Boot issues with Ubuntu 16.04 on new PC

[maw501]

Hello all,

Background

I have just bought a PC with the following spec:

Processor (CPU) Intel® Xeon® Silver 4110 8-Core (2.1 GHz, 3.0GHz Turbo, 11M L3 Cache)
Motherboard ASUS® WS C621E SAGE (DDR4 RDIMM, 6Gb/s, CrossFireX/SLI)
Memory (RAM) 64GB Kingston DDR4 2666MHz ECC Registered (2 x 32GB)
Graphics Card 11GB NVIDIA GEFORCE GTX 1080 Ti - HDMI, 3x DP GeForce - GTX VR Ready!
1st Hard Disk 480GB KINGSTON UV400 2.5" SSD, SATA 6 Gb (550MB/R, 500MB/W)
2nd Hard Disk 2TB SEAGATE BARRACUDA SATA-III 3.5" HDD, 6GB/s, 7200RPM, 64MB CACHE
Power Supply CORSAIR 1000W RMx SERIES™ MODULAR 80 PLUS® GOLD, ULTRA QUIET
Power Cable 1 x 1 Metre UK Power Cable (Kettle Lead)
Processor Cooling INTEL BXSTS300C THERMAL SOLUTION
Thermal Paste STANDARD THERMAL PASTE FOR SUFFICIENT COOLING
Sound Card ONBOARD 8 CHANNEL (7.1) HIGH DEF AUDIO (AS STANDARD)
Wireless/Wired Networking 2 x ONBOARD 10/100/1000 GIGABIT LAN PORTS
USB Options MIN. 2 x USB 3.0 & 6 x USB 2.0 PORTS @ BACK PANEL + MIN. 2 FRONT PORTS

Unfortunately (apportioning no blame) the PC came with Windows installed which I didn’t want and I had a slight headache installing a version of Ubuntu 16.04 – various bios/boot issues and driver errors, detailed below. I eventually wiped the partitions using gparted (and probably the windows boot stuff too) and after a few reinstalls of Ubuntu I now have a working install (which appears okay once I reach it). I also think I have managed to install the GPU - an involved process I do not wish to repeat soon. In order to configure the GPU I had to install a different version of the Ubuntu kernel, version 4.4 XXX which is now set to default.

Issues and current behaviour

When I start the PC by pressing the button it takes about 20 seconds before I hear the beep and anything starts appearing on the screen. The first screen that flashes up is a screen with the AMBIOS/ASUS details and instructions on what to press to enter Setup etc…

Then up comes an Asmedia 106x SATA Controller screen with a few messages (using PCIE Gen 2 x2) and saying ‘Can’t find any device’. Then we flick back to the previous AMBIOS/ASUS screen before a screen saying ‘Initializing Intel Boot Agent GE v1.5.72’ and to ‘press Ctrl + S to enter the Setup Menu’.

Then we go back to the AMBIOS/ASUS screen for the 3rd time and finally into Grub where we are faced with the following:

Ubuntu
Advanced options for Ubuntu
EFI/ubuntu/fwupx63.efi
EFI/ubuntu/mmx64.efi
System setup

The default if I don’t touch anything is ‘Advanced options for Ubuntu’ and defaulting to the version 4.4 kernel. On choosing this (or just not touching anything and it defaulting there) I get a pink grub screen with the following message:

Loading Linux 4.4.0-040400-generic …
Loading initial ramdisk …

Then a black screen with:

[0.336994] Error parsing PCC subspaces from PCCT
/dev/sda6: clean, 238105/1831424 files, 1997552/7323904 blocks

Then finally we are through the OS about a minute later and all seems okay…

Goal
My aim is simply to diagnose the cause of any of the warning messages and errors and resolve as appropriate. Given the time to install the GPU and initial hassle getting Ubuntu on I’m keen to not repeat this process and thus want to ensure I have things in good order to start and if I need to reinstall things then to do it before I set up the PC for use.

I am more than happy to provide any more information or diagnostics as required – please just ask. I can provide screenshots, videos etc… of the startup if it helps. By comparison my 5 year old PC boots in about 10-15s from hitting the button.

Many thanks for any responses in advance.

Mark

P.S. A note about me: I’m using the PC for machine learning research and whilst I am adept as a programmer, with the lower-level OS stuff I’m definitely in the ‘google and try what seems to make sense – usually from Stack Exchange or the like’ camp.

 

[Alabalcho]

I might help you with couple of issues:
- "Intel boot agent" appears because "Boot from LAN" is before booting from your OS drive. Disable that in BIOS
- "Can't find any device" from your SATA controller: Probably this controller supports some form of RAID, and informs you that no RAID drives are defined. Going thru the Setup process (pressing <Ctrl>-S at the right moment) might clear that.
- Above two are probable reasons for long delay before boot
- "Convoluted GPU setup" - My question would be rather why you need that instead of using on-board GPU, you're doing nothing with it under Linux

 

[maw501]

I might help you with couple of issues:
- "Intel boot agent" appears because "Boot from LAN" is before booting from your OS drive. Disable that in BIOS
- "Can't find any device" from your SATA controller: Probably this controller supports some form of RAID, and informs you that no RAID drives are defined. Going thru the Setup process (pressing <Ctrl>-S at the right moment) might clear that.
- Above two are probable reasons for long delay before boot
- "Convoluted GPU setup" - My question would be rather why you need that instead of using on-board GPU, you're doing nothing with it under Linux

Hi, so I disabled the Intel Boot Agent from Ctrl + S and now I'm at grub rescue with:

error: unknown filesystem
grub rescue>

Any thoughts? Have tried following online instructions but to no avail...could it be some UEFI/MBR/GPT issue with my set-up? This bit is confusing me.

Thanks

 

[Alabalcho]

"Intel Boot agent" is the one responsible for booting over LAN, it is not in SATA controller settings. So revert the SATA back to what it was.

These GRUB messages make me think that you have serious problems with your SSD/HDD partitioning - that is, GRUB on one drive, while actual Linux <root> partition on another, or your devices have changed numbers.

 

[maw501]

"Intel Boot agent" is the one responsible for booting over LAN, it is not in SATA controller settings. So revert the SATA back to what it was.

These GRUB messages make me think that you have serious problems with your SSD/HDD partitioning - that is, GRUB on one drive, while actual Linux <root> partition on another, or your devices have changed numbers.

Thanks. Do you think it is better to reinstall Linux? I did a manual partition (as the default gives me 64gb of swap) and set an EFI system partition, swap, root and home partitions - perhaps I don't need the EFI one.

 

[Alabalcho]

I would disconnect the HDD (and probably, your "smart" SATA controller), leave only the essentials (GPU out as well), and reinstall Linux from scratch. Make sure it works the way you want it, make a backup, and start adding hardware. Again - as long as your "machine learning" does not support unloading to GPU, you don't need it there.

 

[maw501]

I would disconnect the HDD (and probably, your "smart" SATA controller), leave only the essentials (GPU out as well), and reinstall Linux from scratch. Make sure it works the way you want it, make a backup, and start adding hardware. Again - as long as your "machine learning" does not support unloading to GPU, you don't need it there.

Thanks again, genuinely appreciate it though I don't think I am confident enough to start unplugging things.

I reinstalled Ubuntu but could only boot from an MBR in BIOS or UEFI iso from usb, not a GPT UEFI one. Here is a boot-repair report of current state:

http://paste.ubuntu.com/p/S4F6Fknpx7/

I get through to the OS now okay but still get the 'Error parsing PCC subspaces from PCCT' message. Also I think the msdos/bios thing maybe isn't right, not sure if this means I'm using some older stuff I shouldn't be?

Mark

P.S. We can forget the gpu for now, priority is a clean Linux install.

 

[electro_neanderthal]

Why not Ubuntu 17.1? Just wondering/suggesting.

 

[maw501]

Why not Ubuntu 17.1? Just wondering/suggesting.

I don't think the GPU toolkit will support it (only uses particular kernels): http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html

 

[electro_neanderthal]

Why not Ubuntu 17.1? Just wondering/suggesting.

I don't think the GPU toolkit will support it (only uses particular kernels): http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html

I may be reading the chart wrong, but unless you're using a Tesla GPU, it looks like it's supported.

 

[maw501]

That is 17.04? Anyway, by the by...I want the LTS version at the moment (though I know going to update soon).

More fundamentally I am still having boot issues. I have figured out that it was in legacy/bios boot mode (CSM was enabled) and as a consequence when I insert a bootable iso in just UEFI mode created from Rufus I couldn't get anywhere.

Disabling CSM allows me through to the install Ubuntu page (from a UEFI bootable iso usb), but when I click yes I get the following errors:

Error parsing PCC subspaces from PCCT
MODSIGN: Couldn't get UEFI db list

and then a black screen that just hangs indefinitely...? Any thoughts welcome - I can only seem to install Ubuntu via a legacy/bios iso.

Mark

 

[electro_neanderthal]

Here's a bit of a crazy idea: Install a second OS and give it a minimum partition space. This should force the PC into a selection menu and ask you to select which one you want to boot up consistently.

I don't have too much experience, just a few PCs that run Ubuntu, Lubuntu, and Xbuntu/Windows XP dual boot.

I also found an article you might find interesting:
https://www.linux.com/learn/how-install-linux-windows-machine-uefi-secure-boot

Turns out manufacturers using UEFI no longer need to allow the disabling of secure boot, which might be why you're only able to use the BIOS.

Though I really don't know how much that will help. Seriously, good luck.

 

[maw501]

Here's a bit of a crazy idea: Install a second OS and give it a minimum partition space. This should force the PC into a selection menu and ask you to select which one you want to boot up consistently.

I don't have too much experience, just a few PCs that run Ubuntu, Lubuntu, and Xbuntu/Windows XP dual boot.

I also found an article you might find interesting:
https://www.linux.com/learn/how-install-linux-windows-machine-uefi-secure-boot

Turns out manufacturers using UEFI no longer need to allow the disabling of secure boot, which might be why you're only able to use the BIOS.

Though I really don't know how much that will help. Seriously, good luck.

Thanks, am in touch with the company that sold me it. Will post the outcome.