CPU at 100% but no process uses the CPU

Hello, I have been using Qubes OS on a Purism Librem Laptop for the last year and a half and I think it is great - I could never go back to using a regular os afterwards.
But I think it still has some issues with stability and maybe even security in extreme cases.

One problem is that sometimes a “phantom” process seems to be using up all the CPU. It happens like this:
-the cpu fan suddenly ramps up to maximum.
-the mouse and the whole system becomes sluggish.
-no vm is above 1% cpu ussage and TOP shows just 2-10% CPU ussage in Dom0.
-I tryed restarting qubes os but the problem persists.
-only fix is to power down the laptop completely and restart the os.

1)Could this be an attack?
2)Is there any way to debug the problem? I can’t seem to find anything in the logs.

Is anyone having similar issues or knows how to debug them?

System: Purism Librem 13 Laptop v3 with disabled the Intel Management engine and coreboot BIOS.
OS: Qubes OS 4.1 (R4.1) Xen 4.14.4

I have noted similar behavior sometimes on my Librem 13 v 3. For me, it seems to happen when coming out of sleep, and it happens about 50 percent of the time. It persists across a restart but a full power down will kill it.

To add insult to injury it slows down the machine enough that powering it down takes a long time. It’s to the point where I have “trained myself” to do a shutdown rather than just closing the lid.

(The fact that it persists even after a reboot tells me this is no process; this is something in the hardware itself.)

I guess this is the key. Did you try to update the Coreboot/Libreboot?

Are you using Qube OS or PureOS?

My laptop is running Qubes.

I ditched PureOS when I realized I was reluctant to use my laptop any more because it didn’t feel safe. (I’ve been using Qubes on my desktop for a bit over a year now.) It’s now basically a mini-me of the desktop, since I could port the salt files over and re-run them on the laptop with a relatively small number of changes (mostly to do with network hardware…the laptop has no ethernet just for instance). With some care I can even move my e-mail client qube between the two systems though it takes 5-15 minutes to do so.

These posts I’d have ignored because they focus on a symptom (the fan) rather than the cause.

Now that you’ve pointed them out and I’ve read the paragraph in the thumbnail, it sounds like only the second thread applies; in the first he can get it to stop by sleeping the machine.)

As for reflashing the BIOS or boot stuff, I’ve never dared to try, it sounds too much like an excellent way to brick my system if One Little Thing goes wrong.

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I disagree. The fans are managed by the BIOS, and they behave wrongly. Faulty BIOS is the cause. Other people in linked threads confirmed that updated systems do not have such problem.

Moreover, BIOS has important security updates which affect the security of Qubes OS (example), so you definitely should update it. I am not sure that it’s sufficient to have latest microcode in the OS. Their update script is quite safe, no complains on the forum that I’ve seen.

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It’s definately not just the fans, the system is also running slow.
I delayed updating the bios for the same reason as SteveC but I will try it and post back if the problem happens again.

Related question:
Has anyone managed to update Coreboot just using the qubes os already installed on the system?
Does it need a live usb with linux instead?

I’m currently trying to use the method described in the first part of this video Update to A Newer Version of PureBoot - YouTube
I found the roms here: Files · master · firmware / releases · GitLab
I just can’t find the rom for my specific version of laptop: Librem Laptop 13 v3.

Apparently the flashrom utility is too old in dom0.

As instructed by support@puri.sm I’ve flashed the [librem_13v2] .rom using the flash option from the boot menu on my Librem Laptop 13 v3.
But somehow I managed to corrupt my QubesOS partition - so always backup your VMs before attempting.
After reinstalling QubesOS everything seems to be working fine…for now.

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