Open Source DNA

Yesterday I was a bit confused when I read this tweet. Manu Sporny, founder and CEO of Digital Bazaar, announced in his blog that he has published his genome..

He send some saliva to 23andme, they analyzed his DNA and provided his genetic code to him (let’s neglect the discussion whether data from 23andme-chips represent a fully sequenced genome..). This process is very smart and not expensive, so this part of his announcement is not spectacular. Lot’s of people are doing so.

The interesting part of this article: He published the results (roughly 1 million SNP markers) from 23andme as open source project to github, licensed under CC0! So he has released all his rights on this data.

In general a very impressing step, he might be the first person who published its DNA under such a license. His intentions are more than exemplary, providing access to genetic data to everyone that wants to work with it, i.e. researchers.

So far, so good, but there are some disadvantages, he still dealt with some of it. For example, what if anybody uses this information against him? I.e. healthcare provider, they might deny him to avoid high costs because they detected some pre-existing conditions in his DNA. It may also affect employment and can lead to discrimination. His reaction:

I’ve thought long and hard about each of those questions and the many more that you ask yourself before publishing this sort of personal data. There are large privacy implications in doing this. However, speaking solely for myself, I think the benefits outweigh the drawbacks.

Very nice, but there are also some ugly implications he apparently didn’t thought about! All these disadvantages don’t only affect himself, they may also affect relatives (children, parents, siblings..). Did they all agree with this publication?

I can’t see the advantages to an anonymously publication. Attach some demographic information like age, gender, educational background and everyone is satisfied. Then you don’t have to bear any consequences with bugs in your DNA.

With all due respect for his engagement, I think this step is not really sophisticated.

Valentine's Day

Yes, it’s that time again, Feb 14th.. It’s Valentine’s Day.

Don’t know who has told my wife, but now I have to do some love, uuurgh..

How ever, this one is for my little valentine:

'            01110000  01101111
                     10                                   '

Love you soo much, of course! ;-)

PS. If you are able to catch one of these flower or praline seller: beat the living daylights out of them!!

java.lang.OutOfMemoryError: Java heap space

I was just contacted concerning this Java memory problem, here is how you can get rid of it.

The amount of Ram for an Java application is limited by the JVM. To provide more memory to a single application you can start your Java process with two more parameters, like:

java -Xms1024m -Xmx1024m YOUR_JAVA_CALL

This allows Java to use up to 1024 MB. Here -Xms specifies the initial heap size, while -Xmx determines the maximum size. For machines with much more mem you might use g instead of m to set the size in gig’s. So -Xmx10g limits the amount of RAM to 10 GB.

Of course it’s annoying to apply these parameters to all your Java runs, so to change this behavior user-wide, you may create an alias like:

alias java='java -Xms1024m -Xmx1024m'

or better: Tell it to the Java Plugin Control Panel! Using XFCE you can find this tool in your panel’s menu in the Settings section. Gnome users may look in System > Preferences. If you don’t want to move your mouse you can also run ControlPanel from your terminal. This opens a window, default parameters can be applied in the tab Java, click View… and add your parameters to the Runtime Parameters column. This tool afterwards writes something like the following line to $HOME/.java/deployment/ :

deployment.javaws.jre.0.args=-Xmx9234m -Xms9234m

So advanced users craving for trouble may edit this file on it’s own :-P

MySQL upgrade failed

Still upgrading some of our servers from lenny to squeeze, actually I run into MySQL trouble…

While upgrading from the package mysql-server 5.0.51a-24+lenny5 -> 5.1.49-3 aptitude told me the following:

Setting up mysql-server-5.1 (5.1.49-3) ...
Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld . . . . . . . . . . . . . . failed!
invoke-rc.d: initscript mysql, action "start" failed.
dpkg: error processing mysql-server-5.1 (--configure):
 subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.1; however:
  Package mysql-server-5.1 is not configured yet.
dpkg: error processing mysql-server (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:

Mmh, a look into the /var/log/syslog pointed to the following errors:

Feb 11 20:50:11 HOST /etc/init.d/mysql[13219]: 0 processes alive and '/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf ping' resulted in
Feb 11 20:50:11 HOST /etc/init.d/mysql[13219]: ^G/usr/bin/mysqladmin: connect to server at 'localhost' failed
Feb 11 20:50:11 HOST /etc/init.d/mysql[13219]: error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'
Feb 11 20:50:11 HOST /etc/init.d/mysql[13219]: Check that mysqld is running and that the socket: '/var/run/mysqld/mysqld.sock' exists!
Feb 11 20:50:11 HOST /etc/init.d/mysql[13219]:
Feb 11 20:50:59 HOST mysqld_safe: Starting mysqld daemon with databases from /var/lib/mysql
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59 [Note] Plugin 'FEDERATED' is disabled.
Feb 11 20:50:59 HOST mysqld: /usr/sbin/mysqld: Table 'mysql.plugin' doesn't exist
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59  InnoDB: Started; log sequence number 0 657837804
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59 [ERROR] /usr/sbin/mysqld: unknown option '--skip-bdb'
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59 [ERROR] Aborting
Feb 11 20:50:59 HOST mysqld:
Feb 11 20:50:59 HOST mysqld: 110211 20:50:59  InnoDB: Starting shutdown...
Feb 11 20:51:05 HOST mysqld: 110211 20:51:05  InnoDB: Shutdown completed; log sequence number 0 657837804
Feb 11 20:51:05 HOST mysqld: 110211 20:51:05 [Note] /usr/sbin/mysqld: Shutdown complete
Feb 11 20:51:05 HOST mysqld:
Feb 11 20:51:05 HOST mysqld_safe: mysqld from pid file /var/run/mysqld/ ended
Feb 11 20:51:14 HOST /etc/init.d/mysql[13584]: 0 processes alive and '/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf ping' resulted in
Feb 11 20:51:14 HOST /etc/init.d/mysql[13584]: ^G/usr/bin/mysqladmin: connect to server at 'localhost' failed
Feb 11 20:51:14 HOST /etc/init.d/mysql[13584]: error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'
Feb 11 20:51:14 HOST /etc/init.d/mysql[13584]: Check that mysqld is running and that the socket: '/var/run/mysqld/mysqld.sock' exists!
Feb 11 20:51:14 HOST /etc/init.d/mysql[13584]:

Many messages at once.. To make a long story short the main problem is this line:

Feb 11 20:50:59 vs-inf-www mysqld: 110211 20:50:59 [ERROR] /usr/sbin/mysqld: unknown option '--skip-bdb'

So edit your /etc/mysql/my.cnf and comment the following line (in my configuration it’s line 94):


That’s it, retry to configure the new version and everything will turn out all right.

Apache not parsing PHP files

I just had a confusing problem: instead of interpreting PHP-scripts in our webserver’s userdir apache serves them for download!

It’s caused by an upgrade from lenny to squeeze and I spend a lot of ours with fixing.

This is really a serious problem, these sites aren’t able to read for those people/search engines etc. that are browsing and, more fatal, if clients are able to access the PHP code of our students/staff they might explore security issues or passwords stored in these PHP files, so first of all I disabled the public access to the webserver.

So what was the problem? When I recognized that phpMyAdmin and other not userdir related stuff still works fine, I searched for issues that differ for userdirs. At long last I took a look into the libapache2-mod-php5 config file located in /etc/apache2/mods-available/php5.conf :

<IfModule mod_php5.c>
    <FilesMatch "\\.ph(p3?|tml)$">
        SetHandler application/x-httpd-php
    <FilesMatch "\\.phps$">
        SetHandler application/x-httpd-php-source
    # To re-enable php in user directories comment the following lines
    # (from <IfModule ...> to </IfModule>.) Do NOT set it to On as it
    # prevents .htaccess files from disabling it.
    <IfModule mod_userdir.c>
        <Directory /home/*/public_html>
            php_admin_value engine Off

As you can see, PHP is disabled if the userdir module was enabled… Disgusting! Commenting these lines out switched PHP for users on. Very annoying!

It's squeeezzed

Yes, Debian’s 6th release, codename squeeze, has become stable yesterday!

Those of you following Debian on twitter should have noticed yet, they announced it in about 4 million tweets ;-)

To mark the occasion the also redesigned the whole web presence, just take a look at their new layout!

This article is just a small THANK YOU to the whole Debian team, they are working hard to make your life much more comfortable! Great work guys!

By the way I send some greetings to all the administrators out there running Debian. Just have a look at figure 1 :-P

freiesMagazin 02/2011 published

The journal freiesMagazin just published it’s February issue, describing all the bots that took part in the programming contest.

Those of you that aren’t convinced by this topic, they also have a nice article about VirtualBox and KVM! So go out and grab a copy!

X deletes input devices

Today I restarted my notebook to boot into another kernel. Unfortunately I couldn’t log-in to the desktop because neither the mouse nor the keyboard was working. The Xorg.log gave me a hint what happened.

That all affected my GRML installation. Unfortunately you can’t change to a virtual terminal while there is no keyboard control, so to change anything you have to connect via SSH or boot from live CD or USB. The error reported in /var/log/Xorg.0.log looks like:

(WW) AllowEmptyInput is on, devices using drivers 'kbd', 'mouse' or 'vmmouse' will be disabled.
(WW) Disabling Mouse0
(WW) Disabling Keyboard0

So you see, all input device are turned off. Annoying!! To avoid this problem you have to add the following section to your /etc/X11/xorg.conf :

Section "ServerFlags"
        Option "AutoAddDevices" "False"
        Option "AllowEmptyInput" "false" 

That should solve the problem. If you don’t have a xorg.conf yet you can create one with:

Xorg -configure

This will create /root/ , so you just have to copy it to /etc/X11/xorg.conf .

Since it was the first reboot for about 30 days and I updated/installed a lot of new software, so I’m not able to blame anyone generating this bug. But if you are feel free to do so ;-)

Alternative to vzprocps

As far as I know the OpenVZ associated vzprocps-tools are just available in version 2.0.11, at least for Debian. Unfortunately they are damn buggy in this version, so unusable…

There are two smart tools included in vzprocps : vztop and vzps . These programs help you a lot dealing with processes of your running containers. But in 2.0.11 they aren’t working:

root@serv: ~ $ vzps
Segmentation fault
root@serv: ~ $ vztop
 00:29:11  up 1 day,  5:18,  3 users,  load average: 1.14, 1.26, 1.23
1949 processes: 1946 sleeping, 2 running, 1 zombie, 0 stopped
CPU0 states:   0.1% user   0.1% system    0.0% nice   0.0% iowait  98.0% idle
CPU1 states:   4.1% user  15.0% system    0.0% nice   0.0% iowait  80.0% idle
CPU2 states:   2.0% user   3.0% system    0.0% nice   0.0% iowait  94.0% idle
CPU3 states:  14.0% user  20.1% system    0.0% nice   0.0% iowait  64.1% idle
Segmentation fault
root@serv: ~ $

It seems that there is an update, but not available as .deb yet. Here is an example for an alternative to vzps to find zombies:

CONTAINER=$(/usr/sbin/vzlist | /bin/grep running | /usr/bin/awk '{print $5}')
for ct in $CONTAINER;
	echo "processing: $ct";
	/usr/sbin/vzctl exec $ct '/bin/ps -ef | /bin/grep defunct';

It’s a bit complicated, but you can write a small script to grep for further things..

YEAH - second in fM contest

As I announced I took place in a programming contest organized by freiesMagazin. In the end I’m proud to tell you I’m second!

I still explained my tactics and my map parsing and all in all five other programmers joined this contest. Today the editorial staffs announced the results:

RankingProgrammer(s)Score in 2500 games
1.Demel and Keiblinger232.595,79

You see I wasn’t able to obtain half of the points of Demel and Keiblinger, looking to the results for each game there was no chance for my bot to beat them. But nevertheless I won the second rank! I couldn’t find any contact information of these guys so I wasn’t able to congratulate personally but if they read this article: Nice work guys ;-) Of course congratulations to the other programmers, even if you didn’t win, taking place is what counts!

By the way the organizer informed me about an IndexOutOfBoundsException in , so that my bot quit working 17 times. But I won’t update my code since it has no sence beyond this contest… It’s just to inform you.

Last but not least my thanks goes to the freiesMagazin itself. It was a very nice contest and I’m really happy about the voucher! I still have a good idea what to buy :-P

P.S.: Since both programmers on the first rank should split their voucher of 50 €, they both won a voucher of 25 €. That means with a voucher of 30 € I won the biggest value ;-)