Using the CLI to backup or copy a Linux system

nevj · 17 January 2026 06:39

There is a nice set of rsync examples here

Last try was:

There are problems with that

I think /dev/* etc should be /dev… ie protect a directory
the source should be /mnt/* … according to examples I find

So I ran

rsync  -avxHAXS --delete  --filter=protect_{/dev,/proc,/sys,/run,/mnt,/media,/tmp} /mnt/*  /

It ran and displayed a long incremental list of files … so /mnt/* was effective
but
on completion the OS collapsed… could not find ls or cat … the background and menu disappeared, and it would not boot… so not sure the --filter option was correct.

So… golden opportunity, … I am going to try with rsync from MX to do a recovery from my backup with both the source and destination directories mounted.
Wish me luck!

Well, my luck is out. … it seems the above rsync attempt not only messed up the destination OS, but also destroyed the source backup filesystem… when I mount it from MX, there is nothing there… it seems --delete deleted the source???

I think the problem was… the --filter=protect option was wrong, so it did not protect /mnt and therefore the backup directory itself came under the --delete operation.

Oh well… start again with a fresh install of Peppermint

ihasama · 17 January 2026 17:02

I’m also trying this rsync to USB now. Actually it’s been running 8hours now.. I’m on Mint, trying to rsync my Gentoo. I tried to exclude my /home/pete/Downloads but it still copied it. At the moment it’s syncing

/gentoo/var/tmp/portage/dev-lang/
ghc-9.0.2-r4  mujs-1.3.3  rust-1.71.1  rust-1.74.1-r101

which takes a lot of time. I don’t know how to exclude these because I used the (added /home/pete/Downloads/*) command as per on the first message.

I can’t give the exact command at the moment for my rsync because it’s still running but will edit this after it stops.

Maybe tar is the right way to do a full system backup? Or just copy /home folder for backing up the data and just re-install OS if needed or use clonezilla?

EDIT: the rsync finished. The command was:

sent 147.839.839.015 bytes received 31.709.647 bytes 4.374.444,91 bytes/sec
total size is 150.170.251.842 speedup is 1,02
root@pete:~# rsync --exclude={/dev/,/proc/,/sys/,/run/} -avxHAXS /gentoo /mnt

It seems that I didn’t add /home/pete/Downloads/* as I thought

nevj · 17 January 2026 21:53

Well, wecome to the mistake makers club… that is how you learn , but it can be painful.

It rendered in discourse as /dev/ but when I quoted it above I got /dev/* in the edit window. ?? The codebox is supposed to protect that??
That started me thinking… /dev/* does not include dot files.
That does not matter in /dev but for /home/pete/Downloads/* I think you might use /home/pete/Downloads/ to include dot files.

That issue arises in specifying the <source> too.
/ is OK, but /abc is not right… it needs to be /abc/
But your /gentoo worked? My feeling is it should be /gentoo/ ?
That only applies to <source>… <destination> can be a directory

The ‘trailing / rule’ applies to pathnames. I am not sure if it applies to items in an --exclude option? The man page is not helpful on this?
I asked duck.ai

"The trailing slash rule in rsync applies differently to source paths compared to exclude patterns.

Trailing Slash in Source Paths When specifying source paths, the presence or absence of a trailing slash determines how rsync interprets the path.

With Trailing Slash: Includes the contents of the directory. Without Trailing Slash: Includes the directory itself and its contents."

"Exclude Patterns For exclude options, the trailing slash has a different effect:

With Trailing Slash: Indicates that you want to exclude directories that match the pattern. This means only directories with that exact name (and their contents) will be excluded. Without Trailing Slash: Excludes all files and directories that match the pattern, regardless of whether they are files or folders."

"Example Exclude a Directory: Exclude option: --exclude=dir/ Excludes the directory dir and its contents. Exclude Files in a Directory: Exclude option: --exclude=dir Excludes both dir and any files named dir.

In summary, yes, the trailing slash rule does apply to exclude options in rsync, and it affects the scope of what gets excluded."

It does not say what dir/* does? That seems to be what everyone uses.
It does say that your /gentoo included the gentoo directory on the backup partition. That is OK , but be careful when you do a recovery.

I am using a hotplug sata disk. rsync copies a 2Gb linux in about a minute.
Usb3 to a flash drive should be about the same time.
You must have heaps in Downloads

Keep at it… There is lots to learn, and even more mistakes are waiting.

What I learnt… when doing a recovery, mount the backup read only … you dont want a mistake to clobber the backup.

Update:

Yes, the trailing slash rule for pathnames

does apply to pathnames within rsync filter rules, including the filter='P ...' (protect) option. The meaning is consistent with the general rsync filter rules:

"* A pattern that ends with a / only matches a directory, not a file. This is useful for protecting a directory and all its contents.

A pattern without a trailing / can match either a file or a directory with that name. "

Update 2:
This is the best doc on exclude rules and filter rules

ihasama · 18 January 2026 11:11

Thanks Neville! I’ll check the linked filter rules. I can confirm that the rsync did copy my system files to the USB. It’s 3rd gen USB and took more than 8 hours. I need to clean my laptop before running the sync again. And also need to pay attention to exclude some of the folders the right way

nevj · 18 January 2026 11:35

Something is wrong. How many Gb is your Gentoo?
I can do 2Gb in 1 minute to my sata disk rated at 6Gb per sec … I think usb3 is rated about the same.
Maybe there is ram buffering? Do you have plenty of ram?

That is the big issue . The documentaion is hard to follow and there are few examples.

Sorry if I gave the impression that rsync for backup is all solved… it is not…there are too many different cases for anyone to be able to write down one simple command or script that would work for everyone.

ihasama · 18 January 2026 11:55

sudo du -hs /
du: cannot access ‘/proc/20089/task/20089/fd/4’: No such file or directory
du: cannot access ‘/proc/20089/task/20089/fdinfo/4’: No such file or directory
du: cannot access ‘/proc/20089/fd/3’: No such file or directory
du: cannot access ‘/proc/20089/fdinfo/3’: No such file or directory
du: cannot access ‘/run/user/1000/doc’: Permission denied
du: cannot access ‘/run/user/1000/gvfs’: Permission denied
74G /

root is 74G
I found one place where I can free space, the /var/tmp/portage is 21G. These files are some leftovers which I can delete. I have only 8GB RAM.

This is a difficult issue and I really appreciate how you two handled this! I really learned a lot (as many of us here have). I think I’ll continue backing up my data and system separately. Using rsync for my home folder is fine.

EDIT: after removing the /var/tmp/portage my system is now 53G, so freed 21G of temp files is great! I wouldn’t have noticed these files if the backup wouldn’t take so long.

nevj · 18 January 2026 12:04

At 2Gb per minute, it should finish in half an hour.

I looked up usb3.0 … it is 5Gb per second… similar to my 6Gbps for sata. That is bits per second… divide by 8 for bytes. … still way faster than I am getting (2GB per min). … Line speed is not the problem.

There is something wrong … is it maybe following links to data outside of Gentoo?

You can mount the backup and look at its filesystem … does it contain more than 74Gb? Are there extra folders?

ihasama · 18 January 2026 14:45

Interesting… sudo du -hs /mnt/gentoo (the USB stick) gives 81G. But 5G difference don’t take 8 hours.. Maybe my USB stick is just fake and it’s not that fast?

I have removed the /var/tmp/portage from my system. Should I try to rsync the USB stick with remove?

Talking about mistakes I once rsynced my system which had a 8Gb Swap file

EDIT: Here’s the root and backup, looks the same.

┌─[pete@gentoo]─[~]
└──╼ ls -a /
.         backup              boot      dots  gentoo  lib64       mnt   root  sys   usr
..        backup19102025.zip  deja-dup  efi   home    lost+found  opt   run   temp  var
.xinitrc  bin                 dev       etc   lib     media       proc  sbin  tmp
┌─[pete@gentoo]─[~]
└──╼ ls -a /mnt/gentoo/
.         backup              boot      dots  gentoo  lib64       mnt   root  sys   usr
..        backup19102025.zip  deja-dup  efi   home    lost+found  opt   run   temp  var
.xinitrc  bin                 dev       etc   lib     media       proc  sbin  tmp

abu · 18 January 2026 14:46

Usually I run rsync with the option -n first, for verifying what will be included.

easyt50 · 18 January 2026 15:22

My God, that’s huge. I have a partition size for root of 35 GB with 22 GB reported as free for my Mint OS.

Rosika · 18 January 2026 15:47

Hi @nevj and all,

sorry, this may be a bit off-topic, because my question aims at backing up not the root partition but some content of either the home or any other data partition.

I was wondering about the parameters of rsync to use in this case.

Would this still be considered to be the preferred method:

rsync -avxHAXS  <source directory> <destination directory>

I was wondering about the -x parameter.

-x, --one-file-system
This tells rsync to avoid crossing a filesystem boundary when recursing.

I´m not sure what that exactly means:
Filesystem boundary is not the same as crossing partitions, or am I getting it all wrong?

A practical example of my query would be saving the hidden .thunderbird folder (containing all e-mails and other stuff), which is located on my 3rd data partition.

Until now I´ve done it this way:

rsync -a --info=progress2 /media/rosika/f14a27c2-0b49-4607-94ea-2e56bbf76fe1/thunderbird_neu/.thunderbird /media/rosika/verbatim2/für_thunderbird/

Sorry again for asking this.

Many greetings from Rosika

ihasama · 18 January 2026 16:02

Not heard that before But yes, you’re right! I learned that on Gentoo the package manager leaves all unfinished builds to a directory and since it’s an old laptop there was appr 20gigs of .tar files. One thing with Gentoo is that you need to make cleaning and I hadn’t checked if there’s something else to clean than just use a program called eclean. My laptop would need a proper cleaning, for an example there’s Sway, Hyprland and Cinnamon and I only use Sway. Then there’s some virtual machine things I could uninstall and I’ve also learned some Python with it so there’s environment for coding also.

nevj · 18 January 2026 21:36

I assume you used a usb3 flash drive?

Yeah , no extra folders and 81G versus 74G is probably just filesystem specs varying on the flash drive

I am wondering about your hardware. … if that laptop is old it may have a slow data bus, or not much memory for buffering. ?
You did not use compression… that would slow it.
I will try an rsync to flash drive on my 2 machines… just to get some idea of timing with a flash drive.

nevj · 18 January 2026 21:48

Hi Rosika

Yes, but for data some of those parameters (eg S) would be unlikely to be needed.

With dot files like your Thunderbird example, be careful how you specify the <source>

No. Filesystem boundry would be the same as crossing partitions. … unless you use something like LVM where partitions mean nothing.

I dont think I intended the topic to apply only to system files… no need to apologise.

Regards
Neville

nevj · 18 January 2026 21:52

There are backup files in there.
@ihasama should probably have excluded those… they may be very large… rsync goes best copying lots of small files.

You may have pointed out the solution. Lets see what @ihasama says

nevj · 18 January 2026 21:54

Yes I have been using --dry-run. I am not very practised at interpreting the output.

nevj · 19 January 2026 10:41

I took a brand new 32Gb usb3.0 flash drive
put it in a usb3 port on my small Dell desktop ( 8Gb ram, i5 processor)
and did the following

Use Gparted. Delete the fat filessytem on the usb drive, make a GPT partiton table, and 2 partitons
esp … 512Mb
ex4 … rest of drive
I took my Downloads directory in Debian which is about 10 Gb

du -s ~/Downloads
10782708	/home/nevj/Downloads

I rsynced it to the usb flash drive

rsync -avxHAXS /home/nevj/Downloads/ /media/nevj/4f5865c2-116e-457c-8999-74fa8710050b


sent 11,044,118,199 bytes  received 308 bytes  17,544,270.86 bytes/sec
total size is 11,041,421,233  speedup is 1.00

No need for excludes . It took about 11 minutes… so about 1Gb per minute. … about half the speed I got in my large machine rsyncing onto a sata disk.
At that speed your 74Gb should have taken 74 minutes.
There is still something wrong… 8hours is too long.

I checked it all got there

# du -s /media/nevj/4f5865c2-116e-457c-8999-74fa8710050b
10745728	/media/nevj/4f5865c2-116e-457c-8999-74fa8710050b

Yes , all there . It is 20 bytes larger? Probably some filesystem difference between the media.

Incidentally , My Gentoo in this machine, is 39G, and my Debian is 34G. … they do get large if you install a lot of software.

oot@mary:/home/nevj/Downloads# du -s /mnt/gentoo/*
9048	/mnt/gentoo/bin
103152	/mnt/gentoo/boot
4	/mnt/gentoo/common
8	/mnt/gentoo/dev
25560	/mnt/gentoo/etc
11686596	/mnt/gentoo/home
3747812	/mnt/gentoo/lib
8008	/mnt/gentoo/lib64
16	/mnt/gentoo/lost+found
4	/mnt/gentoo/media
8	/mnt/gentoo/mnt
1149940	/mnt/gentoo/opt
4	/mnt/gentoo/proc
15056	/mnt/gentoo/root
4	/mnt/gentoo/run
9744	/mnt/gentoo/sbin
544432	/mnt/gentoo/stage3-amd64-desktop-openrc-20230122T154655Z.tar.xz
4	/mnt/gentoo/sys
24	/mnt/gentoo/tmp
21617028	/mnt/gentoo/usr
1698932	/mnt/gentoo/var

So 11G is in /home, 20G of software.

So my smaller machine is definitely slower than my large desktop. Not surprising , it has less ram for buffering, a slower cpu, and probably not as good a motherboard.
So hardware may be an issue with your laptop.

Just checking, did you reformat your usb drive to ext4?
was it a 3.0 drive?
was the port a 3.0 port?

Rosika · 19 January 2026 14:08

Hi Neville,

thank you, Neville, for helping me out with my query.

I see.
The -S parameter does the following:

Try to handle sparse files efficiently so they take up less space on the destination.
Conflicts with --inplace because it’s not possible to overwrite data in a sparse fashion.

O.K., I have to admit I had to look up the definition of “sparse file” in the first place :

A sparse file in Linux is a type of file that efficiently uses disk space by only storing non-empty data and representing empty blocks with metadata, rather than actual zero bytes.
This allows for significant storage savings, especially for files that contain large amounts of empty data, such as virtual machine images and database files

Thanks for your recommendation.

Ah, O.K., I get it.

Once again I had to look it up:

A filesystem boundary in Linux refers to the point where one filesystem ends and another begins, typically marked by mount points. When archiving files, tools like tar can be configured to avoid crossing these boundaries to ensure only files from a specific filesystem are included.

… which effectively is the same as the thing you just pointed out.

In the case of rsync :

-x, --one-file-system
       This  tells rsync to avoid crossing a filesystem boundary when recursing.

This means I would have to avoid the parameter -x as well, I guess.

My .thunderbird folder resides on the 3rd data partition of my (external) HDD and the backup would be placed on another external HDD.
So there´s definitively crossing of partitions involved here.

Thanks for your help, Neville.

Many greetings from Rosika

ihasama · 19 January 2026 14:34

I agree. I’ll try my old SSD (with the same USB3 port) next. I’ll check a proper sized folder to sync and then we see if it’s mobo/laptop issue or USB card issue.

My system recognizes the USB card:

[   24.015915] usb 1-2: new high-speed USB device number 4 using xhci_hcd
[   24.151546] usb 1-2: New USB device found, idVendor=0951, idProduct=1666, bcdDevice= 2.00
[   24.151568] usb 1-2: New USB device strings: Mfr=2, Product=3, SerialNumber=4
[   24.151577] usb 1-2: Product: DataTraveler 3.0
[   24.151584] usb 1-2: Manufacturer: Kingston
[   24.151590] usb 1-2: SerialNumber: E0D55E6C382B1790F9431010
[   24.608823] usb-storage 1-2:1.0: USB Mass Storage device detected
[   24.609012] scsi host2: usb-storage 1-2:1.0
[   24.609119] usbcore: registered new interface driver usb-storage
[   24.611326] usbcore: registered new interface driver uas
[   25.613758] scsi 2:0:0:0: Direct-Access     Kingston DataTraveler 3.0 0000 PQ: 0 ANSI: 4
[   25.614700] sd 2:0:0:0: Attached scsi generic sg0 type 0
[   25.615494] sd 2:0:0:0: [sda] 242155521 512-byte logical blocks: (124 GB/115 GiB)
[   25.615909] sd 2:0:0:0: [sda] Write Protect is off
[   25.615924] sd 2:0:0:0: [sda] Mode Sense: 23 00 00 00
[   25.616124] sd 2:0:0:0: [sda] Write cache: disabled, read cache: enabled, doesn't support DPO or FUA
[   25.642198]  sda: sda1
[   25.642632] sd 2:0:0:0: [sda] Attached SCSI removable disk

It is EXT4 and YES, USB3 drive+port:

ihasama · 19 January 2026 15:00

Now I’m using my laptop’s original SSD with USB3 cable from the same USB3 port of my laptop. I had one partition (EXT4) empty so I use that partition. I choose to rsync my Downloads folder which is 9.6G:


du -sh /home/pete/Downloads/
9.6G	/home/pete/Downloads/

I added --progress and --stats to my command:

gentoo ~ # rsync --progress --stats -avxHAXS /home/pete/Downloads/ /mnt/

And here’s the stats:

       4,796 100%    4.82kB/s    0:00:00 (xfr#2415, to-chk=0/2518)

Number of files: 2,518 (reg: 2,415, dir: 103)
Number of created files: 2,517 (reg: 2,415, dir: 102)
Number of deleted files: 0
Number of regular files transferred: 2,415
Total file size: 10,238,969,764 bytes
Total transferred file size: 10,238,969,764 bytes
Literal data: 10,238,969,764 bytes
Matched data: 0 bytes
File list size: 0
File list generation time: 0.001 seconds
File list transfer time: 0.000 seconds
Total bytes sent: 10,241,635,295
Total bytes received: 46,484

sent 10,241,635,295 bytes  received 46,484 bytes  49,596,521.93 bytes/sec
total size is 10,238,969,764  speedup is 1.00
gentoo ~ #

It took only few minutes to rsync 10 Gb. However, when I check dmesg I see a lot of warnings:

[  957.806085] usb 1-1: new high-speed USB device number 7 using xhci_hcd
[  957.936878] usb 1-1: New USB device found, idVendor=152d, idProduct=a583, bcdDevice= 2.14
[  957.936897] usb 1-1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[  957.936905] usb 1-1: Product: External
[  957.936911] usb 1-1: Manufacturer: JMicron
[  957.936916] usb 1-1: SerialNumber: DD56419883914
[  957.960947] scsi host2: uas
[  957.972206] scsi 2:0:0:0: Direct-Access     JMicron  Tech             0214 PQ: 0 ANSI: 6
[  957.975971] sd 2:0:0:0: Attached scsi generic sg0 type 0
[  960.132218] sd 2:0:0:0: [sda] 500118192 512-byte logical blocks: (256 GB/238 GiB)
[  960.132233] sd 2:0:0:0: [sda] 4096-byte physical blocks
[  960.132477] sd 2:0:0:0: [sda] Write Protect is off
[  960.132488] sd 2:0:0:0: [sda] Mode Sense: 6b 00 00 08
[  960.133059] sd 2:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[  960.133302] sd 2:0:0:0: [sda] Preferred minimum I/O size 4096 bytes
[  960.133316] sd 2:0:0:0: [sda] Optimal transfer size 33553920 bytes not a multiple of preferred minimum block size (4096 bytes)
[  960.199805]  sda: sda1 sda2 sda4 sda5
[  960.200890] sd 2:0:0:0: [sda] Attached SCSI disk
[  961.259434] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[  961.259470] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[  961.259478] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000081/00006000
[  961.259488] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[  961.259495] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[  968.683832] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[  968.683860] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[  968.683869] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000081/00006000
[  968.683879] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[  968.683886] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[  970.629726] pcieport 0000:00:1d.0: AER: Correctable error message received from 0000:01:00.0
[  970.629756] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[  970.629766] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000001/00006000
[  970.629778] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[  971.040859] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[  971.040893] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[  971.040903] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000081/00006000
[  971.040915] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[  971.040923] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[  971.346519] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[  971.346550] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)

---- 
 
[ 1312.841748] NMI watchdog: Enabled. Permanently consumes one hw-PMU counter.
[ 1313.132152] ata1: SATA link down (SStatus 4 SControl 300)
[ 1313.225512] r8169 0000:02:00.0 enp2s0: Link is Down
[ 1313.455660] ata2: SATA link down (SStatus 4 SControl 300)
[ 1313.682164] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1313.682173] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1313.905280] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1313.975301] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1313.975316] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1339.340599] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1339.340611] pcieport 0000:00:1d.0: PCIe Bus Error: severity=Correctable, type=Data Link Layer, (Transmitter ID)
[ 1339.340614] pcieport 0000:00:1d.0:   device [8086:9db0] error status/mask=00001000/00002000
[ 1339.340617] pcieport 0000:00:1d.0:    [12] Timeout
[ 1339.340621] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Transmitter ID)
[ 1339.340623] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=000010c1/00006000
[ 1339.340625] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[ 1339.340627] ath10k_pci 0000:01:00.0:    [ 6] BadTLP
[ 1339.340628] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1339.340630] ath10k_pci 0000:01:00.0:    [12] Timeout
[ 1339.340631] ath10k_pci 0000:01:00.0: AER:   Error of this Agent is reported first
[ 1341.688629] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1341.688665] pcieport 0000:00:1d.0: PCIe Bus Error: severity=Correctable, type=Data Link Layer, (Transmitter ID)
[ 1341.688676] pcieport 0000:00:1d.0:   device [8086:9db0] error status/mask=00001000/00002000
[ 1341.688689] pcieport 0000:00:1d.0:    [12] Timeout
[ 1341.688709] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Data Link Layer, (Receiver ID)
[ 1341.688719] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=000000c0/00006000
[ 1341.688731] ath10k_pci 0000:01:00.0:    [ 6] BadTLP
[ 1341.688740] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1341.688748] ath10k_pci 0000:01:00.0: AER:   Error of this Agent is reported first
[ 1342.945633] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1342.945675] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[ 1342.945689] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000081/00006000
[ 1342.945705] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[ 1342.945718] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1347.408039] NMI watchdog: Enabled. Permanently consumes one hw-PMU counter.
[ 1347.451859] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1347.698493] ata1: SATA link down (SStatus 4 SControl 300)
[ 1347.791924] r8169 0000:02:00.0 enp2s0: Link is Down
[ 1348.021153] ata2: SATA link down (SStatus 4 SControl 300)
[ 1348.241968] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1348.241977] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1350.474993] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1351.282124] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1351.282163] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1369.579216] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1369.579250] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Physical Layer, (Receiver ID)
[ 1369.579260] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000081/00006000
[ 1369.579271] ath10k_pci 0000:01:00.0:    [ 0] RxErr                  (First)
[ 1369.579280] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1402.347057] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1402.347091] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Data Link Layer, (Receiver ID)
[ 1402.347102] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000080/00006000
[ 1402.347113] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1411.767980] pcieport 0000:00:1d.0: AER: Multiple Correctable error message received from 0000:01:00.0
[ 1411.768013] ath10k_pci 0000:01:00.0: PCIe Bus Error: severity=Correctable, type=Data Link Layer, (Receiver ID)
[ 1411.768023] ath10k_pci 0000:01:00.0:   device [168c:0042] error status/mask=00000080/00006000
[ 1411.768034] ath10k_pci 0000:01:00.0:    [ 7] BadDLLP
[ 1413.858556] NMI watchdog: Enabled. Permanently consumes one hw-PMU counter.
[ 1413.907830] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1414.147871] ata1: SATA link down (SStatus 4 SControl 300)
[ 1414.241237] r8169 0000:02:00.0 enp2s0: Link is Down
[ 1414.467852] ata2: SATA link down (SStatus 4 SControl 300)
[ 1414.667900] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1414.667909] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1414.917711] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1414.987739] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1414.987750] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)
[ 1417.348892] NMI watchdog: Enabled. Permanently consumes one hw-PMU counter.
[ 1417.404396] EXT4-fs (sda5): re-mounted 6926e412-9714-4963-94b9-1dd367b830b5.
[ 1417.637828] ata1: SATA link down (SStatus 4 SControl 300)
[ 1417.961160] ata2: SATA link down (SStatus 4 SControl 300)
[ 1418.187846] ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.LPCB.EC0._Q37.POWS], AE_NOT_FOUND (20240827/psargs-332)
[ 1418.187856] ACPI Error: Aborting method \_SB.PCI0.LPCB.EC0._Q37 due to previous error (AE_NOT_FOUND) (20240827/psparse-529)

EDIT: Asked duck.ai about these dmesg errors:
The logs you’ve shared indicate several issues with your system, primarily related to connectivity and hardware errors. Here’s a breakdown of the key messages:

Key Issues Identified

Log Entry	Description
NMI watchdog: Enabled. Permanently consumes one hw-PMU counter.	This indicates a watchdog function is active, monitoring system performance. It may not necessarily indicate a problem but may interfere with system performance tracking.
SATA link down (SStatus 4 SControl 300)	The system is unable to establish a connection with the specified SATA device, suggesting potential issues with the drive or its cable.
Link is Down	Network interface (enp2s0) is unable to establish a connection, which might be due to hardware issues or configuration problems.
ACPI BIOS Error (bug): Could not resolve symbol	ACPI errors indicate issues with the Advanced Configuration and Power Interface, typically related to BIOS. It may require a BIOS update or further investigation on the BIOS settings.
PCIe Bus Error: severity=Correctable	This indicates that the PCI Express bus has encountered a correctable error. It is important to monitor these, as they can lead to hardware malfunctions if persistent.

Suggested Steps to Address Issues

1. Check SATA Connections

Ensure that the SATA cables are properly connected to both the drives and the motherboard.
Test the drives in a different system if possible to rule out hardware failure.

2. Investigate Network Interface

Verify the physical connections for your network hardware.
Try resetting the network interface or updating its drivers.

3. ACPI BIOS Errors

Consider updating your BIOS to the latest version provided by your motherboard manufacturer. This could resolve compatibility and configuration issues.
Check BIOS settings related to power management and ACPI support.

4. Handling PCIe Bus Errors

Monitor for repeat occurrences of the PCIe bus errors. If it continues, check for driver updates for affected devices, particularly the ath10k_pci network card.
If errors persist, consider reseating the PCIe cards or testing with alternate hardware.

5. System Log Review

Continue to monitor system logs for any new errors or patterns. This can provide insight into whether these issues are transient or indicative of larger problems.

It’s essential to address these issues, especially regarding SATA and PCIe connectivity, as they may affect system stability and performance. If you have further questions or need more specific guidance on any of these steps, feel free to ask!