Installed Linux on Gigabyte 970A-DS3P motherboard - lost all data

I am a long-time linux user, for the last 10 years or so have been using linux mint. Recently I have decided to switch to manjaro and after trying it on my laptop for a month I have decided to install in on my desktop, too.

I have a Gigabyte 970A-DS3P motherboard with amd fx 8350 - not the latest hardware but still powerful enough. I have 5 disks in my computer - 2 SSDs (500GB and 250GB - the larger one is used for system) and 3 HDDs (1TB, 2TB and 3TB - I'll call them disks 1, 2 and 3).

Everything started smoothly, after the OS installation I installed additional packages and configured the system and then I rebooted it. From that point my HDDs 1 and 2 were gone - gnome disks showed them as 'unknown' partitions. Suspecting further problems I immediately disconnected disk 3 and then tried to recover disks 1 and 2. Testdisk found lost partitions but could not recover them. At first I thought that my motherboard or disks broke and I put HDDs in another computer. From there I could recover my files and copy them elsewhere but when I returned disks to my computer I could not create new partitions. Gnome disks, Gparted, fdisk and gdisk complained that the partition table was missing but could not write one. I then started gparted distro on another computer and could restore partition tables there.

I reinstalled linux mint on my desktop and tested disks and everything went smoothly. I restored the data, then tried to reinstall manjaro and the same thing happened again. After the first reboot all HDDs were gone - this time deleting partition table on disk 3 also. SSDs were not affected in any way.

After a long weekend of trial end error I found the problem that is 100% reproducible. My motherboard seems to not play nicely with linux but so far the only problem has been usb3 not working and slower startup times which could be prevented by sending "iommu=soft" switch to kernel. If that switch was not set I wouldn't have usb3 support and that was it.

However, in latest manjaro (18.1) failing to send that switch to kernel will lead to partition table deletion in all HDDs. First boot after install seems to work but after the first reboot the disks would lose their partition tables. None of the partitioning tools that I've tried (gparted, gnome disks, fdisk, gdisk, testdisk) could create partition table on those disks afterwards and I was able to create partitions only from gparted distro with "iommu=soft" switch sent to kernel. If the "iommu=soft" switch is immediately added to kernel everything would work.

I do not know if this is a newer kernel bug or is something manjaro specific but I think that those with AMD FX cpus and this motherboard need to be warned.

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This is not Manjaro specific - but a general Linux issue - and related to a specific hardware component - which may spark the thought - it is a hardware issue.

And it as an issue several years old earliest mention 2014.

Probably long time solved using firmware updates.

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Those boards are fine i and a lot of others use them,
But you need to tweek grub if not using a secure boot distro.

There were no problems with the installation from liveusb on usb 3.0.
After the installation and only after first reboot the system deletes partition tables from disks. This is not a known problem and that is why I am reporting it here.

This seems to be manjaro specific and that is why I am reporting here. As I said I have been using mint on the same hardware for 9 years without any problems.

then it's new kernel specific and the same problem would eventually crop up with Linux Mint, try installing kernel 4.19 LTS instead of kernel 5.3

I installed Manjaro yesterday and have the same motherboard (rev 1.0), so far everything has been fine, but i'm a bit concerned.

Which rev. version do you have and have you updated your bios?

That's actually a good idea, I'll try that. But I still think that it is important to post this warning because this can erase data on a newly installed computer.

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I use rev 1.0 the later beta version fails to boot here.
As i said the motherboard is fine just needs the grub tweaking otherwise you get very delayed boot times, Known bug since the 970 series boards 1st came out, unless using secure boot like Linux Mint Fedora, Ubuntu, opensuse.


That is the problem USB3 turns of partway through booting as per Windows secure boot options unless its a secure boot ISO.

Gigabyte lists FX8350 as supported CPU for this motherboard on their own website

Besides, I have the latest firware and bios updates and it was working with linux for almost 10 years.
The links that you've sent are for usb 3.0 problem and I was aware of them. None of them mentions deleting partition tables of hard disks. That is why I've posted it here.

original post deleted

i offered an apology and wanted no further part in this discussion
based on OP later comments apology appears to be dishonoured and is withdrawn

No, I didn't ignore them, I think you didn't read my problem carefully because your links are for a different problem. Your third link is the one that I've sent in my first post, so I was aware of that problem - I wouldn't be able to install linux mint on my computer without that solution. The other two are also solving the usb problem.
And in the end you said "this appears to be solution to USB problem".

But I didn't have usb problem, I already had manjaro installed on my system. And suddenly on reboot it erased partition tables on HDDs. This never happened to me before, and I'm linux user for more that 20 years. And as I've said, I have reinstalled it a few times after that and the problem was always there, 100% reproducible. And yes, I know that iommu=soft switch solves the usb problem, and that is should be there but I'm pretty sure that lack of that switch shouldn't result in data being lost on hard disks. That's why I posted it here.

I own that motherboard as well. I've lost my partition tables on a lot of drives over the years, but never with that mobo.

Most of my lost partition tables were from user error or a flaky external USB HD controller, and most were on Windows not Linux.

I always back up my partition tables and my data so that I never have to worry about that problem. I'd suggest you start implementing a backup regimine as well.

Let me chirp in here 1st iommu=soft does not solve any problems that was the 1st work around and dirty.
iommu=pt is the latest workround i posted the link I would follow that 1st before doing any thing.

The one thing you are correct on is it should not happen,

You can't compare Mint with Manjaro, Mint is a secure boot complaint distro, Manjaro is not and needs secure boot turned off and fast boot turned of.

Is this machine duel booting if it is then it could be windows hibernation.

Note on this I had problems on another machine that if I used gparted to format partitions when I booted MAC or Windows the partition tables disappeared some what like you describe, but only when booting non Linux, not saying this is related to your problem, I solved it by using a win live ISO to partition. non linux partitions

You have given no information on your system inxi -F would help users, A 10 then 20 year Linux user should know that lol.

The other problem is apart from frightening the life out of a new user other users do not seem to face the same problems why do they not is it something to do with hardware?

How are you burning the ISO are you using a USB to write the image if so how are you doing that what program did you use?.

I'm sorry if this sound belittling it is not meant that way, Linux is a strange beast at the best of times it is always a challenge for users.

Please post as much info as possible not pictures just formated text, take notice of what others have to say as i said others use this board one uses it to develop and distribute Arch deepin ISOs so it maybe like me a old board but its very capable.

Have fun

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It could easily be a hardware issue. As I stated, I've seen this before with flaky USB controllers on multi-bay USB hard drive caddies (with Windows).

Well I know for a fact if the bios is not correctly this sort of thing can happen as its not non secure boot friendly board for Linux.

I used Arch and manjaro on it it took till 2017 to get the correct cheat code with no help from Gigabyte

Machine is not dual booting, there is only linux on it. I have reinstalled mint currently because I have to work on that computer but I will get some old HDDs in a few days and will try everything again and I will post more technical information that might lead to some clues about what is happening. I didn't lose any data (yay for my backup service) but I prefer to test on HDDs that do not contain any important data.

You could use etcher to make a bootable USB.
I personally would try something like Endeaver and see if the same happens if successful would rule out the installer at least. if not then try using another distro other than mint Ubuntu based, Debian would fit the bill if Ok.
Then its back to Manjaro not the motherboard it may not be Linux friendly but works just fine if you follow the link I sent you.

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It's surprising to me how problematic this board can be since I have a Gigabyte one too, an AM1M-S2H revision 1.0. That is EFI from the same vendor (AMI) as well and I've never had any such issues with it on any Linux distribution I have tried with it, I use it in EFI only mode. The only snafus I have had to date have been to do with the Athlon 5350 and a couple of sp5100_tco watchdog conflict (easily resolved by getting sp5100_tco loaded first) and a separate DRM error with older kernels. All these have been negated since kernel 4.19 LTS anyhow. I'm wondering if it's more complicated than dodgy firmware revisions and also partly to do with the 970 chipset?

iommu=pt is the common workaround I have seen posted on many forums for the 970A-DS3P.

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