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Thread: Seemingly sporadic slow ZFS IO since 22.04

  1. #61
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Are you using this for anything other than a media server? I mean what other processes are going on when you are watching movies?

    On my workstation, it is dual-boot with Win11 and Ubuntu. I have Plex installed on both OS'es pointing to the same storage, where my media files are. That way my wife can watch movies, no matter what I am doing on that. Watching movies or playing music is just reads.

    I thrash that machine. I game on it. I'll be running many KVM VM's doing testing, while doing program compiles... I have visual system monitoring on my desktop, with Conky statuses, and very rarely am I really taxing that i9... Or the disk through-put, or any of my 18 networking devices on it.

    There has got to be something going on there, to affect that, that we are not seeing yet. We have checked all the other blocks there.

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  2. #62
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by MAFoElffen View Post
    Are you using this for anything other than a media server? I mean what other processes are going on when you are watching movies?

    On my workstation, it is dual-boot with Win11 and Ubuntu. I have Plex installed on both OS'es pointing to the same storage, where my media files are. That way my wife can watch movies, no matter what I am doing on that. Watching movies or playing music is just reads.

    I thrash that machine. I game on it. I'll be running many KVM VM's doing testing, while doing program compiles... I have visual system monitoring on my desktop, with Conky statuses, and very rarely am I really taxing that i9... Or the disk through-put, or any of my 18 networking devices on it.

    There has got to be something going on there, to affect that, that we are not seeing yet. We have checked all the other blocks there.
    This is the thing. This box does pretty much nothing apart from Emby and some dockers that deal with NZB and Torrent and this is what it has done it's entire life without ever having an issue. It doesn't serve a huge SQL DB for example, or run folding at home, or scrub constantly, or have a massive amount of torrents/nzb at any one time (anyway this is irrelevant because they are sent to the 500GB disk first) or idk.... transcode a lot (front ends are Nvidia Shields that can handle most things).

    It's 3 main functions are:

    1. Host music, movies and TV and serve via Emby docker
    2. Use ZFS to maintain data quality
    3. Use a few other dockers that deal with sorting and acquisition like radarr, sonarr, prowlarr, VPN, deluge, sabnzbd etc.

    With that said, ALL these things were running with Bionic. Firefox is always open chewing up memory, but there's plenty free now and again, the firefox behaviour hasn't changed since Bionic. I literally installed Jammy and used Docker compose to fire up my containers and snap to install firefox. Install ksplice and a few other essentials and that's it.

    If I thrashed this, I could understand if ground to a halt. This is something else.
    Last edited by tkae-lp; December 13th, 2023 at 01:00 AM. Reason: Reworded last line. Wrote when tired and it didn't make sense. lol

  3. #63
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    I'm thinking about if you installed sysstat and did something like this:
    Code:
    # syntax: pidstat -d <interval> <times>
    sudo pidstat -d 30 59 | tee -a $HOME/pidstats.log
    Then it might track some of those...

    And if yo added that to a cron job to run every 10 minutes hour or so, then it might get fairly large over a few days.

    Here is a snip from the output of that
    Code:
    mafoelffen@Mikes-ThinkPad-T520:~$ sudo pidstat -d 30 100
    Linux 6.2.0-37-generic (Mikes-ThinkPad-T520)     12/11/2023     _x86_64_    (8 CPU)
    
    12:05:33 PM   UID       PID   kB_rd/s   kB_wr/s kB_ccwr/s iodelay  Command
    12:06:03 PM     0      1169      0.00      4.93      0.00       0  systemd-journal
    12:06:03 PM     0      3181      0.00      0.02      0.00       0  NetworkManager
    12:06:03 PM   104      3210      0.00      0.00      0.00       0  rsyslogd
    12:06:03 PM     0      3224      0.21      0.00      0.00       0  snapd
    12:06:03 PM     0      3821    562.40      0.00      0.00       0  libvirtd
    12:06:03 PM  1000      6222      3.37      0.00      0.00       0  gnome-shell
    12:06:03 PM  1000      6824      0.29      0.00      0.00       0  xdg-desktop-por
    12:06:03 PM  1000    205044    230.79      2.60      0.00       0  firefox
    12:06:03 PM  1000    211290      0.67      0.00      0.00       0  Isolated Web Co
    12:06:03 PM  1000    350276      1.43      0.00      0.00       0  Isolated Servic
    12:06:03 PM  1000    355514      5.06      0.00      0.00       0  Web Content
    
    ##... <<On Dang. That is every 30 seconds for about an hour or so. Maybe run once every hour and limit it to 30 seconds & 60 times ?
    
    12:54:03 PM   UID       PID   kB_rd/s   kB_wr/s kB_ccwr/s iodelay  Command
    12:54:33 PM     0       437      4.27      0.00      0.00       0  z_rd_int_0
    12:54:33 PM     0      1169      0.00     14.93      0.00       0  systemd-journal
    12:54:33 PM   104      3210      0.00      0.04      0.00       0  rsyslogd
    12:54:33 PM     0      3439     16.06      0.00      0.00       0  canonical-livep
    12:54:33 PM     0      3821    563.33      0.00      0.00       0  libvirtd
    12:54:33 PM  1000      6222      3.38      0.00      0.00       0  gnome-shell
    12:54:33 PM  1000      9431    207.62      0.00      0.00       0  update-notifier
    12:54:33 PM  1000    205044     65.84      0.31      0.00       0  firefox
    12:54:33 PM     0    353749    154.20      0.00      0.00       0  kworker/u16:4-events_unbound
    12:54:33 PM  1000    374977      6.50      0.00      0.00       0  Isolated Servic
    
    12:54:33 PM   UID       PID   kB_rd/s   kB_wr/s kB_ccwr/s iodelay  Command
    12:55:03 PM     0      1169      0.00      5.60      0.00       0  systemd-journal
    12:55:03 PM     0      3178      5.42      0.00      0.00       0  cron
    12:55:03 PM   104      3210      0.00      0.01      0.00       0  rsyslogd
    12:55:03 PM     0      3821    563.33      0.00      0.00       0  libvirtd
    12:55:03 PM  1000      6222      3.38      0.00      0.00       0  gnome-shell
    12:55:03 PM  1000    205044      5.34     24.31      0.00       0  firefox
    12:55:03 PM     0    353749      0.00      6.67      0.00       0  kworker/u16:4-iwlwifi
    12:55:03 PM     0    353752      0.00      8.00      0.00       0  kworker/u16:7-events_power_efficient
    
    12:55:03 PM   UID       PID   kB_rd/s   kB_wr/s kB_ccwr/s iodelay  Command
    12:55:33 PM     0      3821    563.33      0.00      0.00       0  libvirtd
    12:55:33 PM  1000      6222      3.38      0.00      0.00       0  gnome-shell
    12:55:33 PM  1000    205044      6.63      0.13      0.00       0  firefox
    12:55:33 PM     0    351618      0.00      5.60      0.00       0  kworker/u16:3-iwlwifi
    
    Average:      UID       PID   kB_rd/s   kB_wr/s kB_ccwr/s iodelay  Command
    Average:        0       437      0.64      0.00      0.00       0  z_rd_int_0
    Average:        0       438      0.38      0.00      0.00       0  z_rd_int_1
    Average:        0       543      0.07      0.00      0.00       0  txg_sync
    Average:        0      1169      0.01      3.18      0.00       0  systemd-journal
    Average:        0      3178      0.42      0.00      0.00       0  cron
    Average:        0      3181      0.00      0.00      0.00       0  NetworkManager
    Average:      104      3210      0.00      0.00      0.00       0  rsyslogd
    Average:        0      3214      0.00      0.00      0.00       0  smartd
    Average:        0      3224      0.15      0.00      0.00       0  snapd
    Average:        0      3426      0.00      0.00      0.00       0  cupsd
    Average:        0      3439      2.66      0.00      0.00       0  canonical-livep
    Average:        0      3821    563.32      0.00      0.00       0  libvirtd
    Average:        0      4999      0.00      0.00      0.00       0  nmbd
    Average:        0      5085      0.01      0.00      0.00       0  samba-bgqd
    Average:        0      5495      0.00      0.00      0.00       0  upowerd
    Average:     1000      5904      0.00      0.00      0.00       0  systemd
    Average:     1000      6222      3.40      0.00      0.00       0  gnome-shell
    Average:     1000      6824      0.01      0.00      0.00       0  xdg-desktop-por
    Average:     1000      7465      0.23      0.00      0.00       0  snap
    Average:     1000      9431      3.92      0.00      0.00       0  update-notifier
    Average:     1000     88253      0.00      0.00      0.00       0  mission-control
    Average:     1000    124715      0.02      0.00      0.00       0  gnome-terminal-
    Average:     1000    205044    137.25     52.22      0.00       0  firefox
    Average:     1000    205412      0.03      0.00      0.00       0  WebExtensions
    Average:     1000    205608      0.00      0.00      0.00       0  Isolated Web Co
    Average:     1000    210615      0.00      0.00      0.00       0  Isolated Web Co
    Average:     1000    211126      0.35      0.00      0.00       0  Isolated Web Co
    Average:     1000    211290      0.01      0.00      0.00       0  Isolated Web Co
    Average:     1000    216895      0.03      0.00      0.00       0  Isolated Web Co
    Average:     1000    232100      0.20      0.00      0.00       0  Isolated Web Co
    Average:     1000    232736      0.01      0.00      0.00       0  Isolated Web Co
    Average:     1000    330037      0.02      0.00      0.00       0  Isolated Web Co
    Average:     1000    340748      0.35      0.00      0.00       0  Isolated Web Co
    Average:     1000    345265      0.02      0.00      0.00       0  Isolated Web Co
    Average:     1000    347837      0.03      0.00      0.00       0  Isolated Web Co
    Average:     1000    347908      0.12      0.00      0.00       0  Isolated Web Co
    Average:        0    351618      4.63      1.15      0.00       0  kworker/u16:3-iwlwifi
    Average:        0    353749      2.78      1.01      0.00       0  kworker/u16:4-events_unbound
    Average:        0    353752      6.93      0.62      0.00       0  kworker/u16:7-iwlwifi
    Average:     1000    355514      0.27      0.00      0.00       0  Isolated Web Co
    Last edited by MAFoElffen; December 11th, 2023 at 10:41 PM.

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  4. #64
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Sorry for the delay. The last few days have been hectic.

    I ran fio and pidstat just now and was just going to post to say I am not currently in a slow down and post a snippet of pidstat BUT THEN my whole system froze! Mouse cursor could move, but no XFCE element would respond, couldn't get to another terminal to go init3 and return to init5, couldn't login via ssh, 3 x Control + Alt + Delete didn't reboot, had to hit the reboot button on the board!

    This happened a few weeks ago (before upgrades) so that rules those out... I didn't think too much of it as it never happened before (we've had a LOT of bad weather here so assumed it was a power fluctuation). But now it's happened again... here is the pidstat snippet: https://paste.ubuntu.com/p/mHHcMwQpBj/

    I started to wonder if perhaps the OS SSD is faulty. I had originally checked the SMART for the array, but not the OS SSD, and sure enough I see this:



    But, the last error occurred 3 months ago as the life hours is now:



    So I guess the next thing is replace that? What I don't get is that the last error was 3 months ago. Nothing since. This does seem to be looking like the likely culprit now though, doesn't it? I just would have expected an error to show 30 mins ago?

    Edit: I can get an Evo 870 500GB SATA SSD here tomorrow. Tbh, if this Sandisk is failing, that's the 2nd one I've had in 2 years. I think I'll stick with Samsung from now on... Never had an issues with their NVMes!
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    Last edited by tkae-lp; December 13th, 2023 at 01:53 AM.

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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by tkae-lp View Post
    Sorry for the delay. The last few days have been hectic.

    This does seem to be looking like the likely culprit now though, doesn't it? I just would have expected an error to show 30 mins ago?
    That seems like a logical guess, but other things were happening before this, Right?
    Dang i hate to post and run, but I've got family in town to-nite.
    Hopefully MAFoElffen will see this. I'm starting to think hardware though, or a bad driver?? Just thinking out loud.
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  6. #66
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by 1fallen View Post
    That seems like a logical guess, but other things were happening before this, Right?
    Dang i hate to post and run, but I've got family in town to-nite.
    Hopefully MAFoElffen will see this. I'm starting to think hardware though, or a bad driver?? Just thinking out loud.
    No worries - as I've said all along, I appreciate your help - enjoy your family time!

    Yes, I would say the problem with ZFS slowing down has been for the past 3 or so months since Jammy. The 1st freeze was only a few weeks ago.

    Edit: I just read that ATA errors can be caused by bad SATA cables, but I have just replaced those. So I suppose, whilst not impossible, we can probably rule those out. The chances of me replacing 1 bad SATA cable with another bad SATA cable on just one (the same) drive are pretty slim!
    Last edited by tkae-lp; December 13th, 2023 at 02:12 AM. Reason: SATA cables and typo

  7. #67
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    I would have the same guess. You just replaced the cables.

    ZFS "zpool status" logs and shows read, write and cksum errors. It hasn't been showing those has it?

    I tend to pay more for Samsung branded because I trust them.

    I keep having errors with 1 Samsung EVO 870 drive which does not show any SMART Errors, and corrects itself with a scrubs... When i first upgraded that array from 4 disks to 5 disks, I replaced that that new SSD 3 times... thinking I just got a bad SSD... and it still goes offline very once in a blue moon. Though inconvenient, I just clear & scrub it and it shows fine and continues on. I still have not tracked down the why of that on mine. But it now only happens about once every 5 months or so. I haven't looked very hard, as it comes back up.

    The funny thing is, it's the 5th disk in a 5 (SSD) disk RAIDZ2 array and the performance is so fast, with 1 disk down in that array, I don't even notice it is degraded until do a "status" on it.

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  8. #68
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by MAFoElffen View Post
    I would have the same guess. You just replaced the cables.

    ZFS "zpool status" logs and shows read, write and cksum errors. It hasn't been showing those has it?

    I tend to pay more for Samsung branded because I trust them.

    I keep having errors with 1 Samsung EVO 870 drive which does not show any SMART Errors, and corrects itself with a scrubs... When i first upgraded that array from 4 disks to 5 disks, I replaced that that new SSD 3 times... thinking I just got a bad SSD... and it still goes offline very once in a blue moon. Though inconvenient, I just clear & scrub it and it shows fine and continues on. I still have not tracked down the why of that on mine. But it now only happens about once every 5 months or so. I haven't looked very hard, as it comes back up.

    The funny thing is, it's the 5th disk in a 5 (SSD) disk RAIDZ2 array and the performance is so fast, with 1 disk down in that array, I don't even notice it is degraded until do a "status" on it.
    Interesting with your 870 experience... I am still inclined to go with it though, I already pushed the button so it will arrive tomorrow but I won't get time to install until Thu/Fri-ish.

    With regards to the zpool output, no, there has never been anything amiss there - output taken now (and I do check regularly):

    Code:
    /mnt/Tank # zpool status Tank
      pool: Tank
     state: ONLINE
      scan: scrub repaired 0B in 07:03:04 with 0 errors on Fri Dec  8 03:03:07 2023
    config:
    
        NAME                                                                STATE     READ WRITE CKSUM
        Tank                                                                ONLINE       0     0     0
          raidz2-0                                                          ONLINE       0     0     0
            ata-ST4000DM000-1F2168_S300XXXX                                 ONLINE       0     0     0
            ata-ST4000DM004-2CV104_ZTT4XXXX                                 ONLINE       0     0     0
            ata-ST4000DM004-2CV104_ZTT4XXXX                                 ONLINE       0     0     0
            ata-ST4000DM000-1F2168_W300XXXX                                 ONLINE       0     0     0
            ata-ST4000DM000-1F2168_W300XXXX                                 ONLINE       0     0     0
            ata-ST4000DM000-1F2168_W300XXXX                                 ONLINE       0     0     0
            ata-ST4000DM000-1F2168_W300XXXX                                 ONLINE       0     0     0
            ata-ST4000DM000-1F2168_W300XXXX                                 ONLINE       0     0     0
        logs    
          nvme-Samsung_SSD_980_PRO_with_Heatsink_2TB_S6WRNS0W53XXXXX-part2  ONLINE       0     0     0
        cache
          nvme-Samsung_SSD_980_PRO_with_Heatsink_2TB_S6WRNS0W53XXXXX-part1  ONLINE       0     0     0
    
    errors: No known data errors
    As you can see, I did a scrub just after I thought we'd cracked it. Nothing flagged.

    SSD arrives tomorrow.. What do I install on it? You think I should still go with Jammy? Mixing it up at this point removes our control from this experiment.... So I guess Jammy it is. Same packages etc. Whenever I do something I always take notes, so I am sure I can replicate the system I have here.

  9. #69
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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by tkae-lp View Post
    Whenever I do something I always take notes, so I am sure I can replicate the system I have here.
    I do the same (with install recipes) of all the commands I used to create someting, and the output, so I have a record of, and can track how it was, and changes I made to things.

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    Re: Seemingly sporadic slow ZFS IO since 22.04

    Quote Originally Posted by MAFoElffen View Post
    all the commands I used to create someting, and the output
    I do the same with commands - I don't do output though. Here's my 22.04 just in case you happen to spot any glaring errors before I reinstall, SSD is here. Will probably be Friday I get round to it.

    Code:
    Installing Ubuntu Server 22.04 and very minimal XFCE Environment
    ----------------------------------------------------------------
    
    1. Grab Ventoy key drive and boot from the Ubuntu server ISO
    
    2. When prompted select Ubuntu Server not Minimalised
    
    3. Partition disks if needed and run through the rest of the installation
    
    Note: If existing home partition, remember not to format and just assign /home
    
    4. On first boot, login with your user and disable cloud-init:
    
    sudo touch /etc/cloud/cloud-init.disabled
    
    5. Edit netplan config: sudo nano /etc/netplan/00-installer-config.yaml to include:
    
    optional: true
    
    ie:
    
    network:
      ethernets:
        enp0s25:
          optional: true
          dhcp4: true
        enp5s0:
          optional: true
          dhcp4: true
      version: 2
    
    
    Note: optional: true prevents boot delays
    
    6. Save the file and rename it:
    
    sudo mv /etc/netplan/00-installer-config.yaml /etc/netplan/00-netcfg.yaml
    
    Then:
    
    netplan generate
    netplan apply
    
    If it moans about permissions do:
    
    chmod 0600 /etc/netplan/00-netcfg.yaml
    
    7. Install some basics: sudo apt install htop curl xfce4 xfce4-goodies xfce4-notes-plugin zathura apt-transport-https ca-certificates avahi-daemon qalculate-gtk
    
    8. hddtemp doesn't seem to work with the XFCE4 sensor plugin. The preferred method for 22.04 seems to be to use hwmon via lm-sensors.
    
    sudo apt install lm-sensors
    sudo modprobe drivetemp
    sensors
    
    To make drivetemp load automatically every boot, add it to /etc/modules:
    
    echo drivetemp | sudo tee -a /etc/modules
    
    This allows adding each HDD to the sensor plugin, (but it's one item in the list per drive)
    
    9. Reboot and install lxdm:
    
    sudo apt install lxdm
    
    Note: LXDM is preferable to LightDM because LightDM is actually not so light and comes with a TON of deps including Network-Manager whereas LXDM contains about 5 packages.
    
    10. Reboot and login by selecting "Desktop: Xfce4 Session" and your credentials
    
    Note: LXDM will be Debian branded (but we can change that later)
    Note2:Upon logging in, if you preserved your home partition, your desktop should be similar but may have some things missing.
    
    11. Setup / config XFCE desktops and addons as required.
    
    12. Install Firefox and other utils:
    
    apt install firefox file-roller gnome-disk-utility gsmartcontrol vlc 
    
    Note: for firefox this will actually install the snap
    
    13. a) Install ZFS and import tank:
    
    apt install zfsutils-linux
    
    b) Import Tank: zpool import Tank
    
    14. Install Docker:
    
    sudo apt-get update
    
    sudo apt-get install ca-certificates curl gnupg
    
    sudo install -m 0755 -d /etc/apt/keyrings
    
    curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
    
    sudo chmod a+r /etc/apt/keyrings/docker.gpg
    
    echo \
      "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
      "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
      sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
    
    sudo apt update
    
    sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
    
    usermod -a tk -G docker
    
    15. Install portainer:
    
    docker volume create portainer_data
    portainer_data
    
    docker run -d -p 8000:8000 -p 9443:9443 --name portainer --restart=always -v /var/run/docker.sock:/var/run/docker.sock -v portainer_data:/data portainer/portainer-ce:latest
    
    Login to portainer and import backup or paste compose files, and start them.
    
    16. Install VNC Viewer / Server and login
    
    17. Install localsend
    
    18. Install tailscale:
    
    curl -fsSL https://tailscale.com/install.sh | sh
    
    Note: Don't forget to config via admin panel.
    
    19. Install ohmyzsh!:
    
    apt install git zsh
    
    sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"
    
    Note: Run this as your own user not root
    Note2: If you're migrating from an old install, ohmyzsh is already installed in home. Just change default shell.
    
    Set zsh as the default shell: chsh -s /bin/zsh
    
    20. Run: sudo lxdm-config to customise login screen appearance
    
    Note: Without sudo, you can only set your own user icon
    
    21. Syncthing:
    
    a. Install by following: apt.syncthing.net
    b. Enable with systemctl enable syncthing@[username].service
    c. Start with: systemctl start syncthing@[username].service
    
    22. Ksplice
    
    a. Download the .deb from here: https://ksplice.oracle.com/try/desktop
    
    b. Install with: apt install ./uptrack.deb
    
    c. Then run: sudo uptrack-upgrade -n and accept the user agreement
    
    d. Edit: /etc/uptrack/uptrack.conf and change autoinstall to yes
    
    e. Now activate with: uptrack-upgrade -y
    
    23. Nvidia Drivers for Hardware Transcoding
    
    The default is Nouveau. This doesn't support h264 etc. Unfortunately the Nvidia Quadro NVS 295 is too old for offical support from Ubuntu for 22.04. But there is a PPA:
    
    add-apt-repository ppa:kelebek333/nvidia-legacy
    apt install nvidia-340
    
    Note: This currenly works well with kernel 5.15.0-88-generic. It could break in future kernels and need reverting.
    
    24. apt update && apt upgrade
    
    25. Remove unused apps:
    
    apt remove xarchiver && apt autoremove
    
    26. Reboot and profit :)
    Last edited by tkae-lp; December 14th, 2023 at 02:51 AM. Reason: code tag out of place, corrected some typos

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