Questions[disk-management](ubuntu)

back story.. i took my 2 seagate 32000641AS drives out of an old dns-323 disk array.. i put them in my dell Precision T5600 since the dns-323 was old and becoming a pain to manage. i then created two separate XFS fs on them and mounted them. The disks i replaced these with were smaller 500G drives.. i copied the data from them onto a 300G usb encrypted thumbdrive. after i put in the seagates i copied the data back.. i use one for local backup and the other to run a virtualbox VM but both drives had the same data from the usb.

i noticed this today in the syslog for both drives.

smartd[809]: Device: /dev/sda [SAT], 19 Currently unreadable (pending) sectors
smartd[809]: Device: /dev/sda [SAT], 19 Offline uncorrectable sectors
smartd[809]: Device: /dev/sda [SAT], 19 Currently unreadable (pending) sectors
smartd[809]: Device: /dev/sda [SAT], 19 Offline uncorrectable sectors

however, no performance issues. also, when i was copying the data back from the usb drive, 1 DIR would not copy back over.. it kept giving me an I/O error.. i didnt need it so i just didnt copy it back.

is this the reason im getting the same exact errors on both drives? or is it coincidence?

so I did mkfs.ext4 on /dev/sdb1

and im now running badblocks -s -v -n -f /dev/sda

Checking for bad blocks in non-destructive read-write mode
From block 0 to 1953514583
Checking for bad blocks (non-destructive read-write test)
Testing with random pattern:   1.43% done, 36:36 elapsed. (0/0/0 errors)

and so far no errors with badblocks, but then i got this in syslog

smartd[809]: Device: /dev/sda [SAT], 19 Currently unreadable (pending) sectors
smartd[809]: Device: /dev/sda [SAT], 19 Offline uncorrectable sectors
smartd[809]: Device: /dev/sda [SAT], SMART Prefailure Attribute: 1 Raw_Read_Error_Rate changed from 116 to 117
smartd[809]: Device: /dev/sda [SAT], SMART Usage Attribute: 190 Airflow_Temperature_Cel changed from 68 to 67
smartd[809]: Device: /dev/sda [SAT], SMART Usage Attribute: 194 Temperature_Celsius changed from 32 to 33
smartd[809]: Device: /dev/sdb [SAT], 35 Currently unreadable (pending) sectors
smartd[809]: Device: /dev/sdb [SAT], 35 Offline uncorrectable sectors
smartd[809]: Device: /dev/sdb [SAT], SMART Prefailure Attribute: 1 Raw_Read_Error_Rate changed from 116 to 113
smartd[809]: Device: /dev/sdb [SAT], SMART Usage Attribute: 195 Hardware_ECC_Recovered changed from 35 to 49

On my Ubuntu desktop, the command fdisk -l shows /dev/loopX up to /dev/loop23. I'm using gnome-fallback on Ubuntu 18.04 LTS.

I'm wondering what possible effects these could have on performance and stabilty of the OS, and if they are just superfluous, how can I remove them?

root@pc5:~# fdisk -l
...
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop15: 3.7 MiB, 3821568 bytes, 7464 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop16: 54.6 MiB, 57274368 bytes, 111864 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop17: 140.7 MiB, 147501056 bytes, 288088 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop18: 14.8 MiB, 15462400 bytes, 30200 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop19: 42.8 MiB, 44879872 bytes, 87656 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop20: 54.5 MiB, 57151488 bytes, 111624 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop21: 4.2 MiB, 4403200 bytes, 8600 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop22: 153.5 MiB, 160935936 bytes, 314328 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes


Disk /dev/loop23: 140.7 MiB, 147501056 bytes, 288088 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

output of df:

Filesystem      1K-blocks       Used  Available Use% Mounted on
udev              8128184          0    8128184   0% /dev
tmpfs             1630464       3716    1626748   1% /run
/dev/sda2       229184876   63255488  154217748  30% /
tmpfs             8152300     142672    8009628   2% /dev/shm
tmpfs                5120          4       5116   1% /run/lock
tmpfs             8152300          0    8152300   0% /sys/fs/cgroup
/dev/loop2         160512     160512          0 100% /snap/gnome-3-28-1804/110
/dev/loop3           4352       4352          0 100% /snap/gnome-calculator/544
/dev/loop0           3840       3840          0 100% /snap/gnome-system-monitor/111
/dev/loop4          91264      91264          0 100% /snap/core/8039
/dev/loop1           1024       1024          0 100% /snap/gnome-logs/81
/dev/loop6          87936      87936          0 100% /snap/shotcut/55
/dev/loop5         406528     406528          0 100% /snap/redis-desktop-manager/332
/dev/loop8          91264      91264          0 100% /snap/core/8213
/dev/loop7         406656     406656          0 100% /snap/redis-desktop-manager/335
/dev/loop9          15104      15104          0 100% /snap/gnome-characters/367
/dev/loop11        157184     157184          0 100% /snap/chromium/949
/dev/loop12         87808      87808          0 100% /snap/shotcut/53
/dev/loop13          1024       1024          0 100% /snap/gnome-logs/73
/dev/loop14         45312      45312          0 100% /snap/gtk-common-themes/1353
/dev/loop16         55936      55936          0 100% /snap/core18/1279
/dev/loop15          3840       3840          0 100% /snap/gnome-system-monitor/107
/dev/loop10        159872     159872          0 100% /snap/gnome-3-28-1804/91
/dev/loop17        144128     144128          0 100% /snap/gnome-3-26-1604/97
/dev/sda1          523248       6232     517016   2% /boot/efi
/dev/loop18         15104      15104          0 100% /snap/gnome-characters/359
/dev/loop19         43904      43904          0 100% /snap/gtk-common-themes/1313
/dev/loop20         55936      55936          0 100% /snap/core18/1265
/dev/loop21          4352       4352          0 100% /snap/gnome-calculator/536
/dev/loop22        157184     157184          0 100% /snap/chromium/958
/dev/loop23        144128     144128          0 100% /snap/gnome-3-26-1604/98
/dev/sdb1       492127240  409174612   57930932  88% /home
tmpfs             1630460         16    1630444   1% /run/user/121
tmpfs             1630460        140    1630320   1% /run/user/1001
tmpfs             1630460          0    1630460   0% /run/user/0

I have an Ubuntu 16.04 virtual machine (local, no cloud) which was created as a clone of another computer. Each time GRUB packages are upgraded using apt upgrade, I get the following message:¹

The GRUB boot loader was previously installed to a disk that is no longer present, or whose unique identifier has changed for some reason. It is important to make sure that the installed GRUB core image stays in sync with GRUB modules and grub.cfg. Please check again to make sure that GRUB is written to the appropriate boot devices.

and then it asks to select an install device.

I am able to finish the GRUB upgrade successfully but the message appears again during the next GRUB upgrade, although the disk is not altered between the upgrades.

How can I “reset” the GRUB configuration to the current one, so it does not ask again?

Examined similar questions

I am not trying to silence upgrade messages as similar questions (https://serverfault.com/questions/662624/how-to-avoid-grub-errors-after-runing-apt-get-upgrade-ubunut, How do I apt-get -y dist-upgrade without a grub config prompt?) suggest. I want to overcome this particular question regarding GRUB upgrade.

The commands from the most upvoted answer to a similar question on ServerFault cannot be applied in my case, I don’t have the mentioned files /boot/grub/menu.lst and update-grub-legacy-ec2 on my machine.

My configuration

I tried to run the commands suggested by oldfred:

$ sudo debconf-show grub-pc
  grub-pc/install_devices_failed_upgrade: true
  grub-pc/mixed_legacy_and_grub2: true
  grub-pc/install_devices_failed: false
  grub-pc/hidden_timeout: false
  grub2/update_nvram: true
  grub-pc/timeout: 5
  grub-pc/install_devices_empty: false
* grub-pc/install_devices_disks_changed: /dev/disk/by-id/ata-VBOX_HARDDISK_VBd7a628c1-923a4727
  grub2/kfreebsd_cmdline:
* grub2/linux_cmdline: consoleblank=0
  grub2/kfreebsd_cmdline_default: quiet splash
  grub-pc/disk_description:
  grub-pc/postrm_purge_boot_grub: false
  grub-pc/partition_description:
* grub-pc/install_devices: /dev/disk/by-id/ata-VBOX_HARDDISK_VBd7a628c1-923a4727
  grub-pc/chainload_from_menu.lst: true
  grub2/force_efi_extra_removable: false
  grub-pc/kopt_extracted: false
* grub2/linux_cmdline_default:
  grub2/device_map_regenerated:

seems to match

$ sudo lshw -C Disk | grep serial
       serial: VBd7a628c1-923a4727

but grub-probe -t device /boot/grub returns the name of the root device of the clone’s master. I tried the suggested command sudo dpkg-reconfigure grub-pc but it did not update the output of sudo grub-probe -t device /boot/grub. How to fix this?

¹ I get the message in a localized version, the pasted English version is copied from https://samrueby.com/2014/09/02/updating-grub-in-ubuntu-amazon-ec2-instance/.

I'm having trouble at the moment because my /home partition appears to be full and its usable space seems to be much smaller than the actual disk, which is the confusing part.

this is the line in fstab where my home partition gets mounted:

#home
UUID=6e6a584b-fa83-439b-bca2-1772b65a3cf2  /home          ext4    defaults      0       0

In gnome disks, this is shown as a 256gb partition covering the entire disk (and that's apparently 99% full, which shouldn't be true): link

The confusing part is the following output of df -Th | sort, where /home is shown as only 28gb in size:

df -Th | sort
/dev/loop10    squashfs   88M   88M     0 100% /snap/core/5328
/dev/loop16    squashfs  5,0M  5,0M     0 100% /snap/canonical-livepatch/42
/dev/sda1      ext4       28G   25G  1,1G  97% /home
/dev/sdb2      ext4      117G   28G   83G  26% /
Filesystem     Type      Size  Used Avail Use% Mounted on
tmpfs          tmpfs     3,9G     0  3,9G   0% /sys/fs/cgroup
tmpfs          tmpfs     3,9G   41M  3,9G   2% /dev/shm
tmpfs          tmpfs     5,0M  4,0K  5,0M   1% /run/lock
tmpfs          tmpfs     789M   16K  789M   1% /run/user/120
tmpfs          tmpfs     789M  1,9M  787M   1% /run
tmpfs          tmpfs     789M   36K  789M   1% /run/user/1000
udev           devtmpfs  3,9G     0  3,9G   0% /dev

I just don't get what's going on here... Can someone help me out? My machine is also slowing down significantly in certain situations now where it hasn't before, which I hope to fix after I understand where all the disk space went.

here's another image of the gnome disk usage analyzer, where home is also 28GB: link edit: BTW, .cache/dconf is less than a kb in size

output of lsblk:

NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda      8:0    0 238,5G  0 disk 
└─sda1   8:1    0 238,5G  0 part /home
sdb      8:16   0 119,2G  0 disk 
├─sdb1   8:17   0   512M  0 part /boot/efi
└─sdb2   8:18   0 118,8G  0 part /
sr0     11:0    1  1024M  0 rom 

What is the Gnome version of KDirStat? I read some 2006 post about program named Baobab , but it looks like it's not included in 10.04 any more, and the home page is not available any more.