Clone was success - M.2 drive showing in Windows - but won't boot

ASUS x99 Deluxe ii motherboard - has been working fine for years with a Samsung PRO SATA SSD as the C-drive / System Drive with Windows 10 64-bit.

I decided to Clone the system drive to a Samsung 980 PRO M.2 drive, and I used the M.2 slot on the motherboard.

To clone I used Macrium Reflect 8 cloning software, and everything went successful with the clone process, and was 100% verified.

The M.2 drive showed up as healthy in Disk Management - (according to Windows 10 64-bit).

I shut down the computer, disconnected the original Samsung PRO SSD SATA cable and it's power cable. 

I went into the BIOS and changed the BOOT Option Priority to the M.2 Samsung 980 PRO hard drive - which was being recognized in the BIOS.

I've checked the motherboard manual, and the ASUS x99 Deluxe ii motherboard is compatible with this Samsung 980 PRO M.2 drive in the M.2 slot.

But upon restarting the computer it does not boot to the M.2 drive.  BIOS version is 1802.

Because the clone process was successful with this M.2 drive in the M.2 slot, and because it was already recognized by Windows 10 and the BIOS,
I'm thinking this no boot problem must be a BIOS boot setting, or some other setting as opposed to the "version" of the BIOS.

Can someone tell me what BIOS settings to check?

Have a look in your BIOS and see if a device with "Windows Boot Manager" is present as a boot option.  If so, set that as the first boot option and try that.

Have a look in your BIOS and see if a device with "Windows Boot Manager" is present as a boot option.  If so, set that as the first boot option and try that.

Thanks jonuk76 - Yes "Windows Boot Manager" is already present as a boot option and that is already set to the first boot option. 

I also attempted to temporarily revert back to the original Samsung PRO SATA 512 GB solid state drive.
I re-connected it's power and SATA cable, and changed the boot order back to that, but suddenly that will not work either?

I have not changed anything else in the BIOS other than the Boot Order. 

Also, when I try to Save and Exit --- the BIOS says I have not made any changes to the BIOS.
Do you know why it would say that, even though I did change the Boot Order?

Just to mention --- previously I had a Samsung 990 PRO in that M.2 slot working as a "Data Drive".

I have the original ASUS PCIe to M.2 bracket to try the Samsung 980 Pro M.2 Clone drive in - should I try that?

Otherwise what are some other BIOS settings should I check to get the 980 PRO M.2 working in the M.2 slot?

I think changes to the boot order not registering as a BIOS change might be a quirk of the Asus BIOS - I see the same on my system (Asus Prime X470 board).  It however does save changes to BIOS boot order.

As for things to change in BIOS, have a look through the boot menu and disable Secure Boot, and anything like "Fast Boot" if present.  Were you using Secure Boot, do you know?  If so I think it's possible that is detecting a change and preventing boot up from the new disk if it's enabled.  Just a thought.

I think changes to the boot order not registering as a BIOS change might be a quirk of the Asus BIOS - I see the same on my system (Asus Prime X470 board).  It however does save changes to BIOS boot order.

 

As for things to change in BIOS, have a look through the boot menu and disable Secure Boot, and anything like "Fast Boot" if present.  Were you using Secure Boot, do you know?  If so I think it's possible that is detecting a change and preventing boot up from the new disk if it's enabled.  Just a thought.

Thanks so much jonuk76  !  Yes, Fast Boot is [Enabled] --- I'm changing that to [Disabled]

Secure Boot is also Enabled, so YES I was using "Secure Boot".  Supposedly the way to change that to disabled is to change the OS Type
from [Windows UEFI mode] --- (which is supposed to represent "ON" state) --- to [Other-OS] --- (which is supposed to represent "OFF" state).

After that Save Changes and Exit --- the changes were noted.

Upon re-boot I saw the ASUS logo, and after a minute or 2 it went to a Blue Screen with an error saying, "INACCESSIBLE BOOT DEVICE".

Then a message came up across the bottom of the ASUS LOGO screen (in white text) that said, "Preparing Automatic Repair".

Then it attempted to re-boot yet again, and after a minute or 2 it went to a Blue Screen with an error saying, "SYSTEM THREAD EXCEPTION NOT HANDLED"  and What Failed? "Ntfs.sys"

I allowed it to attempt re-booting 4 more times (and it alternated between the 2 messages above), this was to see if anything different would happen, and to make sure I typed the error messages above correctly.

Does this possibly mean the clone process did not actually work?
Or could there still be more BIOS settings to check?

Next I shut the computer off, removed the Samsung 980 M.2 1TB drive from the system.
+ Re-connected the original system drive: Samsung PRO 512GB SATA hard drive back onto it's SATA port.
+ Turned the computer back ON.

+ Tapped "DELETE" key to enter BIOS.
+ Clicked ADVANCED. 
+ Clicked the BOOT tab.
+ Changed the Boot Option Priority to: 

BOOT OPTION #1 - Windows Boot Manager (P2: Samsung SSD 860 PRO 512GB)

BOOT OPTION #2 - Disabled

Saved Changes and EXIT --- this time as typical it said, "You have made no changes to the BIOS" - (but as you mentioned the BOOT Priority changes DID actually change)

+ Then Re-booted.

This time the system successfully booted back to original Windows 10 64-bit using the SATA connected original Samsung SSD 860 PRO 512GB C-Drive.

NOTE:  I don't know if this could cause problems with the M.2 port being used as a "SYSTEM" drive port, but I have 6 additional SATA (data only) hard drives attached to other SATA ports.
When I re-attempt the M.2 boot, should I up-plug ALL of my SATA drives during the initial system boot process? 

P1: Crucial CT4000MX500SSD1 (3815447MB) - this is a SATA port connected data drive

P3: Samsung SSD 860 EVO 2TB (1907729MB) - this is a SATA port connected data drive
P4: Samsung SSD 860 EVO 1TB (953869MB) - this is a SATA port connected data drive

P5: Crucial CT4000MX500SSD1 (3815447MB) - this is a SATA port connected data drive

P6: Crucial CT2000MX500SSD1 (1907729MB) - this is a SATA port connected data drive

P8: Samsung SSD 860 EVO 2TB (1907729MB) - this is a SATA port connected data drive

Nothing is plugged into SATA Port 7.

P2: is the C-Drive / System Drive --- Samsung SSD 860 PRO 512GB (488386MB)

Do you think the problem might have been having all those other SATA data drives connected during the initial launch of the M.2 port drive as the new system drive connection?

*** In the BIOS, I have left Fast Boot [Disabled]
and I have left Secure Boot disabled with it set to [Other OS] (DISABLED state)

If you suspect a corrupted M.2 hard drive, should I try Cloning again using again Macrium Reflect 8 software to another new Samsung 980 PRO SSD that I have on hand?
Or do you think the problem is the cloning process did not actually work, and I should just clone again with the same hard drive? 

Or should I purchase a new Samsung 990 PRO M.2 drive and try that instead?  

Or do you think there is some other BIOS setting that still needs to be changed?

Or do you think the problem could be that I expanded the Windows System Drive partition AFTER the cloning process instead of BEFORE the cloning process?

NOTE:  I cloned from a Samsung 860 PRO 512GB SATA drive   TO:  a Samsung 980 PRO 1TB M.2 drive, so on the clone drive a partition needed to be extended.
I didn't extend that partition until AFTER cloning, so maybe at that point the AOMEI Partition Assistant software corrupted a NTFS.sys file that the ASUS BIOS then could not read?

This is what I should have done while I was in the process of cloning the system drive from a smaller size hard drive to a larger size hard drive: 
 

But since I forgot to extend the partition using Macrium Reflect 8 during the cloning process, I extended the partition AFTER the cloning process, using AOMEI Partition Assistant Standard.
I don't yet know if that was the cause of the error saying, "SYSTEM THREAD EXCEPTION NOT HANDLED"  and What Failed? "Ntfs.sys"

Sorry for the delay, a lot of info here to look through. 

Looking up that motherboard, it looks like there's bandwidth sharing between the motherboard M.2 slot and the slot PCIe x16_3  (this is the the third x16 slot away from the main one which probably has your graphics card).  This means effectively that you can't use that slot and the M.2 slot on the motherboard at the same time.  The fact you were using the M.2 drive for storage, and were able to clone an OS to it, seemingly without errors being thrown out, makes me think it's unlikely it's a factor in this case, but thought I'd mention it anyway.

 

 

I allowed it to attempt re-booting 4 more times (and it alternated between the 2 messages above), this was to see if anything different would happen, and to make sure I typed the error messages above correctly.

Does this possibly mean the clone process did not actually work?
Or could there still be more BIOS settings to check?

Maybe...  It sounds like something on that clone is not right anyway.  I may have been fortunate but I've cloned SSD's many times for the purpose of upgrades etc. and never run into problems booting afterwards.  From recollection I've used Acronis True Image, EaseUs Todo, maybe Macrium Reflect, and on one occasion Samsung's own cloning tool that's part of their Magician toolkit to clone drives, without this sort of issue occurring. The Samsung one is more or less a couple of clicks and done - very easy to use (but only works with Samsung drives of course).  I'm clutching at straws a bit but it's important to clone the disk at the drive level, not just clone your "C:" partition.  There are other hidden partitions on the drive which are important for booting up - there will be an "EFI Partition" and "Recovery Partition" present, for example which need to be in the clone.  On a system booting in UEFI mode (as yours is) the partition table on the clone has to be the GPT type rather than MBR.  This is set when the drive is initialised, although it can be changed afterwards (although normally not without wiping all the contents of the drive).

I can't think what other BIOS settings would need changing - Secure Boot is the main one which could cause initial problems, I think. If you are currently able to boot from the old SATA drive then perhaps performing the clone operation from scratch is something you can try.

I don't think having the additional SATA drives connected should cause problems.  However, if I were personally trying to troubleshoot a system, disconnecting them temporarily to "take them out of the equation" is certainly something you can do.  If they are pure storage drives this shouldn't cause a problem.

I would not recommend buying another SSD (the 990) unless it's established that there's something wrong with the one you have (and I don't think there is judging from what you've said).

Edited by jonuk76, 16 September 2024 - 12:42 AM.

IIRC, expanding a partition is best done prior to cloning, not after. 

The fact that the new SSD is visible on all but slot B suggests either a problem with slot B or lane sharing as suggested by Jonuk.

That the clone won't boot successfully suggests a failed cloning, or only cloning C: and not the other partitions on the boot drive as Jonuk pointed out. 

Thanks for the replies.  I will start over and re-try making the Clone again to a Samsung 980 PRO M.2 - and will use the Samsung clone software if possible.

This time I will extend the partition before beginning the clone process. 
 

Do the 2 ports dedicated for U.2 drives on this ASUS x99 Deluxe ii motherboard have PCIe lane sharing?

My NVIDIA video card takes up 2 PCIe slots - uses only slot #1, but covers PCIe slot #2 - which is then not useable by me.

My Firewire card for my external audio soundcard uses PCIe slot #5

My Universal Audio Octo card uses PCIe slot #4.

That means, the only other available PCIe slot would be the PCIe slot #3,
but you said PCIe slot #3 lane shares with the one and only M.2 slot on the motherboard. Is that correct?

So I believe this means if I use the dedicated M.2 slot on the motherboard, that I can not use the PCIe slot #3.  Is that correct?

From the manual, page ix, yes there is lane sharing:

• PCIe x16_3 shares bandwidth with M2 and U.2_2.
• PCIe x16_5 shares bandwidth with U.2_1.
• PCIe x16_2 shares bandwidth with USB3_34 and USB3.1_EA34.

See the manual for more details. 

So, to answer your final question, if I understand correctly, the M.2 slot and U.2 slots will work. Again, assuming that I understand correctly,  if you have a 28-lane CPU, the speed will be x8, and if you have a 40-lane CPU. X16.

That is all in relation to PCIe x16_3, M.2 and U.2_2.

For PCIe x16_4 and U.2_1 with a 28-lane CPU, it will be disabled. 

For PCIe x16_5 and U.2_1 with a 40-lane CPU, the speed will be x4 with U2.1 enabled. 

If I have misunderstood, I hope that someone will correct me. 

Thanks!  My CPU is the Intel Core i7-5960X, and the specs are supposed to be: 3GHz, 8 cores, Gen 3, 40 Lanes.

Does that mean the M.2 dedicated slot, and both U.2_1 and U.2_2 dedicated connection ports can all be used at the same time, but the speed would be x4 on all 3 of those drives?

Will the M.2 and U.2 be faster than SATA connected Samsung 860 PRO solid state hard drives?

With the Intel Core i7-5960X CPU - can I use the 1 dedicated M.2 slot as the C-drive (system drive) and ALSO use both dedicated U.2 ports with Western Digital Gold U.2 drives as data drives?
To use the M.2 and U.2, does that mean I need to leave the PCIe x16_3 slot empty?

 

I'm not sure, to be honest, if everything runs concurrently, which makes sense, or sequentially (like with interrupt requests).

@jonuk76 can you answer? 

Page 51 of the BIOS Manual has some relevant settings in the Advanced/Onboard Devices configuration settings.   To use the config of M.2 slot, and both U.2 slots occupied, the "U2_2 Bandwidth" setting should be U2_2 (not "Auto"), and PCIEX16_5 Slot Bandwidth should be set to X4.

The M.2 and U.2 slots all offer up to a 4 x PCIe 3.0 link speed.  This is way faster than SATA (theoretical throughput of PCIe 3.0 x4 is up to 3.9 GB/s, although in the real world, with a real SSD with real overheads, you can expect somewhat less than this).  SATA tends to max out at around 530-540 MB/s from memory, in ideal conditions.  Using these drives restricts the PCIEX16_3 and PCIEX16_5 slots to 8x and 4x PCIe lanes respectively.

Edited by jonuk76, 02 October 2024 - 05:49 PM.