Lennart's weblog

Open source, computers, Africa and other more (or less) interesting stuff.

Tag: sysadmin (page 1 of 4)

Fixing Emacs tramp mode when using zsh

Today I finally took some time to fix a long-standing problem: when trying to edit a file on a remote host using Emacs tramp mode, long time-outs occurred when typing the remote file name (after hitting C-x C-f). These time-outs were so long and occurred after each key press that tramp was effectively useless.

After some digging (e.g. excluding helm as the problem source) I found this entry in the Emacs Wiki which basically told my that using zsh (the Z shell) on the remote host could be the culprit. Indeed, after adding

[[ $TERM == "dumb" ]] && unsetopt zle && PS1='$ ' && return

at the top of my ~/.zshrc file solved the problem instantly. What this line does is simply replacing the shell prompt with a very simple one (a $ followed by a space) if the terminal is of the dumb type (which is the case for tramp).

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 unix.stackexchange.com 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

Using rsync to backup a ZFS file system to a remote Synology Diskstation

Some time ago I moved from using LVM to using ZFS on my home server. This meant I also had to change the backup script I used to make backups on a remote Synology Diskstation. Below is the updated script. I also updated it such that it now needs a single command line argument: the hostname of the Diskstation to backup to (because I now have two Diskstations at different locations). If you want to run this script from cron you should set up key-based SSH login (see also here and here).

# This script makes a backup of my home dirs to a Synology DiskStation at
# another location. I use ZFS for my /home, so I make a snapshot first and
# backup from there.
# This script requires that the first command line argument is the
# host name of the remote backup server (the Synology NAS). It also
# assumes that the location of the backups is the same on each
# remote backup server.
# Time-stamp: <2014-10-27 11:35:39 (L.C. Karssen)>
# This script it licensed under the GNU GPLv3.
set -u
if [ ${#} -lt 1 ]; then
    echo -n "ERROR: Please specify a host name as first command" 1>&2
    echo " line option" 1>&2
    exit -1
# Some settings
# Options for the remote (Synology) backup destination
# Options for the client (the data to be backed up)
# ZFS options
# Backup source path. Don't forget to have trailing / otherwise
# rsync's --delete option won't work
# rsync options
OPTIONS="--delete -azvhHSP --numeric-ids --stats"
OPTIONS="$OPTIONS --timeout=60 --delete-excluded"
OPTIONS="$OPTIONS --skip-compress=gz/jpg/mp[34]/7z/bz2/ace/avi/deb/gpg/iso/jpeg/lz/lzma/lzo/mov/ogg/png/rar/CR2/JPG/MOV"
EXCLUSIONS="--exclude lost+found --exclude .thumbnails --exclude .gvfs"
EXCLUSIONS="$EXCLUSIONS --exclude .cache --exclude Cache"
EXCLUSIONS="$EXCLUSIONS --exclude .local/share/Trash"
EXCLUSIONS="$EXCLUSIONS --exclude home/lennart/tmp/Downloads/*.iso"
EXCLUSIONS="$EXCLUSIONS --exclude home/lennart/.recycle"
EXCLUSIONS="$EXCLUSIONS --exclude _dev_dvb_adapter0_Philips_TDA10023_DVB*"
# The real work
# Create the ZFS snapshot
if [ -d $SNAPDIR ]; then
    # If the directory exists, another backup process may be running
    echo "Directory $SNAPDIR already exists! Is another backup still running?"
    exit -1
    # Let's make snapshots
# Do the actual backup
# Remove the ZFS snapshot
if [ -d $SNAPDIR ]; then
    echo "$SNAPDIR does not exist!" 1>&2
    exit 2
exit 0

Multiple accounts on an SSH server: managing key files

I’ve got several domains hosted at the same hosting company, and the company provides SSH access for each of them with a different user name, but with the same SSH server address. As I’m using key-based login to the server (see also my post here) I ran into the following problem: How do I set up my SSH config file such that it knows which key to use for which user name?

It turns out that the solution is easy (thanks Kelvin!): if you use the %r variable in the ~/.ssh/config file it contains the user name which you used when logging in. Similarly, the %h contains the host name you used on the command line. So all I needed to do was to create entries like this:

Host ssh.myhoster.com
     IdentityFile ~/.ssh/hosting-%r.key

and make sure that the corresponding key files are named hosting-domain1.key, hosting-domain2.key, etc. and then log in using a command like ssh domain1@ssh.myhoster.com.

SSH with several keys: fix “Too many authentication failures” error

Yesterday I created an SSH key for a new machine. Today I try to log in to a different machine, one that actually doesn’t use keys, and I got the error mentioned in the title. It turns out SSH offers all available keys by default, so I ran out of login attempts before I noticed it.

The solution is simple: Add

IdentitiesOnly yes

to your ~/.ssh/config file.

A more detailed explanation can be found here.

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

Using ‘expect’ to distribute files among users

I’m currently teaching at the Summmer School in Statistical Omics in Split, Croatia. A great experience!

Because of the computations involved in the project work, we have access to a server. However, since the machine is part of a university cluster, I haven’t been given full root permissions (in fact, I’m only allowed to use sudo to install packages).

Now, the problem I had to solve was that I needed to distribute a certain file (.Renviron) to each student’s home directory. Normally I’d use sudo to do that, but the admin hadn’t allowed me to use cp via sudo. Furtunately, I had a list of user names and passwords for the students (because I had to distribute those), so I thought I’d use su - to change to each student’s account and copy the file, something along the lines of

echo PASSWORD | su -

and then loop over each account. Unfortunately, while testing the script I found out it wouldn’t work since su complained:

su: must be run from a terminal

Then I remembered the expect tool, which executes commands based on what it ‘sees’ on the command line. In this case I wanted it to enter the password at su‘s prompt. This is the expect script I came up with, it accepts two command line arguments, the user name and the password:

#!/usr/bin/expect -f
set user [lindex $argv 0]
set pass [lindex $argv 1]
spawn su - $user
expect "Password: "
send "$pass\r"
expect "$ "
send "cp -i /common/WORK/school/lennart/.Renviron .\r"
expect "$ "
send "ls -l .Renviron\r"
expect "$ "
send "exit\r"

The script was wrapped in the Bash script that I had already written:

# This script is used to copy files from this directory to the
# home directories of the users listed in $USERFILE.
while read user passw; do
    ./copy_file_to_users.expect $user $passw
done < $USERFILE
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