Ubuntu

Normal booting affected: Forced to use recovery mode for booting into 22.04.1 LTS after upgrade from 20.04.1 LTS

Asked by Anand Manthena

SUMMARY REPORT

Link Reference: http://paste.ubuntu.com/p/zhknRNbqDz/

12 November, 2022

PRELUDE:

    1. I am a regular and an active Ubuntu software user for more than 5 years, having started with Ubuntu 16.04 LTS (Xenial Xerus) in April 2017 as a learner.
    2. Starting as an Ubuntu-One client with Username manan49 in 2020, I am now an active “Ubuntu Advantage” client with the benefit of ESM (Extended Security Maintenance).
    3. Until recently, I had been a hassle-free and satisfied user of Ubuntu 20.04.5 LTS, Focal Fossa system through the self-learning process, by troubleshooting and overcoming system software issues with self-effort, external forums and online support.
    4. I chose to upgrade my computer from Ubuntu Focal Fossa, 20.04.5 LTS system to Ubuntu Jammy Jellyfish, 22.04.1 LTS system very recently on 07/11/2022.
    5. While I didn’t face any major problems earlier with the Ubuntu upgrades from 2017 onwards in the past and had had a fairly good enjoyable learning experience, I must confess that my experience with upgrading Ubuntu from Focal Fossa to Jammy Jellyfish version has been far from being smooth, and a very rough ride, indeed. Despite all my sincere efforts to resolve the undermentioned upgrading (predominantly python related, I guess, on Dell desktop computers with Intel graphic cards ???) issues, I feel frustrated in having failed to resolve them by myself so far, or even through online forums support.

MY DESKTOP COMPUTER SPECS:

anand@jjfish 16:21:02 ~
$ inxi -Fxz
System:
Kernel: 5.15.0-52-generic x86_64 bits: 64 compiler: gcc v: 11.2.0
Desktop: GNOME 42.5 Distro: Ubuntu 22.04.1 LTS (Jammy Jellyfish)
Machine:
Type: Portable System: Dell product: Inspiron N5010 v: A11
serial: <superuser required> --> ?
Mobo: Dell model: 0P2H9M v: A11 serial: <superuser required> BIOS: Dell
v: A11 date: 01/06/2011
CPU:
Info: dual core model: Intel Core i3 M 380 bits: 64 type: MT MCP
arch: Westmere rev: 5 cache: L1: 128 KiB L2: 512 KiB L3: 3 MiB
Speed (MHz): avg: 1444 high: 1463 min/max: 931/2527 cores: 1: 1390
2: 1463 3: 1463 4: 1463 bogomips: 20216
Flags: ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
Device-1: Intel Core Processor Integrated Graphics vendor: Dell driver: N/A
bus-ID: 00:02.0
Device-2: Microdia Laptop_Integrated_Webcam_1.3M type: USB
driver: uvcvideo bus-ID: 1-1.6:4
Display: x11 server: X.Org v: 1.21.1.3 driver: X: loaded: vesa
unloaded: fbdev,modesetting gpu: N/A resolution: 1024x768
OpenGL: renderer: llvmpipe (LLVM 13.0.1 128 bits) v: 4.5 Mesa 22.0.5
direct render: Yes
Audio:
Device-1: Intel 5 Series/3400 Series High Definition Audio vendor: Dell
driver: snd_hda_intel v: kernel bus-ID: 00:1b.0
Sound Server-1: ALSA v: k5.15.0-52-generic running: yes
Sound Server-2: PulseAudio v: 15.99.1 running: yes
Sound Server-3: PipeWire v: 0.3.48 running: yes
Network:
Device-1: Intel Centrino Wireless-N 1000 [Condor Peak] driver: N/A
bus-ID: 12:00.0
Device-2: Realtek RTL810xE PCI Express Fast Ethernet vendor: Dell
driver: r8169 v: kernel port: e000 bus-ID: 13:00.0
IF: enp19s0 state: up speed: 100 Mbps duplex: full mac: <filter>
IF-ID-1: docker0 state: down mac: <filter>
Bluetooth:
Device-1: Dell Wireless 365 Bluetooth type: USB driver: btusb v: 0.8
bus-ID: 2-1.6.3:6
Report: hciconfig ID: hci0 rfk-id: 0 state: up address: <filter>
bt-v: 1.2 lmp-v: 2.1
Unknown error: 1 --> ?
Drives:
Local Storage: total: 465.76 GiB used: 201.99 GiB (43.4%)
ID-1: /dev/sda vendor: Crucial model: CT500MX500SSD1 size: 465.76 GiB
Partition:
ID-1: / size: 195.19 GiB used: 180.09 GiB (92.3%) fs: ext4 dev: /dev/sda1
ID-2: /home size: 95.56 GiB used: 21.91 GiB (22.9%) fs: ext4
dev: /dev/sda3
Swap:
ID-1: swap-1 type: file size: 8 GiB used: 81 MiB (1.0%) file: /swapfile
Sensors:
System Temperatures: cpu: 68.0 C mobo: N/A
Fan Speeds (RPM): cpu: 3720
Info:
Processes: 254 Uptime: 2h 2m Memory: 3.64 GiB used: 2.11 GiB (58.1%)
Init: systemd runlevel: 5 Compilers: gcc: 11.3.0 Packages: 2629 Shell: Bash
v: 5.1.16 inxi: 3.3.13

ISSUES/BUGS:

    1. Ever since my computer system got upgraded to Ubuntu 22.04.1 LTS on 07/11/2022 using the Software Updater, I have NOT been unable to boot normally. I am confronted with the following booting error on a black screen:
     [ 66.756939] hdaudio hdaudioCOD3; unable to configure, disabling
I have been unsuccessful in troubleshooting the above problem and I am forced to boot ONLY through the “Recovery Boot” option, each time.

    2. From the beginning, I had been using the howdy face recognition software successfully. After upgrading, it failed to work. So, I reinstalled the latest Jammy compatible version of howdy, but I am confronted with the following errors, with the terminal command:

      $ sudo howdy add
 Traceback (most recent call last):
# Error-1: File “/usr/local/bin/howdy”, line 95, in <module>
  import cli.add
# Error-2: File “/usr/lib/security/howdy/cli/add.py”, line 10, in
  <module> import numpy as np
  ModuleNotFoundError: No module named “numpy”
    3. On exercising the following terminal command:

$ sudo apt install python3-pip
Traceback (most recent call last):
# Error-3: File “/lib/security/howdy/compare.py”, line 17, in
<module> import dlib
ModuleNotFoundError: No module named “dlib”
Unknown error: 1

    4. Suspecting booting issues with the bootloader, I successfully executed the boot-repair with the Linux “Boot Repair Disk, Version 1.2.5” on 12/11/22, but the booting problem still persists.

    5. As a supplementary troubleshooting exercise for taking care of dependencies issues, I created an exclusive virtual environment, venv for processing and retention/saving of python related work in a venv folder in the path: /home/user(self)/venv, and installed therein, the following packages’ versions:

Python 3.10.6; numpy 1.23.4; dlib 19.24.0; cli.add 0.1; wheel 0.38.4; scipy 1.9.3 & scikit-image 0.19.3

    6. Even after installation of the latest packages as above and attempting to reboot, the booting problem remains unresolved and the same errors as detailed above continue to appear.

    7. Looking for technical support at my email address: <email address hidden>

INDICATIVE TERMINAL OUTPUT:

anand@jjfish 08:18:48 ~
$ sudo nano /etc/default/grub
Traceback (most recent call last):
  File "/lib/security/howdy/compare.py", line 17, in <module>
    import dlib
ModuleNotFoundError: No module named 'dlib'
Unknown error: 1
[sudo] password for anand:

anand@jjfish 08:26:23 ~
$ ubuntu-drivers devices

anand@jjfish 08:26:52 ~
$ sudo howdy add
Traceback (most recent call last):
  File "/usr/local/bin/howdy", line 95, in <module>
    import cli.add
  File "/usr/lib/security/howdy/cli/add.py", line 10, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'

anand@jjfish 08:27:36 ~
$ sudo apt-get dist-upgrade -y
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

anand@jjfish 08:27:57 ~
$ sudo apt-get update && sudo apt-get dist-upgrade -y
Ign:1 https://repo.vivaldi.com/stable/deb stable InRelease
Hit:2 https://repo.vivaldi.com/stable/deb stable Release
Hit:3 http://archive.ubuntu.com/ubuntu jammy InRelease
Get:4 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [114 kB]
Hit:5 https://ppa.launchpadcontent.net/boltgolt/howdy/ubuntu jammy InRelease
Get:7 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [99.8 kB]
Get:8 https://esm.ubuntu.com/infra/ubuntu jammy-infra-security InRelease [7,453 B]
Get:9 http://archive.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/main i386 Packages [372 kB]
Get:11 https://esm.ubuntu.com/infra/ubuntu jammy-infra-updates InRelease [7,452 B]
Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [698 kB]
Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 DEP-11 Metadata [95.1 kB]
Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/restricted i386 Packages [23.3 kB]
Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [417 kB]
Get:16 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 DEP-11 Metadata [255 kB]
Get:17 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 DEP-11 Metadata [940 B]
Get:18 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 DEP-11 Metadata [11.7 kB]
Get:19 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 DEP-11 Metadata [20.1 kB]
Get:20 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 DEP-11 Metadata [13.2 kB]
Fetched 2,247 kB in 2s (902 kB/s)
Reading package lists... Done
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

* * *

NB: I am able to use the latest version Ubuntu 22.04.1 LTS, Jammy Jellyfish system, however by booting ONLY in the RECOVERY MODE on the grub prompt.

Question information

Language:
English Edit question
Status:
Solved
For:
Ubuntu Edit question
Assignee:
No assignee Edit question
Solved by:
Bernard Stafford
Solved:
Last query:
Last reply:
Revision history for this message
Manfred Hampl (m-hampl) said : 		#1

One of the first lines in the output of boot-repair:

sda1 is 98 % full

Apparently you are running out of free space. You have to remove obsolete files.

Revision history for this message
Anand Manthena (manan49) said : 		#2

Anand's answer:

Thanks for your prompt reply and advice. I created additional free space
(38GB free) in sda1 today by deleting unwanted/obsolete files and tried
booting again. The stated problem still persists.

On Mon, Nov 14, 2022 at 8:22 PM Manfred Hampl <
<email address hidden>> wrote:

> Your question #703818 on Ubuntu changed:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> Status: Open => Answered
>
> Manfred Hampl proposed the following answer:
> One of the first lines in the output of boot-repair:
>
> sda1 is 98 % full
>
> Apparently you are running out of free space. You have to remove
> obsolete files.
>
> --
> If this answers your question, please go to the following page to let us
> know that it is solved:
> https://answers.launchpad.net/ubuntu/+question/703818/+confirm?answer_id=0
>
> If you still need help, you can reply to this email or go to the
> following page to enter your feedback:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> You received this question notification because you asked the question.
>

Revision history for this message
Manfred Hampl (m-hampl) said : 		#3

What exactly happens when you try booting normally (nor selecting recovery mode)?

Is there anything in the system logs that might shed a light on the root cause of your problems?

The message "[ 66.756939] hdaudio hdaudioCOD3; unable to configure, disabling ..." indicates just a problem with the sound system, but should not prevent the boot process at all.

Revision history for this message
Anand Manthena (manan49) said : 		#4

*Answer to Question 1*:

 " *What exactly happens when you try booting normally (not selecting
recovery mode)?*" -->

(a) Earlier (With Focal Fossa, before upgrading): The system used to boot
normally and straight away take me to the 'howdy' face recognition system
for auto login, or Authentication Window (if time lapsed) for entering the
password.

Now, with [Jammy Jellyfish (abbr:JJ), after upgrading]: The system is
taking me to the frozen black screen (without booting normally) ; then
the *root;
clean (.....Nos. of files) & (.....Nos. of Blocks)* is getting displayed.

Immediately thereafter, the error
* "[ 66.756939] hdaudio hdaudioCOD3; unable to configure, disabling ..."*
is getting flashed, cursor blinking endlessly and booting prevented. In
every booting effort, the digits after 66 are getting changed; today it is
*66.600381*

The above audio system error, preventing normal booting is indeed, very
intriguing,

(b) Even in recovery boot login, *howdy* is not working (with suspected
python errors). In the "Authentication Required" window (where login
password is required to be entered), Orange colored *"Unknown error: 1"* is
displayed below the window.

(c) After booting through recovery mode, I accessed the /var/log/*syslog*
folder as a *root user*; it is displaying an alert on the top: "*There was
a problem opening the file, and it has opened with some invalid characters.
If you continue editing this file, you could corrupt this document*"; the
same alert can be seen in all the other similar folders like - *syslog.1,
kern.log, kern.log.1 *etc

*Answer to Question*: 2

 " *Is there anything in the system logs that might shed light on the root
cause of your problems?"*

I am puzzled and unable to figure out the likely root cause(s) for the
problem, even from the system logs which are quite exhaustive.

(i) As regards *system logs*, (c) above answers part of the question.
However, for the purpose of focussed troubleshooting, should you feel that
any *specific terminal outpu*t would be of help (suggesting the terminal
command) in isolating the likely/suspected problem area within the system,
I shall send the same.

I may add that free space of more than 40 GB has already been created for
the parent drive partition sda1, but the problem persists. There is no
problem either with the sound system, when the computer is used in the
recovery boot mode - it functions normally.

My */Home* folder containing my personal files, folders and documents etc
are located/housed in a separate sda3 (not in the bootable system
partition, sda1) ext4 filesystem (non-bootable) partition of the SSD - if
that could help, in easier diagnosis of the problem.

Awaiting further directions for troubleshooting,

Anand

On Thu, Nov 17, 2022 at 1:06 PM Manfred Hampl <
<email address hidden>> wrote:

> Your question #703818 on Ubuntu changed:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> Status: Open => Needs information
>
> Manfred Hampl requested more information:
> What exactly happens when you try booting normally (nor selecting
> recovery mode)?
>
> Is there anything in the system logs that might shed a light on the root
> cause of your problems?
>
> The message "[ 66.756939] hdaudio hdaudioCOD3; unable to configure,
> disabling ..." indicates just a problem with the sound system, but
> should not prevent the boot process at all.
>
> --
> To answer this request for more information, you can either reply to
> this email or enter your reply at the following page:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> You received this question notification because you asked the question.
>

Revision history for this message
Anand Manthena (manan49) said : 		#5

Further to my above message, I am attaching 4 files of today's "GNOME-LOGS"
of my Ubuntu System - categorized under "applications", "hardware",
"security" and "system" respectively for your perusal and troubleshooting.

I shall await further advisory directions for resolving the problem.

Regards,

Anand

---------- Forwarded message ---------
From: Anand Manthena <email address hidden>
Date: Thu, Nov 17, 2022 at 2:56 PM
Subject: Re: [Question #703818]: Normal booting affected: Forced to use
recovery mode for booting into 22.04.1 LTS after upgrade from 20.04.1 LTS
To: <email address hidden>

Your question #703818 on Ubuntu changed:
https://answers.launchpad.net/ubuntu/+question/703818

    Status: Needs information => Open

You gave more information on the question:
*Answer to Question 1*:

 " *What exactly happens when you try booting normally (not selecting
recovery mode)?*" -->

(a) Earlier (With Focal Fossa, before upgrading): The system used to boot
normally and straight away take me to the 'howdy' face recognition system
for auto login, or Authentication Window (if time lapsed) for entering the
password.

Now, with [Jammy Jellyfish (abbr:JJ), after upgrading]: The system is
taking me to the frozen black screen (without booting normally) ; then
the *root;
clean (.....Nos. of files) & (.....Nos. of Blocks)* is getting displayed.

Immediately thereafter, the error
* "[ 66.756939] hdaudio hdaudioCOD3; unable to configure, disabling ..."*
is getting flashed, cursor blinking endlessly and booting prevented. In
every booting effort, the digits after 66 are getting changed; today it is
*66.600381*

The above audio system error, preventing normal booting is indeed, very
intriguing,

(b) Even in recovery boot login, *howdy* is not working (with suspected
python errors). In the "Authentication Required" window (where login
password is required to be entered), Orange colored *"Unknown error: 1"* is
displayed below the window.

(c) After booting through recovery mode, I accessed the /var/log/*syslog*
folder as a *root user*; it is displaying an alert on the top: "*There was
a problem opening the file, and it has opened with some invalid characters.
If you continue editing this file, you could corrupt this document*"; the
same alert can be seen in all the other similar folders like - *syslog.1,
kern.log, kern.log.1 *etc

*Answer to Question*: 2

 " *Is there anything in the system logs that might shed light on the root
cause of your problems?"*

I am puzzled and unable to figure out the likely root cause(s) for the
problem, even from the system logs which are quite exhaustive.

(i) As regards *system logs*, (c) above answers part of the question.
However, for the purpose of focussed troubleshooting, should you feel that
any *specific terminal outpu*t would be of help (suggesting the terminal
command) in isolating the likely/suspected problem area within the system,
I shall send the same.

I may add that free space of more than 40 GB has already been created for
the parent drive partition sda1, but the problem persists. There is no
problem either with the sound system, when the computer is used in the
recovery boot mode - it functions normally.

My */Home* folder containing my personal files, folders and documents etc
are located/housed in a separate sda3 (not in the bootable system
partition, sda1) ext4 filesystem (non-bootable) partition of the SSD - if
that could help, in easier diagnosis of the problem.

Awaiting further directions for troubleshooting,

Anand

On Thu, Nov 17, 2022 at 1:06 PM Manfred Hampl <
<email address hidden>> wrote:

> Your question #703818 on Ubuntu changed:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> Status: Open => Needs information
>
> Manfred Hampl requested more information:
> What exactly happens when you try booting normally (nor selecting
> recovery mode)?
>
> Is there anything in the system logs that might shed a light on the root
> cause of your problems?
>
> The message "[ 66.756939] hdaudio hdaudioCOD3; unable to configure,
> disabling ..." indicates just a problem with the sound system, but
> should not prevent the boot process at all.
>
>
> To answer this request for more information, you can either reply to
> this email or enter your reply at the following page:
> https://answers.launchpad.net/ubuntu/+question/703818
>
> You received this question notification because you asked the question.
>

--
You received this question notification because you asked the question.

Revision history for this message
Manfred Hampl (m-hampl) said : 		#6

Attaching files does not work, see https://answers.launchpad.net/ubuntu/+question/703818

Revision history for this message
Best Bernard Stafford (bernard010) said : 		#7

Fresh install ?
https://ubuntu.com/download/desktop

Revision history for this message
Anand Manthena (manan49) said : 		#8

Thanks Mr. Bernard,

The soft option of a 'Fresh Install' was always available to me, which I have already implemented successfully and Ubuntu 22.04.1 LTS system is working without any problem, however in a different partition (sda6) of the SSD, auto-chosen by the Grub bootloader in the fresh install [my /home partition fortunately being located in a different partition too (sda3)].

Being a Linux learner, I was just curious to arrive at the hard option of a possible solution by troubleshooting myself, but failed apparently even after several attempts. To my mind, the looping booting error of "hdaudioCOD3-unable to configure, disabling" appeared to be a bug yet awaiting resolution by the experts through the traditional "Software Updater" route , with the technical glitches seemingly caused by the introduction of snap software.

What do I do with corrupted version of Ubuntu 22.04.1 LTS, currently not booting and housed in the defunct sda1 partition of the SSD? Kindly advise whether I can erase it fully and reformat for future use, say with another Linux distro.

Thanks once again.

The Question #703818 can be closed; however, I shall appreciate if I could be informed of the technical solution if arrived at by experts to the cited problem.

Anand