Mac Pro being held captive by phantom SSD

[pighuddle]

I have a mysterious problem with my 2009 Mac Pro (upgraded to 5,1 12-core 3.33ghz) running 10.11.5

For some reason the machine will not boot without a certain, specific 500GB SSD in a bay. Recently I decided I wanted a bigger primary project-drive (I do audio production) so I copied all my current project files from the old 500GB SSD Evo840 project-drive to a new 1TB Evo850 via an eSATA dock. I shut down, removed the sled, residing in Bay 1 with the 500GB SSD and replaced it with the 1TB SSD. After replacing the sled the Mac Pro would not boot. I get a Chime and then nothing. If I put the old 500GB back it boots up no problem. If I put the new 1TB in another bay it boots np. But no matter what I do I can't get the MP to boot without that 500GB SSD in a bay. Also, if I move the mysterious 500GB SSD to any other bay than Bay 1 it takes almost two minutes longer for the Mac to boot.

I've tried PRAM and SMC resets. My boot drive resides in the extra optical bay so I tried putting the enigmatic 500GB SSD in the optical bay and putting the boot drive in Bay 1. That config prevents booting as well.

Everything runs fine as long as that particular drive is present in Bay 1. I trashed all the files on the 500GB SSD drive so it's just an empty volume now! I don't like that my entire system (and my career!) is beholden to that particular SSD. Any ideas on how I can be free of this phantom SSD?

Thanks!

 

[h9826790]

You "copy" the project files to the new SSD, but did you install OS on to it first?

 

[pighuddle]

No. I always keep my project-files on a different drive than my OS. The "boot drive", I refer to, contains only OS related files, apps and app support files. thx!

 

[DPUser]

Hopefully someone here can help you figure this out! See you at MOTUNation.

One minor point: I am quite sure your Mac is a 2009, not 2008, as you can't upgrade a 2008 to a 5,1.

 

[h9826790]

No. I always keep my project-files on a different drive than my OS. The "boot drive", I refer to, contains only OS related files. thx!

I see, make sense now.

So, if you holding "option" key to boot. Or holding Command + R. Did you get anything?

 

[pighuddle]

[Ah. Yes DPuser. That's a mistake. I do indeed have a 2009 MP. Thx! ..yes, see you at mn]

h9, I have tried those start-up operations. I am able boot into Recovery mode (Cmnd+R), but holding the option key is NOT letting me choose the startup drive as it should, with or without another viable boot drive in a bay.

Here's another anomaly/clue. I tried taking out the 500GB SSD and putting a spinner clone of my boot drive in a Bay. With that drive in any bay the MP does boot (after 3 mins!) but it uses that drive (cloned spinner) to boot into, not the one in the optical bay. In fact the one in the optical bay isn't seen at all by the system when I boot like that!

Thank you

 

[h9826790]

If you can boot to recovery partition. How about re-install the OS to the boot drive?

1) This should NOT delete anything, but just re-install the OS again on your current OS. It may able to fix some strange boot issue.

2) I assume you have full backup, just in case the installation going south, you still have everything in your backup drive.

3) This may upgrade your OS, be careful to check if that's the correct installer in the recovery partition.

Anyway, do you have any PCIe SATA III card installed?

 

[pighuddle]

If you can boot to recovery partition. How about re-install the OS to the boot drive?

1) This should NOT delete anything, but just re-install the OS again on your current OS. It may able to fix some strange boot issue.

2) I assume you have full backup, just in case the installation going south, you still have everything in your backup drive.

3) This may upgrade your OS, be careful to check if that's the correct installer in the recovery partition.

Anyway, do you have any PCIe SATA III card installed?

Yes, I have a Time Machine backup of the boot drive, but, yeah. I don't want to upgrade to Sierra at the moment if I can avoid it.

As a matter of fact I do have an eSATA III PCIe card. And this may have all started around the time I installed it. However, I been unhooking the external drives on that bus while I was troubleshooting all this.
[doublepost=1498956445][/doublepost]So it looks like Recovery will install the same version of the OS that's on the drive. The internet isn't crystal clear on the subject, but it looks like Recovery will not erase my user data just as you say h9. Guess I'll give that a try when I have a moment.

Thank you h9!

 

[pighuddle]

Well, I reinstalled the OS via Recovery and nothing has changed. I also tried pulling the eSATA III, but still my MP will not boot without that dang 500GB SSD in a bay!

One thing. Above I said the MP will boot into Recovery mode, but not without the phantom SSD in a bay. The recovery took place with it in the bay.

 

[h9826790]

Sorry, can't help. It's totally out of my knowledge now.

As you said, that's just a pure data SSD, should not affect the boot process.

A PRAM reset should clear the preference of the selected boot drive. But that doesn't work for you, and the boot option is broken without reason.

If I understand correctly, you are actually booting (including recovery partition) from another SSD, but only when the data SSD is there. Which doesn't make any sense to me.

I trust you, but that's out of my knowledge. Hopefully some other members can help you.

 

[pighuddle]

Yep. The phantom 500GB SSD is used for data only. But currently it's empty. I'm afraid to reformat it. I fear I won't be able boot at all without it. It.makes.no.sense.

Thanks for your help h9. Hopefully someone else will have an idea.

 

[AidenShaw]

Yep. The phantom 500GB SSD is used for data only. But currently it's empty. I'm afraid to reformat it. I fear I won't be able boot at all without it. It.makes.no.sense.

Thanks for your help h9. Hopefully someone else will have an idea.

Where is your UEFI partition? If it's on the SSD, this all makes sense.

 

[pighuddle]

Thank you Aiden!

Googled UEFI partition. It does appear that a bad EFI partition would cause this behavior, but how would my EFI partition end up on a data drive? More importantly, how do I determine where it is and/or how do I move it to the Boot SSD where it belongs?

Based on this, I had the thought to unmount the phantom 500GB SSD with Disk Utility and re-reinstall the OS in Recovery mode, but once I select Disk Utility (in Recovery mode) I can see no way to get back the Reinstall dialogue.

Now what?

 

[Synchro3]

Start the Terminal app and type: diskutil list

Then you will see all partitions on all drives, included the hidden drives, example:
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *1.0 TB disk0
1: EFI 209.7 MB disk2s1
2: Apple_HFS PCI Express SSD 999.7 GB disk0s2
3: Apple_Boot Recovery HD 650.0 MB disk0s3

Is there a hidden partition on your 500GB SSD?

Caution: With this command you can erase a volume:
diskutil eraseVolume HFS+ Blank /dev/disk0s3

 

[pighuddle]

Thanks!

That operation begets this:
----------------------------
/dev/disk2 (internal, physical):
IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk2
1: EFI EFI 209.7 MB disk2s1
2: Apple_HFS Boot SSD 499.2 GB disk2s2
3: Apple_Boot Recovery HD 650.0 MB disk2s3

/dev/disk3 (internal, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk3
1: EFI EFI 209.7 MB disk3s1
2: Apple_HFS 500GB Project Drive 499.8 GB disk3s2
----------------------------
I'm not entirely sure what I'm looking at. "Boot SSD" is the boot drive, "500GP Project Drive" is the problem drive. It looks okay to me. Is it?
[doublepost=1499030589][/doublepost]Per a suggestion elsewhere I changed the CR2032 NV RAM battery, but I used a battery that I happen to have around. Now I'm wondering if the replacement was good.

Can anyone here confirm a dead NV RAM battery might cause this?

 

[Synchro3]

Thanks!

That operation begets this:
----------------------------
/dev/disk2 (internal, physical):
IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk2
1: EFI EFI 209.7 MB disk2s1
2: Apple_HFS Boot SSD 499.2 GB disk2s2
3: Apple_Boot Recovery HD 650.0 MB disk2s3

/dev/disk3 (internal, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *500.1 GB disk3
1: EFI EFI 209.7 MB disk3s1
2: Apple_HFS 500GB Project Drive 499.8 GB disk3s2
----------------------------
I'm not entirely sure what I'm looking at. "Boot SSD" is the boot drive, "500GP Project Drive" is the problem drive. It looks okay to me. Is it?
[doublepost=1499030589][/doublepost]Per a suggestion elsewhere I changed the CR2032 NV RAM battery, but I used a battery that I happen to have around. Now I'm wondering if the replacement was good.

Can anyone here confirm a dead NV RAM battery might cause this?

Looks also ok for me. No hidden recovery partition on '500GB Project Drive'.

Could you uninstall all drives, and install a new drive? Do you have an OS X Install DVD or USB stick?

 

[pighuddle]

Looks also ok for me. No hidden recovery partition on '500GB Project Drive'.

Could you uninstall all drives, and install a new drive? Do you have an OS X Install DVD or USB stick?

Uninstall drives? I'm not sure what that means. I can remove them of course. I'd need to create a bootable USB stick. That's not a bad idea to pull all the drives and boot from a fresh OS on a separate disk. That's gotta work. Unfortunately that route has me rebuilding my entire setup and reinstalling all my apps. Exactly what I'm trying to avoid. ...none the less that's probably my best next move.

Thanks again.

 

[pighuddle]

Well, it looks like simply updating to 10.11.6 fixed the problem . When I went to create the USB stick I noticed I hadn't updated to the latest version of El Cap. I also did a few other random actions like repairing permissions again and running First Aid again (things I'd done before) but I suspect whatever is in that update fixed the issue so I am now free of the phantom 500GB SSD.

Thanks all for your help and thoughtful advice! Onward!

 

[DPUser]

Bravo!