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Tag: Ubuntu (Page 3 of 5)

Using BibTeX from org-mode

22 August 2013 / / 1 Comment

I use Emacs‘ org-mode a lot for writing notes, todo lists, presentations and writing short reports. Recently I started writing a larger report which I normally would have done in LaTeX. This time, since the notes related to the project were already in org format, I decided to write the whole report in org-mode. The one thing I needed for that was using BibTeX bibliographies (and RefTeX) from org-mode. A quick web search revealed that that can easily be done by adding the following to your .emacs file:

;; Configure RefTeX for use with org-mode. At the end of your
;; org-mode file you need to insert your style and bib file:
;; \bibliographystyle{plain}
;; \bibliography{ProbePosition}
;; See http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/
(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name)
       (file-exists-p (buffer-file-name))
       (reftex-parse-all))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
  )
(add-hook 'org-mode-hook 'org-mode-reftex-setup)

After that, RefTeX works, but exporting the org document to PDF (via LaTeX) didn’t include the bibliography entries. A quick look at the error log showed that bibtex hadn’t been run, so the question was: how to tell org-mode to do that too when exporting. The answer is to tell org-mode to use the latexmk Perl script (on Debian/Ubuntu it is easily installed from the package repositories) when exporting to PDF. I added the following lines to my .emacs file:

;; Use latexmk for PDF export
(setq org-latex-to-pdf-process (list "latexmk -pdf -bibtex %f"))

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Setting up (or fixing) an encrypted swap partition

31 July 2013 / / 0 Comments

Today I tried to clone my laptop’s harddrive to a new drive (thanks to Lenovo for sending me a replacement since the old drive was showing signs of breaking down). At first I tried dd, but that failed at around 90%, either because the old disk is indeed failing or because something fishy with the USB connection or enclosure in which I put the new disk. So I started gparted to check which partitions were copied OK and which weren’t. It turns out that all partitions were fine, except for my (encrypted) swap partition. gparted didn’t even recognise the partition type (on the original drive!). So after I replaced the harddrive I wanted to recreate the encrypted swap partition. It turn’s out to be easy if you follow the steps outlined in this blog post from Puny Geek. Thanks Puny Geek!

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Fixing the NFS check plugin in Nagios (in Ubuntu)

11 June 2013 / / 0 Comments

For some time (probably after an upgrade, I actually don’t remember anymore) we had problems with the NFS check in Nagios on our Ubuntu 12.04 servers. The check would return UNKNOWN: RPC program nfs udp is not running. When running the actual check from the command line:

/usr/lib/nagios/plugins/check_rpc -H '$HOSTADDRESS$' -C nfs -c2,3

the output would be: Can't fork for rpcinfo.
It turns out that the file /usr/lib/nagios/plugins/utils.pm has the wrong path to the rpcinfo binary. Instead of /usr/sbin/rpcinfo it lists /usr/bin/rpcinfo. So, like most of the times, the fix is easy, but pinpointing the exact problem isn’t.

Don’t forget to restart Nagios after changing the path as utils.pm needs to be reloaded.

As Ubuntu is based on Debian, I expect this fix to work there as well. According to this Launchpad bug report this issue was fixed in January in version 1.4.16-1ubuntu1 of the nagios-plugins package, which is not in Ubuntu 12.04.

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Converting from bzr to git

6 June 2013 / / 0 Comments

I’m in the process of moving several of my projects that used Bazaar (bzr) for revision control to Git. Converting a repository from bzr to git is very easy when using the fastimport package. In a Debian-based distribution run the following command to install the package (don’t be fooled by its name, it also contains the fastexport option):

sudo aptitude install bzr-fastimport

The go into the directory that contains your bzr repo and run:

git init
bzr fast-export `pwd` | git fast-import

You can now check a few things, e.g. running git log to see whether the change log was imported correctly. This is also the moment to move the content of your .bzrignore file to a .gitignore file.

If all is well, let’s clean up:

rm -r .bzr 
git reset HEAD

Thanks to Ron DuPlain for his post here, from which I got most of this info.

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Solving “RTNETLINK answers: File exists” when running ifup

28 March 2013 / / 11 Comments

On a server with multiple network cards I tried to configure the eth3 interface by editing /etc/network/interfaces (this was an Ubuntu 12.04 machine).

This was the contents of /etc/networking/interfaces:

# The loopback network interface
auto lo
iface lo inet loopback

auto eth0
iface eth0 inet static
        address xxx.yyy.zzz.mmm
        netmask 255.255.255.0
        gateway xxx.yyy.zzz.1
        dns-nameservers xxx.yyy.zzz.aaa xxx.yyy.zzz.bbb
        dns-search mydomain.nl

auto eth3
iface eth3 inet static
        address 192.168.4.1
        netmask 255.255.255.0
        gateway 192.168.4.1

When I tried to bring the interface up I got an error message:

$ ifup eth3
RTNETLINK answers: File exists
Failed to bring up eth3.

It took me a while to figure it out, but the problem was the gw line in the eth3 entry. Of course you can only have one default gateway in your setup. I missed this because I was also trying to add routes to networks behind the machine on the other end of eth3.
In the end, removing the gw line in the eth3 entry solved the problem.

My final /etc/networking/interfaces looks like this:

# The loopback network interface
auto lo
iface lo inet loopback

auto eth0
iface eth0 inet static
        address xxx.yyy.zzz.mmm
        netmask 255.255.255.0
        gateway xxx.yyy.zzz.1
        dns-nameservers xxx.yyy.zzz.aaa xxx.yyy.zzz.bbb
        dns-search mydomain.nl

auto eth3
iface eth3 inet static
        address 192.168.4.1
        netmask 255.255.255.0
        post-up /sbin/route add -net 192.168.1.0 netmask 255.255.255.0 gw 192.168.4.250
        post-up /sbin/route add -net 192.168.2.0 netmask 255.255.255.0 gw 192.168.4.250
        post-up /sbin/route add -net 192.168.3.0 netmask 255.255.255.0 gw 192.168.4.250
        post-down /sbin/route del -net 192.168.1.0 netmask 255.255.255.0
        post-down /sbin/route del -net 192.168.2.0 netmask 255.255.255.0
        post-down /sbin/route del -net 192.168.3.0 netmask 255.255.255.0

Update 2013-08-19: Removed network entries as per Ville’s suggestion.

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Pairing a device with a Logitech unifying receiver in Linux

8 February 2013 / / 2 Comments

My girlfriend’s keyboard and mouse stopped working some time ago. It turned out that her Logitech unifying receiver (a small USB dongle for keyboard and mouse) was a bit broken, only when twisted in a certain way it would work. So, I called Logitech, explained the situation and they offered to send us a replacement for free. Well done Logitech support!

Now, since we both use Linux as our main OS, the question was how to pair the mouse and keyboard with the new receiver. Logitech provides a piece of Windows software, but nothing for Linux. It turns out it’s not that difficult and you can find various little C programmes that do it for you. I tried Travis Reeder’s solution and it worked like a charm on my Ubuntu 12.04 machine.

These are the steps I took.
First I switched off the keybord and the mouse, then ran the following:

$ git clone https://github.com/treeder/logitech_unifier.git
Cloning into 'logitech_unifier'...
remote: Counting objects: 35, done.
remote: Compressing objects: 100% (26/26), done.
remote: Total 35 (delta 11), reused 33 (delta 9)
Unpacking objects: 100% (35/35), done.
$ cd logitech_unifier/
$ ./autopair.sh 
Logitech Unified Reciever unify binary not compiled, attemping compilation
Logitech Unified Reciever unify binary was successfully compiled
Auto-discovering Logitech Unified Reciever
Logitech Unified Reciever found on /dev/hidraw0!
Turn off the device you wish to pair and then press enter
[sudo] password for lennart: 
The receiver is ready to pair a new device.
Switch your device on to pair it.

I ran the autopair.sh script twice, once for the mouse and once for the keyboard.

Thanks Travis!

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Comparing rsnapshot and obnam for scheduled large backups

4 January 2013 / / 4 Comments

Introduction

The home directories of the servers I administer at work total about 6.5TB of data. The home directories are stored on a file server (using ext4 partitions) and served to the other server over NFSv3 with a bonded 1Gbps LAN link.

As you all know backups are a good idea but how to implement a backup strategy for this kind of data? We decided quite early that using tapes as backup medium was out of the question. We simply can’t afford them given the amount of disk space we need. Moreover, tapes usually require operator involvement and neither me nor my colleague feels like going to the data centre every week. Our idea was to back up to another server with enough disk space in a different part of the data centre. For off-site backups we can always make an annual (maybe monthly) backup either on tape at SurfSARA/BigGrid or on a remote server.

Before implementing a given strategy several things need to be known and tested. The major questions we wanted to have an answer to were:

  1. How often do we want to backup the data? Daily snapshots? Weekly? Monthly?
  2. How many of the backups mentioned above do we want to keep? And for how long?
  3. In order to answer these questions (given a roughly fixed amount of backup space) we need to know
    • How much data changes per night/week/etc.
    • How much duplication is there in the data? How many people store the same file (or blocks, if you go for block-level deduplication)?
  4. Is NFS/network speed a limiting factor when running the backups?
  5. Can the tool preserve additional file system attributes like POSIX ACLS?

Candidates

After looking around the web and looking back at my own experiences I came up with three possible candidates. Each of them allows for backup rotation and preserves Posix ACLs (so points 1 and 5 above have been taken care of).

  1. Bacula: enterprise-level backup application that I’ve used in combination with tapes in the past. Easily supports multiple clients, tape robots, etc. No deduplication. All metadata etc. are stored in a (MySQL) database, so restoring takes some effort (and don’t forget to make a backup of the database as well!).
  2. rsnapshot: based on rsync, makes snapshots using hard links. Easy to restore, because files are simply copied to the backup medium.
  3. rdiff-backup: similar to rsnapshot, but doesn’t allow for removal of intermediate backups after a given time interval. Consequently it was the first candidate to fall of my list.
  4. Obnam: a young tool that promises block level data deduplication. Stores backed up data in its own file format. Tools for browsing those archives are not really well developed yet.

Tests

Because I already had quite some experience with Bacula but none with the other two candidates (although I use rsync a lot) I decided to start a test run with Obnam, followed by a run with rsnapshot. These are the results:

Obnam

After backing up /home completely (which took several days!), a new run, several days later took (timing by the Linux time command):

Backed up 3443706 files, uploaded 94.0 GiB in 127h48m49s at 214.2 KiB/s average speed830 files; 1.24 GiB (0 B/s)

real    7668m56.628s
user    4767m16.132s
sys     162m48.739s

From the obname log file:

2012-11-17 12:41:34 INFO VFS: baseurl=/home read=0 written=0
2012-11-21 23:09:36 INFO VFS: baseurl=/backups/backup_home read=2727031576964 written=150015706142
2012-11-21 23:09:36 INFO Backup performance statistics:
2012-11-21 23:09:36 INFO * files found: 3443706
2012-11-21 23:09:36 INFO * uploaded data: 100915247663 bytes (93.9846482715 GiB)
2012-11-21 23:09:36 INFO * duration: 460128.627629 s
2012-11-21 23:09:36 INFO * average speed: 214.179341663 KiB/s
2012-11-21 23:09:36 INFO Backup finished.
2012-11-21 23:09:36 INFO Obnam ends
2012-11-21 23:09:36 INFO obnam version 1.2 ends normally

So: ~5 days for backing up ~100 GB of changed data… Load was not high on the machines, neither in terms of CPU, nor in terms of RAM. Disk usage in /backups/backup_home was 5.7T, disk usage of /home was 6.6T, so there is some dedup, it seems.

rsnapshot

A full backup of /home to (according to the log file):

[27/Nov/2012:12:55:31] /usr/bin/rsnapshot daily: started
[27/Nov/2012:12:55:31] echo 17632 > /var/run/rsnapshot.pid
[27/Nov/2012:12:55:31] mkdir -m 0700 -p /backups/backup_home_rsnapshot/
[27/Nov/2012:12:55:31] mkdir -m 0755 -p /backups/backup_home_rsnapshot/daily.0/
[27/Nov/2012:12:55:31] /usr/bin/rsync -a --delete --numeric-ids --relative --delete-excluded /home /backups/backup_home_rsnapshot/daily.0/localhost/
[28/Nov/2012:23:16:16] touch /backups/backup_home_rsnapshot/daily.0/
[28/Nov/2012:23:16:16] rm -f /var/run/rsnapshot.pid
[28/Nov/2012:23:16:16] /usr/bin/rsnapshot daily: completed successfully

So: ~1.5 days for a full backup of 6.3TB. An incremental backup a
day later took:

[29/Nov/2012:13:10:21] /usr/bin/rsnapshot daily: started
[29/Nov/2012:13:10:21] echo 20359 > /var/run/rsnapshot.pid
[29/Nov/2012:13:10:21] mv /backups/backup_home_rsnapshot/daily.0/ /backups/backup_home_rsnapshot/daily.1/
[29/Nov/2012:13:10:21] mkdir -m 0755 -p /backups/backup_home_rsnapshot/daily.0/
[29/Nov/2012:13:10:21] /usr/bin/rsync -a –delete –numeric-ids –relative –delete-excluded –link-dest=/backups/backup_home_rsnapshot/daily.1/localhost/ /home /backups/backup_home_rsnapshot/daily.0/localhost/
[29/Nov/2012:13:25:09] touch /backups/backup_home_rsnapshot/daily.0/
[29/Nov/2012:13:25:09] rm -f /var/run/rsnapshot.pid
[29/Nov/2012:13:25:09] /usr/bin/rsnapshot daily: completed successfully

So: 15 minutes… and the changed data amounted to 21GB.

This gave me a clear winner: rsnapshot! Not only is it very fast, but given its simple way of storing data restoring a backup of any file is quickly done.

We now also have answers to our questions: Our daily changing volume is of the order of ~ 100GB, there isn’t much data that can be deduplicated. We also monitored the network usage and, depending on the server load it can be limiting, but since a daily differential backup takes only 15-30 minutes that isn’t a problem.
For a remote backup sever that was connected with a 100Mbps line we did see that the initial backup took a very long time. We should try to get a faster connection to that machine.

The future

The next challenge we face is how to back up some of the large data sets we have/produce. These include aligned BAM files of next-generation sequencing data, VCF files of the same data, results from genomic imputations (both as gzip-ed text files and as binary files in DatABEL format). This also totals several TB. Luckily these files usually don’t change on a daily basis.

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Booting an Ubuntu server with a degraded software RAID array

4 January 2013 / / 0 Comments

My home server runs Ubuntu 12.04 with a software RAID 5 array and since a couple of days I’ve been getting e-mails from the SMART daemon warning me of uncorrectable errors on one of the drives. Today I took the time to take the failing drive out and check it with the tools from the manufacturer.

Because I didn’t want to run the risk of unplugging the wrong drive with the system on (and thus losing the whole RAID array) I shut the server down, removed the harddrive and started it again. The idea was that it would boot right back into the OS, but with a degraded RAID array. Unfortunately the server didn’t come up… After connecting a keyboard and monitor to it it turned out that the system was waiting with an initramfs prompt. From there I could check that the RAID array was indeed degraded, but functioning fine as I could manually mount all partitions.

Some Googling later I found out that by default Ubuntu doesn’t boot into a degraded software RAID array. This is to make sure you as administrator know something is wrong. A good idea for a laptop or PC, but not for a standalone server. The solution is the following:

  • From the initramfs prompt mount your original filesystems, for example in /mnt.
  • Use chroot /mnt to change root into your server’s hard disks.
  • In the file /etc/initramfs-tools/conf.d/mdadm add or change the line to 
    BOOT_DEGRADED=true
  • Then run 
    update-initramfs -u

    to regenerate the initial ramdisk.

  • Type exit to exit the chroot environment.
  • Unmount your file systems and reboot

Now your server should continue booting even though it has a degraded RAID array.

Links

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ProbABEL v0.3.0 released

4 January 2013 / / 0 Comments

On New Year’s day I released version 0.3.0 of ProbABEL, almost two months after the previous release.

This update contains a few small bug fixes, but the most important feature of this new release is that thanks to the work of Maarten Kooyman we have a four to five-fold speed increase for the types of GWAS we run at work. In his e-mail to the GenABEL developers list he explains what he did to achieve this. The take-home-message of it is that you should always look for a suitable library for important tasks of any program you write. The old ProbABEL was based on a self-written matrix class that handled things like matrix multiplication and matrix subsetting. In the new release we make use of the Eigen C++ template library, maintained and developed by people who know much more about fast implementations of linear algebra than we do.

For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

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ProbABEL 0.2.2 released

21 November 2012 / / 1 Comment

On November 7th I released version 0.2.2 of ProbABEL, a set of programs that allow scientists (usually geneticists and epidemiologists) to run Genome-wide association studies (GWAS) in a fast and efficient way, even on machines with low amounts of RAM.

ProbABEL is part of the GenABEL suite, wich is a set of open source package for statistical genomics. Its main developer is Yurii Aulchenko, my former supervisor at the Erasmus Medical Centre.

This update contains a few small bug fixes and an update of the probabel.pl wrapper script that enables the use of chunked imputation output files as input. For more detailed changes, check the announcement.
For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

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