The New Yorker has a nice article about the GNU manifesto, which turned thirty earlier this month.
It nicely summarises what lead RMS to publish the manifesto and start the Free Software Foundation and also briefly explains the difference between Free Software and Open Source software.
Category: Linux (Page 3 of 9)
A quick note to self: I wanted to find out what Subversion version was run on R-forge, which I access via SSH. This is how to do it:
$ ssh username@svn.r-forge.r-project.org svnserve --version svnserve, version 1.6.17 (r1128011) compiled Nov 20 2011, 01:10:33 Copyright (C) 2000-2009 CollabNet. Subversion is open source software, see http://subversion.apache.org/ This product includes software developed by CollabNet (http://www.Collab.Net/). The following repository back-end (FS) modules are available: * fs_base : Module for working with a Berkeley DB repository. * fs_fs : Module for working with a plain file (FSFS) repository. Cyrus SASL authentication is available.
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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
ignorance.
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
account):
$ 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/ \
/storage/JaarlijkseBackupsOrganized
$ 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
sectors:
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:
$ 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
now.
Creating the new ZFS pool
$ zpool create -o ashift=9 JaarlijkseBackupPool \
/dev/disk/by-partlabel/JaarlijkseBackups-HD103SI-S1VSJD6ZB0
$ zpool status JaarlijkseBackupPool
pool: JaarlijkseBackupPool
state: ONLINE
scan: none requested
config:
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
TIME SENT SNAPSHOT
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
^C
$ 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
command.
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
#!/bin/sh # # 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` olddate="2013-02-04" srcdir="/mnt/backupsrc/" destdir="/mnt/backupdest/JaarlijkseBackups/$today" prevdir="/mnt/backupdest/JaarlijkseBackups/$olddate" # LVM options VG=raid5vg LV=home # 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 fi # 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 $rsynccommand |
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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).
#!/bin/bash # # 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 fi ############################### # Some settings ############################### # Options for the remote (Synology) backup destination DESTHOST=$1 DESTUSER=root DESTPATH=/volume1/Backups/ DEST=${DESTUSER}@${DESTHOST}:${DESTPATH} # Options for the client (the data to be backed up) # ZFS options ZFS_POOL=storage ZFS_DATASET=home ZFS_SNAPSHOT=rsync_snapshot SNAPDIR="/home/.zfs/snapshot/$ZFS_SNAPSHOT" # Backup source path. Don't forget to have trailing / otherwise # rsync's --delete option won't work SRC=${SNAPDIR}/ # 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 else # Let's make snapshots zfs snapshot $ZFS_POOL/$ZFS_DATASET@$ZFS_SNAPSHOT fi # Do the actual backup rsync -e 'ssh' $OPTIONS $EXCLUSIONS $SRC $DEST # Remove the ZFS snapshot if [ -d $SNAPDIR ]; then zfs destroy $ZFS_POOL/$ZFS_DATASET@$ZFS_SNAPSHOT else echo "$SNAPDIR does not exist!" 1>&2 exit 2 fi exit 0 |
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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.
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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.
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If you’re interested in a short (14 minute) talk on what Free Foftware is all about, have a look at Richard Stallman’s TEDx Geneva presentation. It’s an excellent introduction by the master himself!
Note: the video above is only half the size of the original because I wanted it to fit the width of this blog.
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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!
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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 |
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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:
#!/bin/bash # # This script is used to copy files from this directory to the # home directories of the users listed in $USERFILE. USERFILE=accounts.txt SRCFILE=/common/WORK/school/lennart/.Renviron while read user passw; do ./copy_file_to_users.expect $user $passw done < $USERFILE |