HankB's questions

Following upgrade from 18.10 to 19.04 I find the desktop is unusable. Following login I note the following:

• No items show up in the Dash-to-Dock dock on the left side except for the square with nine dots (task drawer?) Clicking on it does nothing.
• Moving the mouse cursor to the upper left corner does not bring up the overview.
• Clicking on the upper left corner takes me back to the login screen.

This works for all logins I have tried:

• Gnome
• Gnome on Xorg
• Ubuntu on Xorg

I suppose some configuration item or shell extension is causing this. Before the upgrade I fully updated 18.10 but I have shell extensions installed through extensions.gnome.org and did not think to check them for updates. (The software manager did pop up a message about not being able to contact the gnome shell extensions site.)

Is there any benefit to reporting this as a bug before I move on to resolve it?

Eventually I'll try disabling shell extensions and next configuration files. At worst I'll have a go with XFCE and at worst, nuke and repave.

If I should file a bug, what's the best way (considering I cannot run any GUI programs.)

If it helps, I've captured a bit of /var/log/syslog that may reflect the issue and put at https://pastebin.com/UwdegT7Q. The salient line might be:

Jun  4 08:47:34 karakum gnome-shell[6106]: Connection to xwayland lost

Thanks!

Edit: Extensions I had installed were

hbarta@karakum:~/Downloads$ ls -l extensions
total 36
drwxrwxr-x 3 hbarta hbarta 4096 Apr 13 10:28 [email protected]
drwxrwxr-x 2 hbarta hbarta 4096 Jan 31 21:08 [email protected]
drwxrwxr-x 4 hbarta hbarta 4096 Apr 13 10:34 [email protected]
drwxrwxr-x 5 hbarta hbarta 4096 Mar 27 07:45 [email protected]
drwxrwxr-x 5 hbarta hbarta 4096 Feb  4 15:20 multi-monitors-add-on@spin83
drwxrwxr-x 4 hbarta hbarta 4096 Feb  4 15:21 [email protected]
drwxrwxr-x 3 hbarta hbarta 4096 Apr 13 10:29 [email protected]
drwxrwxr-x 3 hbarta hbarta 4096 Jan 30 19:23 [email protected]
drwxrwxr-x 2 hbarta hbarta 4096 Jan 30 19:20 [email protected]
hbarta@karakum:~/Downloads$ 

Moving all of them to a different location has resolved the issue.

I ran sudo dmesg --follow shortly after rebooting and found these messages at the end of the output. It seems to come out several times. A few lines around that are

[  139.356270] ------------[ cut here ]------------
[  139.356272] Unknown pixelformat 0x00000000
[  139.356309] WARNING: CPU: 1 PID: 3056 at /build/linux-7kdHqT/linux-4.15.0/drivers/media/v4l2-core/v4l2-ioctl.c:1291 v4l_fill_fmtdesc+0xf41/0x1250 [videodev]

More dmesg output can be seen at https://pastebin.com/4YxinP3Z

System is a Dell XPS-13 9370 with Intel video adapter.

hbarta@karakum:~$ cat /etc/issue
Ubuntu 18.04.2 LTS \n \l

hbarta@karakum:~$ uname -a
Linux karakum 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
hbarta@karakum:~$ lspci|grep VGA
00:02.0 VGA compatible controller: Intel Corporation UHD Graphics 620 (rev 07)
hbarta@karakum:~$ 

What problem is being reported? Should I be concerned? How can I fix and should I file a bug report?

I was not looking for an issue when I say this so on the surface, it seems innocuous.

Thanks!

I'm trying to install ZFS on a 17.10 install on my Lenovo laptop and the zfs module is not loading. I suspect this may be because I'm using a different kernel to resolve the corrupted BIOS issue I encountered earlier. Here is a scrape of the relevant commands:

root@kigelia:~# apt install zfsutils-linux
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.13.0-32 linux-headers-4.13.0-32-generic linux-image-4.13.0-32-generic linux-image-extra-4.13.0-32-generic
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  libnvpair1linux libuutil1linux libzfs2linux libzpool2linux zfs-zed
Suggested packages:
  nfs-kernel-server samba-common-bin zfs-initramfs | zfs-dracut
The following NEW packages will be installed:
  libnvpair1linux libuutil1linux libzfs2linux libzpool2linux zfs-zed zfsutils-linux
0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 957 kB of archives.
After this operation, 3,286 kB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 libuutil1linux amd64 0.6.5.11-1ubuntu3.1 [46.3 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 libnvpair1linux amd64 0.6.5.11-1ubuntu3.1 [35.2 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 libzpool2linux amd64 0.6.5.11-1ubuntu3.1 [387 kB]
Get:4 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 libzfs2linux amd64 0.6.5.11-1ubuntu3.1 [119 kB]
Get:5 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 zfsutils-linux amd64 0.6.5.11-1ubuntu3.1 [329 kB]
Get:6 http://us.archive.ubuntu.com/ubuntu artful-updates/main amd64 zfs-zed amd64 0.6.5.11-1ubuntu3.1 [41.2 kB]
Fetched 957 kB in 0s (2,026 kB/s)  
Selecting previously unselected package libuutil1linux.
(Reading database ... 332030 files and directories currently installed.)
Preparing to unpack .../0-libuutil1linux_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking libuutil1linux (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package libnvpair1linux.
Preparing to unpack .../1-libnvpair1linux_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking libnvpair1linux (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package libzpool2linux.
Preparing to unpack .../2-libzpool2linux_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking libzpool2linux (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package libzfs2linux.
Preparing to unpack .../3-libzfs2linux_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking libzfs2linux (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package zfsutils-linux.
Preparing to unpack .../4-zfsutils-linux_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking zfsutils-linux (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package zfs-zed.
Preparing to unpack .../5-zfs-zed_0.6.5.11-1ubuntu3.1_amd64.deb ...
Unpacking zfs-zed (0.6.5.11-1ubuntu3.1) ...
Setting up libuutil1linux (0.6.5.11-1ubuntu3.1) ...
Setting up libnvpair1linux (0.6.5.11-1ubuntu3.1) ...
Processing triggers for libc-bin (2.26-0ubuntu2.1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Setting up libzpool2linux (0.6.5.11-1ubuntu3.1) ...
Setting up libzfs2linux (0.6.5.11-1ubuntu3.1) ...
Setting up zfsutils-linux (0.6.5.11-1ubuntu3.1) ...
Created symlink /etc/systemd/system/zfs-mount.service.wants/zfs-import-cache.service → /lib/systemd/system/zfs-import-cache.service.
Created symlink /etc/systemd/system/zfs.target.wants/zfs-import-cache.service → /lib/systemd/system/zfs-import-cache.service.
Created symlink /etc/systemd/system/zfs-share.service.wants/zfs-mount.service → /lib/systemd/system/zfs-mount.service.
Created symlink /etc/systemd/system/zfs.target.wants/zfs-mount.service → /lib/systemd/system/zfs-mount.service.
Created symlink /etc/systemd/system/zfs.target.wants/zfs-share.service → /lib/systemd/system/zfs-share.service.
Created symlink /etc/systemd/system/multi-user.target.wants/zfs.target → /lib/systemd/system/zfs.target.
zfs-import-scan.service is a disabled or a static unit, not starting it.
Job for zfs-import-cache.service failed because the control process exited with error code.
See "systemctl  status zfs-import-cache.service" and "journalctl  -xe" for details.
Job for zfs-mount.service failed because the control process exited with error code.
See "systemctl  status zfs-mount.service" and "journalctl  -xe" for details.
Job for zfs-share.service failed because the control process exited with error code.
See "systemctl  status zfs-share.service" and "journalctl  -xe" for details.
Setting up zfs-zed (0.6.5.11-1ubuntu3.1) ...
Created symlink /etc/systemd/system/zed.service → /lib/systemd/system/zfs-zed.service.
Created symlink /etc/systemd/system/zfs.target.wants/zfs-zed.service → /lib/systemd/system/zfs-zed.service.
Processing triggers for libc-bin (2.26-0ubuntu2.1) ...
root@kigelia:~# zpool create -f tank -O compression=lz4 -m /test /dev/disk/by-id/wwn-0x5002538d40dca5d9-part11
The ZFS modules are not loaded.
Try running '/sbin/modprobe zfs' as root to load them.
root@kigelia:~# /sbin/modprobe zfs
modprobe: FATAL: Module zfs not found in directory /lib/modules/4.15.3-041503-generic
root@kigelia:~#

Here is the kernel and available modules.

hbarta@kigelia:~$ uname -a
Linux kigelia 4.15.3-041503-generic #201802120730 SMP Mon Feb 12 07:31:14 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
hbarta@kigelia:~$ find /lib/modules -name "*zfs*"
/lib/modules/4.13.0-32-generic/kernel/zfs
/lib/modules/4.13.0-32-generic/kernel/zfs/zfs
/lib/modules/4.13.0-32-generic/kernel/zfs/zfs/zfs.ko
/lib/modules/4.13.0-21-generic/kernel/zfs
/lib/modules/4.13.0-21-generic/kernel/zfs/zfs
/lib/modules/4.13.0-21-generic/kernel/zfs/zfs/zfs.ko
/lib/modules/4.13.0-36-generic/kernel/zfs
/lib/modules/4.13.0-36-generic/kernel/zfs/zfs
/lib/modules/4.13.0-36-generic/kernel/zfs/zfs/zfs.ko
hbarta@kigelia:~$ 

Should I switch back to a mainstream kernel? File a bug report against the special kernel? Add modules to the kernel I'm running?

I'd appreciate suggestions on the best course of action (as well as pointers instructions for doing this properly.)

Thanks!

Edit.0: I booted Debian Stretch on this laptop and performed the same steps. I noted that the install of the ZFS utilities included 'zfs-dkms' which was not a dependency on Ubuntu. I then booted Ubuntu and attempted to install this package. The process reported some errors and then hung. The scrape from the terminal window is

hbarta@kigelia:~$ sudo apt install zfs-dkms
[sudo] password for hbarta: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.13.0-32 linux-headers-4.13.0-32-generic linux-image-4.13.0-32-generic linux-image-extra-4.13.0-32-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  spl spl-dkms
The following NEW packages will be installed:
  spl spl-dkms zfs-dkms
0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
Need to get 1,486 kB of archives.
After this operation, 11.3 MB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://us.archive.ubuntu.com/ubuntu artful/universe amd64 spl-dkms all 0.6.5.11-1ubuntu1 [385 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu artful-updates/universe amd64 zfs-dkms all 0.6.5.11-1ubuntu3.1 [1,081 kB]
Get:3 http://us.archive.ubuntu.com/ubuntu artful/universe amd64 spl amd64 0.6.5.11-1ubuntu1 [19.5 kB]
Fetched 1,486 kB in 0s (3,350 kB/s)
Preconfiguring packages ...
Selecting previously unselected package spl-dkms.
(Reading database ... 332214 files and directories currently installed.)
Preparing to unpack .../spl-dkms_0.6.5.11-1ubuntu1_all.deb ...
Unpacking spl-dkms (0.6.5.11-1ubuntu1) ...
Setting up spl-dkms (0.6.5.11-1ubuntu1) ...
Loading new spl-0.6.5.11 DKMS files...
Building for 4.15.3-041503-generic
Building initial module for 4.15.3-041503-generic
ERROR (dkms apport): kernel package linux-headers-4.15.3-041503-generic is not supported
Error! Bad return status for module build on kernel: 4.15.3-041503-generic (x86_64)
Consult /var/lib/dkms/spl/0.6.5.11/build/make.log for more information.
Selecting previously unselected package zfs-dkms.
(Reading database ... 332501 files and directories currently installed.)
Preparing to unpack .../zfs-dkms_0.6.5.11-1ubuntu3.1_all.deb ...
Unpacking zfs-dkms (0.6.5.11-1ubuntu3.1) ...
Selecting previously unselected package spl.
Preparing to unpack .../spl_0.6.5.11-1ubuntu1_amd64.deb ...
Unpacking spl (0.6.5.11-1ubuntu1) ...
Setting up spl (0.6.5.11-1ubuntu1) ...
Processing triggers for man-db (2.7.6.1-2) ...
Setting up zfs-dkms (0.6.5.11-1ubuntu3.1) ...
WARNING: Building ZFS module on an unknown kernel.
Loading new zfs-0.6.5.11 DKMS files...
Building for 4.15.3-041503-generic
Building initial module for 4.15.3-041503-generic
configure: error: 
    *** Please make sure the kmod spl devel <kernel> package for your
    *** distribution is installed then try again.  If that fails you
    *** can specify the location of the spl objects with the
    *** '--with-spl-obj=PATH' option.
ERROR (dkms apport): kernel package linux-headers-4.15.3-041503-generic is not supported
Error! Bad return status for module build on kernel: 4.15.3-041503-generic (x86_64)
Consult /var/lib/dkms/zfs/0.6.5.11/build/make.log for more information.
hbarta@kigelia:~$ find /lib/modules -name "*zfs*"
/lib/modules/4.13.0-32-generic/kernel/zfs
/lib/modules/4.13.0-32-generic/kernel/zfs/zfs
/lib/modules/4.13.0-32-generic/kernel/zfs/zfs/zfs.ko
/lib/modules/4.13.0-21-generic/kernel/zfs
/lib/modules/4.13.0-21-generic/kernel/zfs/zfs
/lib/modules/4.13.0-21-generic/kernel/zfs/zfs/zfs.ko
/lib/modules/4.13.0-36-generic/kernel/zfs
/lib/modules/4.13.0-36-generic/kernel/zfs/zfs
/lib/modules/4.13.0-36-generic/kernel/zfs/zfs/zfs.ko
hbarta@kigelia:~$ 

I have found that white space seems to be significant in ZFS commands, but only apparently under some conditions.. For example, both of the following commands work:

root@grandidier:~# zfs list -t snap -r tank/srv 
NAME                  USED  AVAIL  REFER  MOUNTPOINT
tank/srv@initial     4.22G      -  2.45T  -
tank/srv@2018-01-09   106G      -  3.40T  -
tank/srv@2018-01-14  50.0M      -  3.27T  -
tank/srv@2018-01-17  48.8M      -  3.16T  -
tank/srv@2018-01-19  56.9M      -  3.09T  -
tank/srv@2018-01-30  48.6M      -  2.72T  -
tank/srv@2018-02-12   104M      -  2.49T  -
root@grandidier:~# zfs list -t snap  -r tank/srv 
NAME                  USED  AVAIL  REFER  MOUNTPOINT
tank/srv@initial     4.22G      -  2.45T  -
tank/srv@2018-01-09   106G      -  3.40T  -
tank/srv@2018-01-14  50.0M      -  3.27T  -
tank/srv@2018-01-17  48.8M      -  3.16T  -
tank/srv@2018-01-19  56.9M      -  3.09T  -
tank/srv@2018-01-30  48.6M      -  2.72T  -
tank/srv@2018-02-12   104M      -  2.49T  -
root@grandidier:~#

(Note: added space between "...snap -r") However if I put the command in a pipe and use back tick substitution to get the result of the command, I get:

root@grandidier:~# export NEW=`zfs list -t snap -r tank/srv | tail -1 | awk '{print $1}'`; echo $NEW
tank/srv@2018-02-12
root@grandidier:~# export NEW=`zfs list -t snap  -r tank/srv | tail -1 | awk '{print $1}'`; echo $NEW
cannot open ' -r': invalid dataset name
cannot open 'tank/srv': operation not applicable to datasets of this type

root@grandidier:~# 

I find this baffling and disconcerting. I think I can sidestep the issue by crafting my scripts without any extra white space but I'd really like to know why this is happening in the first place.

This is on
Ubuntu 16.04 LTS (up to date)
bash 4.3.48
ZFS 0.6.5.11-1ubuntu3

Edit: to answer the first three comments (and retain code formatting)

root@grandidier:~/bin# printf '%q\n' "$IFS"
$' \t\n'

It seems that the $(...) syntax is also subject to this problem (see next comment.)

I'm not sure where something that looks like a space could come from but it seems that is the issue. I have copied this string to/from a Google doc and perhaps it did some sort of translation on the spaces. If I add the extra space in the google doc and copy/paste to an xterm, the error is reported. If I edit the command (on the command line) and delete/reenter the two spaces, the command works w/out error.

Clearly Google Docs is not a good programming editor. (I'm not really using it that way but rather to take notes and save copies of commands as I work my way through something. I probably should stick to something like vim for that.)

I followed instructions in another post that basically said to create the RAID and install after selecting the RAID partitions to which to install. I've done this a number of times but find myself stymied this time.

I had a system running on a pair of 512GB SSDs that had two RAID0 partitions. One was for system (about 40GB) and most of the rest is allocated to /home. This was running on a 17.x version of Linux Mint. Following an unclean shutdown the system was borked. It appeared that some files were missing or corrupted. I decided that it was a good time to update so I downloaded the current Linux Mint (Cinnamon) .iso and copied it to a USB drive. I booted the USB, assembled the RAIDs and proceeded with the installation. I selected /dev/md1 for the system, EXT4 format and reformat the drive. I selected /dev/md2 for /home without a reformat. The install seemed to go well with the installer even recognizing that my $HOME is encrypted. When it got to the point where it needed to install GRUB, it reported an error and gave me three choices. Regardless of the choice I made, the dialog did not proceed.

Next I downloaded and tried to install Xubuntu 16.04 LTS and had exactly the same result. At present I've booted the USB drive, assembled the RAIDs and tried to install GRUB to both /dev/sda and /dev/md0 with the following results.

xubuntu@xubuntu:~$ sudo grub-install --boot-directory=/media/xubuntu/c31e9230-d979-4c7d-81ee-34dda0bac330 /dev/md0
Installing for i386-pc platform.
grub-install: warning: File system `ext2' doesn't support embedding.
grub-install: warning: Embedding is not possible.  GRUB can only be installed in this setup by using blocklists.  However, blocklists are UNRELIABLE and their use is discouraged..
grub-install: error: will not proceed with blocklists.
xubuntu@xubuntu:~$ 


xubuntu@xubuntu:~$ sudo grub-install --boot-directory=/media/xubuntu/c31e9230-d979-4c7d-81ee-34dda0bac330 /dev/sda
Installing for i386-pc platform.
grub-install: warning: this GPT partition label contains no BIOS Boot Partition; embedding won't be possible.
grub-install: error: embedding is not possible, but this is required for RAID and LVM install.
xubuntu@xubuntu:~$ 

Here is how /dev/sda is partitioned.

xubuntu@xubuntu:~$ sudo parted -l /dev/sda
Model: ATA Samsung SSD 850 (scsi)
Disk /dev/sda: 500GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system  Name                 Flags
 4      17.4kB  1049kB  1031kB               BIOS boot partition  boot, esp
 3      1049kB  1074MB  1073MB  ext4                              boot, esp
 1      1074MB  21.5GB  20.4GB  ext4                              raid
 2      21.5GB  500GB   479GB                                     raid

And the RAIDs

xubuntu@xubuntu:~$ cat /proc/mdstat
Personalities : [raid0] [raid1] 
md0 : active raid1 sde2[0] sdg2[1]
      186839936 blocks super 1.2 [2/2] [UU]

md3 : active raid1 sda3[0] sdb3[1]
      1047488 blocks [2/2] [UU]

md2 : active raid0 sda2[0] sdb2[1]
      934827008 blocks super 1.2 512k chunks

md1 : active raid0 sdb1[0] sda1[1]
      39846912 blocks super 1.2 512k chunks

unused devices: <none>
xubuntu@xubuntu:~$ 

I did some searching and found https://blog.hostonnet.com/grub-install-warning-this-gpt-partition-label-contains-no-bios-boot-partition-embedding-wont-be-possible Based on the suggestion to mark the drive 'bios_grub on' I executed the following commands:

xubuntu@xubuntu:~$ sudo parted /dev/sda set 1 bios_grub on
Information: You may need to update /etc/fstab.

xubuntu@xubuntu:~$ sudo grub-install --boot-directory=/media/xubuntu/c31e9230-d979-4c7d-81ee-34dda0bac330 /dev/sda
Installing for i386-pc platform.
Installation finished. No error reported.
xubuntu@xubuntu:~$ 

Thrilled to see "Installation finished. No error reported." I rebooted and found myself facing a "grub>" prompt. :(

Worse yet, this operation seems to have corrupted /dev/md0 and it no longer assembles when I boot the thumb drive.

I'd really like to know what to do differently to get this to work. Thanks for any help.

Edit: I recall seeing options to 'boot other drive' form some install media. As a stopgap I would be happy to be able to use something like that (which would require the ability to boot an image on RAID) until I can figure out what needs to happen to get GRUB installed properly