Notes about open source software, computers, other stuff.

Tag: Ubuntu (Page 1 of 4)

Using the Lenovo Thunderbolt 3 Essential Dock with Linux

Today the Lenovo Thunderbolt 3 Essential dock I had ordered just before the new year arrived. My current laptop is a 6th Gen Lenovo Thinkpad X1 Carbon, which actually has two Tunderbolt 3 (TB3) ports. For a while the cable mess on my desk had been bothering me and a dock looked like a good way to get rid of both the clutter and the fact that I had to plug in a power cable, an HDMI cable, a USB cable and a network cable. The latter was especially tricky, because my laptop doesn’t have a dedicated ethernet port, but instead has a dongle that plugs into one of the TB3 ports. Of course, I didn’t want it to happen that I was on the road without the dongle, so double checking and making sure I had it in my bag was a regular worry.

With the TB3 Essential dock all this should be over. The dock is pretty well equipped:

  • 1 ethernet port (1Gbps)
  • 1 HDMI 2.0 port
  • 1 DisplayPort 1.4
  • 2 USB A 3.0 1.5Gbps ports
  • 2 USB C 10Gbps ports (no video support)
  • 1 3.5 mm audio jack.

The one thing that remained to be seen, of course, was whether the all those ports would work under Linux as well. I read some promising reports for other TB3-based docks from Lenovo, so I decided to order it.

After connecting the various cables to the dock came the moment supreme: I plugged in the TB3 cable to the laptop. And… The display connected to the HDMI port lit up. So far, so good! No USB functionality, however. Time to dive into the BIOS, because I remembered having seen some settings there, including some security related ones.

In the BIOS I couldn’t change the TB3 security setting because, as the help message explained, the graphics memory was set to 512MB. I’m not sure why this is an issue, but I looked up the graphics RAM setting and reduced it to 256MB. Next, I went back to the TB settings and set the security level to the first option: “No security”, followed by a reboot. Now, everything worked. That is one step in the right direction.

However, I wasn’t willing to forgo all security, so I went back to the BIOS settings and set the security level to “Secure Connection” (according to this blog post at this is security level 2 or SL2). I rebooted and indeed, no USB. So I went to Ubuntu’s Thunderbolt settings and there I had to press the ‘Unlock’ button in the top right corner, after which I could click on a button authorise the dock. After that all connections worked again. From the commandline, the boltctl utility can be used to see more information on the connected thunderbolt devices. This is the output for an unauthorised device:

$ boltctl list
? Lenovo Thunderbolt 3 Essential Dock
  ?? type:          peripheral
  ?? name:          Thunderbolt 3 Essential Dock
  ?? vendor:        Lenovo
  ?? uuid:          00b00089-417d-0801-ffff-ffffffffffff
  ?? status:        connected
  ?  ?? domain:     ca030000-0070-6f08-2382-4312b0238921
  ?  ?? authflags:  none
  ?? connected:     ma 04 jan 2021 16:26:45 UTC
  ?? stored:        ma 04 jan 2021 16:20:57 UTC
     ?? policy:     iommu
     ?? key:        no

And this is the output after clicking the “Authorise” button in the Ubuntu settings:

? boltctl list
? Lenovo Thunderbolt 3 Essential Dock
  ?? type:          peripheral
  ?? name:          Thunderbolt 3 Essential Dock
  ?? vendor:        Lenovo
  ?? uuid:          00b00089-417d-0801-ffff-ffffffffffff
  ?? status:        authorized
  ?  ?? domain:     ca030000-0070-6f08-2382-4312b0238921
  ?  ?? authflags:  none
  ?? authorized:    ma 04 jan 2021 16:30:07 UTC
  ?? connected:     ma 04 jan 2021 16:26:45 UTC
  ?? stored:        ma 04 jan 2021 16:20:57 UTC
     ?? policy:     iommu
     ?? key:        yes (new)


However, my joy was shortlived, because after disconnecting and reconnecting the dock, the USB ports had stopped working again. The device had to be authorised again. This seemed tedious, so I set about reading more in the boltctl man page and found that there was a way to enroll a device permanently. So that is what I did. First I removed its UUID from the database:

$ boltctl forget 00b00089-417d-0801-ffff-ffffffffffff

And then added it again, this time with the auto policy:

$ boltctl enroll --policy auto 00b00089-417d-0801-ffff-ffffffffffff
 ? Lenovo Thunderbolt 3 Essential Dock
   ?? type:          peripheral
   ?? name:          Thunderbolt 3 Essential Dock
   ?? vendor:        Lenovo
   ?? uuid:          00b00089-417d-0801-ffff-ffffffffffff
   ?? dbus path:     /org/freedesktop/bolt/devices/00b00089_417d_0801_ffff_ffffffffffff
   ?? status:        authorized
   ?  ?? domain:     ca030000-0070-6f08-2382-4312b0238921
   ?  ?? parent:     ca030000-0070-6f08-2382-4312b0238921
   ?  ?? syspath:    /sys/devices/pci0000:00/0000:00:1d.0/0000:05:00.0/0000:06:00.0/0000:07:00.0/domain0/0-0/0-1
   ?  ?? authflags:  secure
   ?? authorized:    ma 04 jan 2021 22:33:08 UTC
   ?? connected:     ma 04 jan 2021 22:32:43 UTC
   ?? stored:        ma 04 jan 2021 16:20:57 UTC
      ?? policy:     auto
      ?? key:        yes

As you can see from the boltctl list output below, the policy is now set to auto (instead of the previous iommu):

$ boltctl list
 ? Lenovo Thunderbolt 3 Essential Dock
   ?? type:          peripheral
   ?? name:          Thunderbolt 3 Essential Dock
   ?? vendor:        Lenovo
   ?? uuid:          00b00089-417d-0801-ffff-ffffffffffff
   ?? status:        authorized
   ?  ?? domain:     ca030000-0070-6f08-2382-4312b0238921
   ?  ?? authflags:  secure
   ?? authorized:    ma 04 jan 2021 22:41:46 UTC
   ?? connected:     ma 04 jan 2021 22:41:45 UTC
   ?? stored:        ma 04 jan 2021 16:20:57 UTC
      ?? policy:     auto
      ?? key:        yes

Now I can disconnect and reconnect the dock without problems :-).

I also tested the 3.5mm audio port, which worked (at least for listening, I didn’t have a headset with microphone at hand). Same for the two USB A and the two USB C ports. Finally, I tested the DisplayPort and that worked too. In fact, connecting my 3440×1440 screen via both HDMI and DP to the dock worked fine. The Ubuntu display settings showed a “3 monitor” setup, two 3440×1440 screens and the latop’s own screen at 2560×1440.

So, in conclusion: the Lenovo Thunderbolt 3 Essential dock is fully supported under Ubuntu 20.04.

Thanks to this blog post at for pointing me to the boltctl utility!

Installing parted during Ubuntu installation

When installing Ubuntu (I guess a regular Debian installation won’t be any different), I sometimes would like to manually create or change partitions (by jumping to another terminal, e.g. using Alt-F2) before doing the actual install. My preferred tool for that is parted, however, on regular Ubuntu installation images (at least the server variety), parted isn’t available from the console by default.

Today I noticed that (at least on today’s daily image of Ubuntu 16.04 Xenial), a udeb file for parted is available. This is how you install it:

udpkg -i /cdrom/pool/main/p/parted/parted-udeb_3.2-15_amd64.udeb

after which you can use parted to your heart’s content.

For more information on udebs see the Debian Installer Internals documentation.

Setting the console font when using an nVidia card

Even though I do most of the work I do on my workstation in a graphical desktop environment, I sometimes want or need to switch to one of the virtual terminals (consoles), for example when trying to fix a connection problem or hanging desktop environment.

Whenever I had to do this I was always bothered by the fact that the font was so large (or, the other way around, the resolution so low). What made my annoyance worse was that I knew from my early Linux days So, instead of being annoyed I decided to fix this. Thanks to the help of mchid on I solved in a matter of minutes. The tricky part for me was to realise I am using an nVidia graphics card, which means things are just a little bit different than normally.

Just in case StackExchange ever goes down or this answer gets lost I will reproduce it below.

For newer Debian & Ubuntu distros using nvidia, I had to do the following: First, edit /etc/default/grub. Change the following line:


to this:


replacing 1280×800 with the desired resolution.


echo "echo FRAMEBUFFER=y" | sudo tee /etc/initramfs-tools/conf.d/splash
sudo update-initramfs -u
sudo update-grub

To simply change the font size, you can do so using the following command:

sudo dpkg-reconfigure console-setup

Moving annual backups from an external disk with Ext4 to an external disk with ZFS

For a few years I have used the Christmas holidays to create a full
backup of my /home on an external hard disk. For that I used a
Bash script around rsync that uses hard links to keep the used disk
space under control. Each backup was saved in a directory named with
the date of the backup. POSIX ACLs were also backed up.

Since last year’s backup I have moved to ZFS (using ZFS on Linux
with Ubuntu 14.04
) as filesystem for /home (and others). Since ZFS
makes checksums of data and metadata it has the possibility to
detect corrupted files (and if the data is redundant it can also fix
them). This is a feature I’d like to have for my backups as
well: I’d rather know it when corruption occurs than live in

So the plan is to move the old backups from the external disk to the
ZFS pool in my server. and instead of using hard links I’ll transfer
the backups in order from old to new to the ZFS pool making a
snapshot for each. Additionally I will also turn on compression
(using the lz4 algorithm). Once that is done I will reformat the
external drive and create a ZFS pool called “JaarlijkseBackupPool” on
it (jaarlijks means annual in Dutch).

The old situation

In the current/old situation, this is how much disk space is used
on the external disk (with and without taking the hard links into

$ sudo du -csh /mnt/JaarlijkseBackups/*
102G    /mnt/JaarlijkseBackups/2010-11-28
121G    /mnt/JaarlijkseBackups/2013-02-04
101G    /mnt/JaarlijkseBackups/2013-12-23
324G    total
$ sudo du -clsh /mnt/JaarlijkseBackups/*
102G    /mnt/JaarlijkseBackups/2010-11-28
193G    /mnt/JaarlijkseBackups/2013-02-04
255G    /mnt/JaarlijkseBackups/2013-12-23
549G    total

Copying the data from the Ext4 disk to a temporary ZFS filesystem on my server

The ZFS pool in my server is called storage. In order to save the
POSIX ACLs of the Ext4 system, they need to be enabled when
creating the ZFS filesystem as well. Setting xattr=sa means the
ACLS are stored more efficiently (although this option is not
compatible with other ZFS implementations at this time, so if I
would try to import the ZFS pool in FreeBSD for example, that
information would be inaccessible).

$ zfs create storage/JaarlijkseBackupsOrganized \
      -o compression=lz4 \
      -o acltype=posixacl \
      -o xattr=sa
$ sudo rsync -ahPAXHS --numeric-ids \
     /storage/JaarlijkseBackups/2010-11-28/ \
$ zfs snapshot storage/JaarlijkseBackupsOrganized@2010-11-28

Followed by the same for the same rsync and zfs snapshot
commands for the other two dates.
Once that is finished, this is the status of that ZFS FS:

$ zfs list -r -t all storage/JaarlijkseBackupsOrganized
NAME                                            USED  AVAIL  REFER  MOUNTPOINT
storage/JaarlijkseBackupsOrganized              275G   438G   272G  /storage/JaarlijkseBackupsOrganized
storage/JaarlijkseBackupsOrganized@2010-11-28  1,03G      -  88,9G  -
storage/JaarlijkseBackupsOrganized@2013-02-04  2,33G      -   196G  -
storage/JaarlijkseBackupsOrganized@2013-12-23      0      -   272G  -
$ zfs get -r -t all compressratio storage/JaarlijkseBackupsOrganized
NAME                                           PROPERTY       VALUE  SOURCE
storage/JaarlijkseBackupsOrganized             compressratio  1.13x  -
storage/JaarlijkseBackupsOrganized@2010-11-28  compressratio  1.19x  -
storage/JaarlijkseBackupsOrganized@2013-02-04  compressratio  1.14x  -
storage/JaarlijkseBackupsOrganized@2013-12-23  compressratio  1.12x  -

Partitioning the external disk

The external disk is as 1TB Samsung SATA 3Gbps SpinPoint F2 EcoGreen disk
(type HD103SI, serial number: S1VSJD6ZB02657). The disk uses 512B

sudo hdparm -I /dev/sdf |grep Sector
     Logical/Physical Sector size:           512 bytes

Before using it with ZFS, it needs to be partitioned. I used

$ parted /dev/sdf
GNU Parted 2.3
Using /dev/sdf
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) p
Model: ATA SAMSUNG HD103SI (scsi)
Disk /dev/sdf: 1000GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number  Start   End     Size    Type     File system  Flags
 1      1049kB  1000GB  1000GB  primary  ext4

(parted) mklabel
New disk label type? gpt
(parted) u
Unit?  [compact]? MB
(parted) p
Model: ATA SAMSUNG HD103SI (scsi)
Disk /dev/sdf: 1000205MB
Sector size (logical/physical): 512B/512B
Partition Table: gpt

Number  Start  End  Size  File system  Name  Flags

(parted) mkpart
Partition name?  []? JaarlijkseBackups-HD103SI-S1VSJD6ZB02657
File system type?  [ext2]? zfs
Start? 1M
End? 1000204M
(parted) p
Model: ATA SAMSUNG HD103SI (scsi)
Disk /dev/sdf: 1000205MB
Sector size (logical/physical): 512B/512B
Partition Table: gpt

Number  Start   End        Size       File system  Name                                  Flags
 1      1,05MB  1000204MB  1000203MB  ext4         JaarlijkseBackups-HD103SI-S1VSJD6ZB0

(parted) q

This removes the old partition table and creates a new GPT
partition table (which allows naming partitions). Next I set the
units to MB so I can leave 1MB at the beginning and end of the
partition (can be helpful when importing this pool in
e.g. FreeBSD). The disk also shows up in /dev/disk/by=partlabel

Creating the new ZFS pool

$ zpool create -o ashift=9 JaarlijkseBackupPool \
$ zpool status JaarlijkseBackupPool
  pool: JaarlijkseBackupPool
 state: ONLINE
  scan: none requested

        NAME                                    STATE     READ WRITE CKSUM
        JaarlijkseBackupPool                    ONLINE       0     0     0
          JaarlijkseBackups-HD103SI-S1VSJD6ZB0  ONLINE       0     0     0

errors: No known data errors

Migrating the data

Now that the new ZFS pool and filesystem are all in place, it is
time to move the backups to the new place, starting with the oldest
backup. The -R option also make sure the attributes like
compression and xattr are transferred to the new FS. The
following commands send each snapshot to the new pool (the -n
option of zfs receive is for doing a dry run, just to show how it
works). After the first snapshot is sent, the other two are sent
using the -i option to zfs send so that only the incremental
differences between the snapshots are sent.

$ zfs send -vR storage/JaarlijkseBackupsOrganized@2010-11-28 | \
      zfs receive -Fvu JaarlijkseBackupPool/oldRsyncBackups
$ zfs send -vR -i storage/JaarlijkseBackupsOrganized@2010-11-28 \
    storage/JaarlijkseBackupsOrganized@2013-02-04 | \
    zfs receive -Fvu JaarlijkseBackupPool/oldRsyncBackups
$ zfs send -vR -i storage/JaarlijkseBackupsOrganized@2013-02-04 \
      storage/JaarlijkseBackupsOrganized@2013-12-23 | \
      zfs receive -Fvu JaarlijkseBackupPool/oldRsyncBackups -n
send from @2013-02-04 to storage/JaarlijkseBackupsOrganized@2013-12-23 estimated size is 84,3G
total estimated size is 84,3G
would receive incremental stream of storage/JaarlijkseBackupsOrganized@2013-12-23 into JaarlijkseBackupPool@2013-12-23
14:09:16   4,22M   storage/JaarlijkseBackupsOrganized@2013-12-23
14:09:17   8,46M   storage/JaarlijkseBackupsOrganized@2013-12-23
14:09:18   18,4M   storage/JaarlijkseBackupsOrganized@2013-12-23
14:09:19   24,8M   storage/JaarlijkseBackupsOrganized@2013-12-23
$ zfs send -vR -i  storage/JaarlijkseBackupsOrganized@2013-02-04 \
      storage/JaarlijkseBackupsOrganized@2013-12-23 | \
      zfs receive -Fvu JaarlijkseBackupPool/oldRsyncBackups

Add this year’s backup

At first I tried to add the new backups also to the
oldRsyncBackups FS, but that didn’t work (at least not with an
incremental backup), so I ended up making a new backup. The extra
cost in disk space is not a real problem. Disk space is rather
cheap and the current configuration will last me at least one more
year. So after creating a snapshot called 2014-12-26 of my
/home I ran:

   $ zfs send -v  storage/home@2014-12-26 | \
      zfs receive -Fu JaarlijkseBackupPool/home
$ zfs list -r -t all JaarlijkseBackupPool
NAME                                              USED  AVAIL  REFER  MOUNTPOINT
JaarlijkseBackupPool                              581G   332G    30K  /JaarlijkseBackupPool
JaarlijkseBackupPool/home                         311G   332G   311G  /JaarlijkseBackupPool/home
JaarlijkseBackupPool/home@2014-12-26             51,2M      -   311G  -
JaarlijkseBackupPool/oldRsyncBackups              271G   332G   267G  /JaarlijkseBackupPool/oldRsyncBackups
JaarlijkseBackupPool/oldRsyncBackups@2010-11-28   974M      -  87,1G  -
JaarlijkseBackupPool/oldRsyncBackups@2013-02-04  2,23G      -   193G  -
JaarlijkseBackupPool/oldRsyncBackups@2013-12-23      0      -   267G  -
$ zfs get -r compressratio JaarlijkseBackupPool
NAME                                             PROPERTY       VALUE  SOURCE
JaarlijkseBackupPool                             compressratio  1.15x  -
JaarlijkseBackupPool/home                        compressratio  1.17x  -
JaarlijkseBackupPool/home@2014-12-26             compressratio  1.17x  -
JaarlijkseBackupPool/oldRsyncBackups             compressratio  1.13x  -
JaarlijkseBackupPool/oldRsyncBackups@2010-11-28  compressratio  1.19x  -
JaarlijkseBackupPool/oldRsyncBackups@2013-02-04  compressratio  1.14x  -
JaarlijkseBackupPool/oldRsyncBackups@2013-12-23  compressratio  1.12x  -

Finishing up

In order to be able to disconnect the external drive without
damaging the filesystems use

zpool export JaarlijkseBackupPool

Later, the drive/pool can be imported using the zpool import

Now that the migration is done, the intermediate filesystem
(including the snapshots) can also be removed:

zfs destroy -r storage/JaarlijkseBackupsOrganized

For reference: the old rsync script

# Time-stamp: <2013-02-04 16:48:31 (root)>
# This scripts helps me create my annual backups to an external hard
# disk. The script uses rsync's hard link option to make hard links to
# the previous backups for files that haven't changed. It makes the
# backup based on an LVM snapshot it creates of the LV that contains
# the /home partition.
# This script needs to be run as root.
today=`date +%F`
# LVM options
# rstnc options
options="-ahPAXHS --numeric-ids"
exclusions="--exclude 'lost+found/'"
#  --exclude '*/.thumbnails'"
# exclusions="$exclusions --exclude '*/.gvfs/'"
# exclusions="$exclusions --exclude '*/.cache/' --exclude '**/Cache'"
# exclusions="$exclusions --exclude '*/.recycle/'"
# Check to see if the previous backup directory exists
if [ ! -d $prevdir ]; then
    echo "Error: The directory with the previous back up ($prevdir) doesn't exist" 1>&2
    exit 1
# Make a snapshot of the home LV that we can backup
lvcreate -L15G -s -n snap$LV /dev/$VG/$LV
mount /dev/$VG/snap$LV $srcdir
# Start the backup, first a dry-run, then the full one
rsynccommand="rsync $options $exclusions --link-dest=$prevdir $srcdir $destdir"
$rsynccommand -n
# Wait for user input
echo "This was a dry run. Press a key to continue with the real stuff or"
echo "hit Ctrl-c to abort."
read dummy

Enabling external commands in the Nagios web interface

After an upgrade of one of my Ubuntu server that runs Nagios, I ran into the following error message (again…) when I tried to issue a command from the web interface:

Error: Could not stat() command file ‘/var/lib/nagios3/rw/nagios.cmd’!

This post by Barry O’Donovan shows very nicely how this problem can/should be fixed in Ubuntu. Much cleaner than chmod/chown-ing the directories myself. Thanks Barry!

Fixing font errors when running qmon on a remote server

Sun Grid Engine (SGE) is a bath queue system that can be used to distribute computation intensive tasks across one or more servers/CPUs. SGE has a graphical configuration utility called qmon, but when you start it on a remote machine (using SSH), you may end up with errors like this:

Warning: Cannot convert string "-adobe-courier-medium-r-*--14-*-*-*-m-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-courier-bold-r-*--14-*-*-*-m-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-courier-medium-r-*--12-*-*-*-m-*-*-*" to type FontStruct
X Error of failed request:  BadName (named color or font does not exist)
  Major opcode of failed request:  45 (X_OpenFont)
  Serial number of failed request:  329
  Current serial number in output stream:  340

The warnings are not really a problem, but the error is. It can be solved by running the following on the client (i.e. your local) machine (assuming it runs Debian or Ubuntu):

sudo apt-get install xfonts-75dpi
xset +fp /usr/share/fonts/X11/75dpi
xset fp rehash

Fixing backlight control with Ubuntu on my ThinkPad T440s

Some time ago I bought a ThinkPad T440s for work. It’s an amazing machine! Before that I used a ThinkPad X121, which served me very well on my daily commute. This machine was getting a bit old, and given that my new job (more about which in a later post) also requires me to have a better machine with more screen real estate, it was high time to upgrade.

Ubuntu (13.10 and 14.04) runs well on the T440s, only two things didn’t work as expected:

  • The WWAN interface (mobile internet, from Ericsson) seems to connect when I select it in the network manager, but the adaptor seems to disappear almost immediately after that. A few seconds it appears again. [edit 20140514]I just found out that it’s working, probably this was fixed in Ubuntu 14.04[/edit]
  • The screen’s backlight brightness can be reduced/increase using the Fn-F5 and Fn-F6 keys, but only in a weird way: several key presses are needed for one unit of decrease/increase.

This last bug can be fixed by booting with the following kernel argument:


Simply add this to the GRUB_CMDLINE_LINUX_DEFAULT line in /etc/default/grub:

  GRUB_CMDLINE_LINUX_DEFAULT="acpi_backlight=vendor quiet splash"

and run sudo update-grub. Reboot and you will be able to change the backlight brightness in finer steps.

I found this solution somewhere on the internet a few weeks ago, wrote it down, but can’t remember anymore what the original URL was. My apologies.

Fixing colours in git output after upgrading to Ubuntu 14.04

After upgrading my Ubuntu 13.10 installation to 14.04, I noticed that the output of several git commands (e.g. git diff and git log) didn’t show colours as they used to, but showed ESC[ ANSI codes instead.
A quick internet search lead to this post on where the LESS environment variable was ‘blamed’. Indeed, I have my LESS variable (re-) defined in my .bashrc and .zshrc files.

The solution was to add -R to the environment variable, which allows raw control characters to be displayed. I now have the environment variable defined as:

LESS='--quiet -X -F -R'

Fixing the compose key in Emacs on Ubuntu 13.10

After upgrading to Ubuntu 13.10 some time ago I noticed that my compose key (i.e. the key that you press followed by e.g. c and , to create a ç) didn’t work anymore in Emacs. I found two bug reports on this issue [1, 2], both effectively suggesting the same solution: start Emacs like this

XMODIFIERS=@im=none emacs

So I added the following line to my ~/.zshrc and ~/.bashrc files:

alias emacs='XMODIFIERS=@im=none emacs'

(of course somewhere before I set my EDITOR variable). I also changed the command in the launcher I use (GLX-Dock/Cairo-Dock).
This doesn’t make it a system-wide (or even user-wide) fix, e.g. the Firefox add-on “It’s all text” doesn’t get it, but it covers most of my use cases.

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