.
  10. flehman macrumors 6502


    Feb 21, 2015
    I did not personally experience what you are describing when I upgraded my own MP 3,1 because IIRC the liquid metal thermal compound was only used on the 3.2 gHz processor models. I was upgrading from 2.8 gHz processors so it must have been garden-variety thermal compound. The Arctic Silver solvent worked for me and I did not have to resort to any extraordinary measures.

    If you find yourself resorting to more invasive/forceful methods to remove the liquid metal compound, my advice would be to remove the CPU from the motherboard to work on it. This way you minimize the risk of getting any liquid, particles, pieces, etc. in the motherboard if you are sanding the processor's heat spreader. Maybe put the CPU in a vise with some padding on both sides? Invest in several grades of sandpaper, starting with some coarser stuff to work on the larger pieces and then some ultra-fine 1600-3000 grade sandpaper like you would use for autobody work. Sandpaper that fine should not damage the heat spreader very much. Even if you get a scratch or two on the heat spreader, thermal compound is designed to fill in imperfections in the heat spreader and/or heat sink to conduct heat away anyway.

    Worst case scenario, if you do damage one or both of the processors, you can get replacement processors. A pair of 3.2 gHz processors for a 3,1 cost me 150 about a year ago and they are probably even cheaper now. I think I still have a pair of clean 3.2 gHz processors in my spare parts - if you end up needing them you can PM me to discuss (assuming I can find them). I was going to upgrade a second MP 3,1 and later decided to get a 4,1 and spend my time upgrading that machine instead. I probably will not circle back to the other 3,1 at this point.

    EDIT: You could also attempt to remove the material with a Dremel tool. Try a buffing attachment first, then a sanding attachment, then a grinding attachment if you must. You can adjust speed to low/high as situation warrants. Slow and steady wins the race.
  11. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    I'm thinking that in worst case scenario, I could tape down some 2000 paper on a table, and rub the CPU/HS back and forth to at least try to make it as flat as possible. But some of these IHS are actually convex, and are flattened after mounting the heatsink, which is why I'd rather not have to sand this thing... And again why I'm asking if there is any way at all to remove it with any solvent, or if it is OK to just ignore any residue on the HS and CPU after cleaning, if it is so hard that it actually needs to be sanded to be removed.
  12. flehman macrumors 6502


    Feb 21, 2015
    Yeah we are definitely talking about a delicate, nerve-wracking process if it comes to that. You could collect a couple different solvents to try out when you make the attempt, and if you don't get results right away you could then switch to the abrasive methods if you start running out of time.
  13. DIY_glenn, Sep 11, 2015
    Last edited: Sep 11, 2015

    DIY_glenn thread starter macrumors member

    Sep 7, 2015
    So I started the process, and it definitely is a nightmare!! I started cleaning off with paper with acetone, got most of the stuff off, but now it was down to the residue. The CPU die was scraped over with a knife blade, no scratches, but a LOT of goo came off, removing the rock-pattern that was there before, it got smooth, but it has a dull gray surface, and marks after the heatsink, obviously some residue here.
    I also used the knife first on the heatsink, not a good idea, it created a couple off chips, and scraped up the surface. I sanded it down with 1500 paper, and got rid of most scratches, then polished with Autosol. It was all grey at first instead of copper, but after polishing for a couple of hours (paper solid black after 5 seconds each time) I'm seeing about 70% copper now, continuing to remove the rest. It is now VERY shiny!

    The CPU was polished as well. After an hour, i could see the residue getting thinner, but it is still more dull than what's been under the gasket. I started seeing the name/info on top after a while, getting clearer and clearer, then going away, proving that I'm now starting to polish the actual surface of the die. Still some residue around the edges, just inside where the gasket was, and I've probably not polished it perfectly flat either, but I think I'm getting there.
    Some say sanding is better than polishing because that ensures it is flat, but I honestly think polishing is better, because it's easier to stop when you reach copper on the heatsink etc, not removing anything else than the thermal compound.

    Will see how this goes, can't be sure before I'm finished with the assembly and can check the temperature.

    After I'm happy with the results of this CPU, I'll document my process with pictures on the next one.
  14. Ludacrisvp macrumors regular

    May 14, 2008
    Just take care that you don't electrostatically destroy those processors. But a new (used) pair from eBay would work to replace them. I also upgraded from dual quad 2.8 with normal paste to dual quad 3.2 with arctic 5 ... I'd say it runs as cool or cooler than it did before. Good luck with that crazy thermal compound. May be easier to buy new procs and heatsinks though.
  15. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Hehe, thanks.
    I got both the Mac Pro 2006 and 2008 for free, as both are outdated, and both have some problems. I think I'm getting through the compound, but it is taking a lot of time!

    I finished the 2008 teardown last night. There are some differences by the DVD tray and PSU compared to 2006, but I don't think I'll be able to move the whole HDD-tray etc over to the 2006 model. I'll probably just do some small mods to make the cables go through.
    2006 = rubber damper + 4 individual cables
    2008 = aluminium shield + one large cable

    I'm starting the 2006 teardown today, to see which parts I can move over. I want to use as much of the parts from the 2008 as possible.
  16. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    I finished the build. The 2008 hardware is now in the 2006 chassis. Some fans were taken from the 2006, as I could hear some slight grinding noise when rotating them manually, so some were more worn than others.

    This was a crazy build, with a lot of modifications to the chassis, but still trying to make it be a stock 2008 setup.

    I thought the worst part would be knocking off the old standoffs from the 2008 chassis and gluing them to the 2006 one, but what actually turned out to be the worst computer-related thing I've ever done, was removing the liquid metal thermal paste.

    I used 1500 grid sandpaper on the heatsinks until I could see copper color, then polished it to make it a bit smoother, and this took a LONG time. I wasn't able to remove everything, and I really don't think it matters. If it's really that stuck, etched into the heatsink, it's probably filling some unevenness, so I just cleaned them and put new thermal paste on (Noctua NT-H1) and mounted the HS back on.
    I'm seeing heatsink temps of about 35C on idle, and cores on 38-45C. Seems normal for hardware this old.

    The Northbridge is just below 70C, and the same with one of the memory modules.
    Is this normal?

    I'll post an update with some pics when I got them gathered.

    Oh, and I also removed the RAID card from my 2008, "A1247, EMC 2156". It got very warm under normal use, I figured I really didn't need it (stupid design, RAID card sits just below the hard drives, making them even warmer!)

    Is it worth anything?
  17. flehman macrumors 6502


    Feb 21, 2015
    The 2008 was a bit of an odd bird because it bridged the 2006-2007 models and the 2009-2012 models. You can upgrade a 1,1 to a 2,1 and you can upgrade a 4,1 to a 5,1 but the 3,1 sits right there in the middle, a transition/hybrid between those groupings of compatible models that came before and after it.
  18. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Heh, you definitely got that right! ;)
    A lot of strange things, f.ex. the 2006 Logic board has a lot of rubber supports underneath, nothing on the 2008, although it's marked on the board! It has two more supports though, and another two extra compared to 2006.
    The PSU is also different, the fan holder etc is different (doesn't have cutout for the PSU cables) there's an aluminium shield behind the DVD tray covering the PSU cables.

    I've moved everything over, somethings had to be glued down with epoxy as it broke off the other chassis.

    I can't recommend doing this modification to anyone, it's just too much work, and a high risk of damaging components. But it is doable.

    I removed the extra standoffs from the 2006 chassis with a hammer (easy) and drilled the bottom off with a drill press, then put the Logic board in place, marked through the extra holes with a drill bit, then out with the board again, sand around the marks from the drill, mount the standoffs to the extra holes in the Logic board, mix and apply 5 min metal epoxy, then put the Logic board back in, mount it down and hold it down. It worked, but a lot of job doing it. Same with standoffs at the bottom, the right one for the RAM cage. And two for the aluminium plate behind the DVD. In total 9 had to be mounted again. Also all the routing of cables etc.
    The worst was the fan enclosure by the PSU, which broke it screws on disassembly, it is also very easy to damage the top of the chassis. I got a small dent. But other than that the chassis is now 99% like new.

    But hours and hours of work, and I still have to assemble the 2006 hardware in the 2008 chassis to sell it!
  19. austinpike macrumors 6502

    Oct 5, 2008
    Wait, maybe I missed it but what was the goal of this whole exercise? If you had two functional machine to start with, was it just that the 2006 chassis was cleaner so you wanted to keep that one?

    A 2006 mac pro isn't worth much to start with and I'd imagine one with the guts frankensteined into a 2008 chassis would be worth even less, but I suppose if you have the time....
  20. flehman macrumors 6502


    Feb 21, 2015
    I was never really clear on the purpose either...but I have done crazier stuff out of curiosity and boredom so I was not going to judge. More power to you OP.
  21. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Hehe, exactly, two working computers, but the 2008 chassis is really beat up, and the 2006 hardware is so outdated, 32-bit EFI etc.

    I got them both for free, so I'm just trying to make a machine that will work for a few years, and maybe get a quick buck on the old one. $100-200 or so.

    Getting the 2006 hardware into the 2008 chassis is a bit less work, but yeah, still some work. Nothing will be visible until you remove all the hardware inside, so it really won't be a frankenstein build.

    I'm going to fix the chassis up a bit before installing the hardware, but all in all I just want it out of the house, I've got what I was after: a nice-looking 2008 Mac Pro.

    Maybe a bit crazy, but yeah... At least I know my computer inside-out.
  22. Twimfy macrumors 6502a


    Sep 11, 2011
    Nice work but that compound you spent all of that time to remove coulda stayed put, it's designed to last a lifetime as long as it doesn't oxidise, it goes into a liquid and then solid state over and over again and the gasket keeps it in place.

    Doesn't really matter I guess, the replacement compound will do just a good a job. I just hope you wore gloves, that liquid metal alloy that Apple used is horrendously toxic in contact with the skin, I can't remember it's specific name but it's not 100% pure liquid metal and compound mixed in with it is nasty stuff, more modern compounds are non-toxic.

    Overall a neat idea. My 2008 case got damaged in transit and although the damaged side (breached corners) are facing against the wall and I don't see them, it bothers me knowing they're there.
  23. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    The reason I removed it, was because if it is exposed to air over a long time, it might damage the components or harden, making it even more difficult to remove.
    My initial idea was to remove the heatsinks, remove the logic board, then reinstall the heatsinks while waiting for the 2006 chassis to be disassembled. It seemed doable from what I could see in the manual. But one of the replies here voted against it:
    I didn't wear gloves, but I removed the liquid metal with a knife blade before starting the sanding/polishing process. AFAIK the thermal paste (probably gallium) isn't toxic, but the grease used on the gasket is. In any case, this was two CPU's, not 500, so there's probably little risk involved with the microscopic amounts available.
    Eating tuna every day might give you mercury poisoning as well, so I think it is safe enough to handle, but if handling a lot of these, it definitely wouldn't hurt to use protective gear.

    The CPUs are at 60-68C when running Geekbench 3 stress test (been running for 50 hours now). The absolute hottest is memory module B with up to 80C!

    My scores are 12.550 avg, 12.780 top, latest 12.750.

    Seems stable enough, and the temperatures seems to be correct. Don't understand why they bothered with the liquid metal, and I'm pretty sure they haven't since?
  24. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    Here are some pictures from the whole process:
    Fastening the PSU fan with rubber pins to the newly glued fan cage (screw mounts were cut on the outer side of the fan to make it easier to reach the rubber mount, they are never in use anyways).
    I used precision pliers (locking) to grab the top of them and pull them through.

    Mounts were drilled in a drill press:
    (Pictures will be uploaded)

    Then I mounted them behind the DVD, and for the Logic board/memory cage:

    The CPU's; Removing the liquid metal thermal paste with alcohol, a knife, sanding and polishing
    (next post):
  25. DIY_glenn thread starter macrumors member

    Sep 7, 2015
    After some work I was left with this, ROCK HARD left on the HS and CPU:


    I started seeing the writings after a while:

    I continued polishing and polishing, and got rid of pretty much everything. Sorry for the blurry photos, late evening...:

    Same with the heatsink, It was all grey after a lot of polishing, so I sanded a little, then continued polishing when I started seeing copper. I couldn't remove it all, but I think it was enough:
    (Still some grey traces)

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