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I have a Thinkpad L13 that has been running Windows 11 and Linux Mint with no problems. I decided to try Ubuntu after about 10 years absence, so I made a live USB stick, and it boots OK on my desktop, but on the laptop, it takes at about 15 minutes or so to finally boot. This is after the GRUB prompt while trying to boot the OS, not the USB itself. I tried another USB stick, another flavor of Ubuntu, from a verified iso file, with the same results. Then I tried my existing Mint disk, with the same problem. Pressing escape shows the message:

The disk contains an unclean file system (0,0) 
The file system wasn't safely closed on Windows. Fixing.

This is followed by a lot of I/O errors.

If I leave it, it finally boots although I'm not sure if everything is OK. But it's able to access the internal drive. Also, Windows and Linux Mint both run OK, and I had Windows check all the drives it was able to check.

This seems to be a hardware problem, but so far, I've been unable to fix it because I don't fully understand where the problem is.

Since this is before ever trying to choose what disk to even install to, my question is whether an existing hard drive affects the USB drive's boot process. It seems like it should not matter - what if I just want to wipe the drive and install Linux?

Any help is appreciated, but knowing if it's the internal drive causing the problem would help a lot.

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    Would recommend checking SMART data (from any OS or bios if supported) before doing anything with your disk. (smartctl in linux can do this). If SMART indicates the disk is failing, back it up immediately and then replace it...
    – user10489
    Commented Jul 17 at 5:44
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    Isn't that message what you get when you haven't fully shut Windows down? I haven't used Windows in decades now, but I've seen something along the lines that the default "shut down" of Windows actually hibernates and that can cause issues with other OSs. See Unable to mount Windows (NTFS) filesystem due to hibernation
    – terdon ♦
    Commented Jul 17 at 10:46

1 Answer 1

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Thanks for the suggestions, but I believe I've answered my own question after a bit of tinkering. It wasn't Windows not shutting down - I don't use it often, but have it only for certain specific uses. But I know all about sleeping, hibernating, full shutdown, etc. - been building computers from scratch since the mid 80s (I'm a retired software engineer).

The main confusion was that I didn't think the hard drive mattered, since I was booting from USB, and had no use, so far, for the internal drive. You'd hope to be able to boot from a USB drive in case of hard drive problems, after all.

It didn't seem to be related to any drives, actually. I went into the BIOS and poked around a bit. All I ended up doing was changing the default boot order a bit, which I didn't (don't?) think mattered, but after saving and exiting, the USB drives worked as expected, and I was able to install Ubuntu without problems - well, I had some problems with Ubuntu Cinnamon, but decided Gnome actually might make more since to me, to compare to Mint Cinnamon that I've been using.

So, maybe the boot order made a difference, or maybe just rewriting the BIOS fixed some error. But it's working again, so thanks.

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