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My SSD is in SATA port 1. All other ports are empty at present.
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I have tried using the Install High Sierra downloaded via the App store. I have also tried using a USB thumb drive with the Install Hugh Sierra on it that was set up to be bootable. The MP 5,1 will not recognize the thumb drive as bootable however. Possibly because it will not boot from High Sierra without the firmware update?

I have pondered a clean install of Sierra on the SSD. I have tried everything "logical" that I can think of. I have only resisted the flashing of the GTX 680 because I am not really a PC person. While I did build a Windows gaming machine last year, I am not conversant with Command line prompts or the Windows OS beyond very limited basics. In fact, I had built that machine to be a hackintosh but never felt comfortable getting the macOS on to it. Remembering the correct connections to the power supply and attaching the GTX 680 to it for flashing purposes is just uncomfortable. I am not sure I even have the right cables to do it. I really am not inept. This problem just confounds me.
1) Do you have any PCIe cards installed?

2) Do you have a empty HDD?

You could install El Capitan from the Mac App Store on a empty disk, boot from it, download 10.13.6 and then try to do the firmware upgrade.
 
My SSD is in SATA port 1. All other ports are empty at present.
[doublepost=1533598698][/doublepost]

I have tried using the Install High Sierra downloaded via the App store. I have also tried using a USB thumb drive with the Install Hugh Sierra on it that was set up to be bootable. The MP 5,1 will not recognize the thumb drive as bootable however. Possibly because it will not boot from High Sierra without the firmware update?

I have pondered a clean install of Sierra on the SSD. I have tried everything "logical" that I can think of. I have only resisted the flashing of the GTX 680 because I am not really a PC person. While I did build a Windows gaming machine last year, I am not conversant with Command line prompts or the Windows OS beyond very limited basics. In fact, I had built that machine to be a hackintosh but never felt comfortable getting the macOS on to it. Remembering the correct connections to the power supply and attaching the GTX 680 to it for flashing purposes is just uncomfortable. I am not sure I even have the right cables to do it. I really am not inept. This problem just confounds me.

Nah if your High Sierra installer drive was truly bootable it would have shown up in the boot picker on the Mac Pro--that would not be affected by firmware at all. Sounds to me like your HS installer drive wasn't created properly or got corrupted or something. If you have another HDD/SDD you can experiment with then as tsialex just said you can download El Capitan from the Mac App Store via this link https://support.apple.com/en-us/HT206886. Install the second HDD in one of the other bays, run the El Capitan installer and make sure you tell it to install to the other HDD. It will set the cMP to boot from that drive automatically as part of the install. Then once it's done you can download the 10.13.6 full installer and try the FW upgrade again. Assuming it works (and you've verified the new firmware versions shows in System Profiler) then you can shut down, remove the 2nd hard drive and boot back into your existing Sierra to proceed with the upgrade to High Sierra.
 
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I've seen problems with individual OS installs where rebooting didn't work properly, and you couldn't change the boot disk via system preferences (it'd come up with an error when closing sysprefs), bur cloning the OS install to a new drive cured the problem. There can be odd behaviour at times related to an install on a particular drive.
 
My boot SSD is an SM951 mounted in an Angelbird Wings PX1 in PCI slot #4. It updates the FW just fine.

Lou
Standard AHCI/SATA SSDs are not the problem, but some RAID ones like OWC Mercury Accelsior E2 or SSDs on PCIe SATA RAID cards.

BTW, I have SM951 512GB + Angelbird Wings PX1 too.
 
GhostImage

Can you shut down the cMP ?

If so . .. after shut down . . wait 20 seconds . . once again try holding down the Power Button 'til the chime . . who knows . .it might work this time.

Good Luck.
 
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I am thrilled to report SUCCESS!

After looking at everyone's ideas, I was struck by tsialex's questions. I bought a new HDD and an Apple NVIDIA GeForce GT 120 512 MB. I also created completely new bootable macOS Sierra and macOS High Sierra thumb drives. I was able to install Sierra on the HDD using the thumb drive which was not an issue before. Then, I booted from the High Sierra drive. I got the same must update the firmware window. I crossed my fingers and clicked the Shut Down button. Nothing happened. I left the machine sit for 30 minutes but no shut down. I eventually shut the MP5,1 down and tried the process again. Still no shut down. Clicking the button didn't do anything. I was quite upset. So I decided to shut down the machine again after waiting five minutes. I figured, what the heck, and held down the power button through the flashing light and tone. When it started, the firmware update screen appeared and the update proceeded. I was able to install and update macOS High Sierra. I am writing this on the updated machine.

I know my frustration showed through but I really appreciate everyone's ideas. I was ready to give up. I feel your ideas and support let me press on.

To everyone, THANK YOU SO MUCH. You all rock!!!
 
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Then, I booted from the High Sierra drive. I got the same must update the firmware window. I crossed my fingers and clicked the Shut Down button. Nothing happened. I left the machine sit for 30 minutes but no shut down. I eventually shut the MP5,1 down and tried the process again. Still no shut down. Clicking the button didn't do anything.
This is definitely a bug in the installer.
I had exactly the same issue a few days ago when booting from a High Sierra 10.12.6 USB flash drive.
Click the shutdown button on the firmware upgrader and nothing happens.
I ended up having to install Sierra and then run the upgrader from there.
 
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So I have reinstalled my SSD and wanted to install High Sierra on it to make it my StartUp disk but Disk Utility does not give me the GUID formatting option. I vaguely recall this being an issue before when reading other threads. Could someone point me towards how to get my SSD to be formatted correctly to install macOS High Sierra and so I can use Migration Assistant to transfer my things from my old MP3,1?
 
So I have reinstalled my SSD and wanted to install High Sierra on it to make it my StartUp disk but Disk Utility does not give me the GUID formatting option. I vaguely recall this being an issue before when reading other threads. Could someone point me towards how to get my SSD to be formatted correctly to install macOS High Sierra and so I can use Migration Assistant to transfer my things from my old MP3,1?

Huh? You mean it's forcing you to use MBR? Or do you mean it's not letting you use "Mac OS Extended (Journaled)" aka HFS+ and is only giving you APFS options? If so, that's because your SSD was already formatted in APFS format. You should just be able to choose "APFS" from that menu and install onto it just fine.

It actually does little good to format it to HFS+, because once you install HS onto it it will convert it back to APFS. If you're intent to run it as HFS+ though then it can be done. See this article: https://www.techrepublic.com/article/how-to-revert-back-to-apples-hfs-from-apfs/

Edit: Even if you are talking about a situation where you can only select MBR for the partition table, the instructions in that article should help you erase the SSD via the diskutil command. Then you can either recreate the partition using diskutil or via the graphical disk utility.

Just be extra sure of what disk you choose in those terminal commands. Diskutil is powerful!
 
Huh? You mean it's forcing you to use MBR? Or do you mean it's not letting you use "Mac OS Extended (Journaled)" aka HFS+ and is only giving you APFS options? If so, that's because your SSD was already formatted in APFS format. You should just be able to choose "APFS" from that menu and install onto it just fine.

It actually does little good to format it to HFS+, because once you install HS onto it it will convert it back to APFS. If you're intent to run it as HFS+ though then it can be done. See this article: https://www.techrepublic.com/article/how-to-revert-back-to-apples-hfs-from-apfs/

Edit: Even if you are talking about a situation where you can only select MBR for the partition table, the instructions in that article should help you erase the SSD via the diskutil command. Then you can either recreate the partition using diskutil or via the graphical disk utility.

Just be extra sure of what disk you choose in those terminal commands. Diskutil is powerful!

When I attempt to install macOS High Sierra on the SSD, which is formatted with Mac OS Extended (Journaled), the Install macOS application says it cannot install on the SSD because it is not using the GUID partitioning scheme. When I attempt to use the Disk Utility to resolve this, the GUID partition option is not available.

The article actually is going the opposite direction than what I want. I want to get to APFS eventually. I just need a clean install of High Sierra on the SSD. I suspect that using the tools to get Sierra and High Sierra on an unauthorized MP 3,1 has cause some corruption I had hoped to escape. When I was finally able to run the Migration Assistant to get my apps on the MP 5,1 HDD, it too was acting erratically. Flickering screen, stalled performance, inability to run certain apps all were in evidence. I am going to wipe the HDD and try a clean install of High Sierra.

Something is definitely wrong!
 
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When I attempt to install macOS High Sierra on the SSD, which is formatted with Mac OS Extended (Journaled), the Install macOS application says it cannot install on the SSD because it is not using the GUID partitioning scheme. When I attempt to use the Disk Utility to resolve this, the GUID partition option is not available.

The article actually is going the opposite direction than what I want. I want to get to APFS eventually. I just need a clean install of High Sierra on the SSD. I suspect that using the tools to get Sierra and High Sierra on an unauthorized MP 3,1 has cause some corruption I had hoped to escape. When I was finally able to run the Migration Assistant to get my apps on the MP 5,1 HDD, it too was acting erratically. Flickering screen, stalled performance, inability to run certain apps all were in evidence. I am going to wipe the HDD and try a clean install of High Sierra.

Something is definitely wrong!
I've asked you before, #341, If you had used any hacks…
 
Huh... well now you know why your firmware updates were failing.

I was going to type out the diskutil commands to do this but then I googled and found this tip on how to fix it using disk utility: https://apple.stackexchange.com/questions/300297/how-to-choose-guid-with-high-sierras-disk-utility

Try that first and if it doesn't work then reply and I'll write out the diskutil method.

Success again!!!

This whole process had me so frustrated that I was not thinking clearly. I used a non-Apple disk utility program to reformat the MP 5,1 SSD to GUID partition scheme using my old MP3,1. I then had no problem installing High Sierra. The new machine (MP 5,1) is up and running well using the SSD. My Geekbench numbers look good.

To get a bit more speed, I am planning to switch the SSD to a PCI spot. I had good luck with OWC Mercury Accelsior S in my MP 3,1. I hope I can find another. :) If others have had problems, let me know?

Again, I appreciate everyone's help, understanding, and support.
 
I've used the Accelsior S PCIe SATA III adapter in both my cMPs (both have Samsung 850 EVO SSDs), the first one for ~2 years, and second one for the last two months, and I've never had problems at all.

I think the problems that were reported were either do with the Accelsior E2 PCIe card which has the SSD module(s)/blades(?) onboard, and the Accelsior S PCIe adapters that shipped with OWC SSD drives are the problem – as opposed to the empty Accelsior S adapters where you add your own SSD. I recall reading people having problems with the E2 as well as OWC SSD drives.
 
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