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:

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:

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
2.Scharm104.412,12
3.Kirsch98.675,43
4.Pirra97.129,97
5.Robbert75.739,36
6.Schulz35.854,39

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 de.binfalse.martin.fmcontest.map.DMap.dirTo(DMap.java:192) , 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 ;-)

apt-get install WP

Finally I also upgraded my blog to Wordpress@3.0.4, eliminating a critical bug.

Rumpel frequently reminded me to do that, but I was too lazy to find my own modifications to the WP core… But today I did! And thinking ahead, here I record what I’m changing to this version! Majorly for me, but maybe you like it ;-)

Display whole tag cloud in wp-admin

When you create an article WP by default only displays the 45 most-used tags in the sidebar. I want to see all of them:

File to change: wp-admin/includes/meta-boxes.php

File to change: wp-admin/admin-ajax.php

Remove http:// from JavaScript prompts

If I want to insert a link into an article I often use the button above the textarea. It’s very friendly from WP to remind the users to start links with http:// , but for me it’s only disgusting because I usually copy&paste the URL from the browsers address bar and have to delete the http:// from the pop-up… To delete them permanently edit wp-includes/js/quicktags.js . Unfortunately this script is just one line, so a diff won’t help you, but I can give you a vim substitution command:

Update 07. July 2011: For WP > 3.2 you also need to apply this regex for wp-includes/js/tinymce/plugins/wplink/js/wplink.js to also eliminate this disgusting http:// from the new link-overlay…

ShortCut[GPG]: Mysterious crypto mails

When I write mails to people for the first time they usually answer them immediately with something like

What is that crazy crypto stuff surrounding your mails? Wondering why I can't read it!?

There are lots of legends out there belonging to this clutter, most of them are only fairy tales, here is the one and only true explanation!

As a friend of security I always try to encrypt my mails via GPG. That is only possible if the recipient is also using GPG and I have his/her public key. If this is not the case, I just sign my mail to give the addressee the chance to verify that the mail is from me and nobody else on its way has modified the content of the mail. So the clutter is the electronic signature of the mail! It’s a simple ASCII code, however not readable for human eyes but readable for some intelligent tools.

There are two kinds of signatures:

• inline signature: it surrounds the message with cryptographic armor. That has the disadvantage that you can't sign attachments or HTML mails and the text is more or less hidden between PGP-goodies.
• attached signatures: the crypto stuff is attached as signature.asc. With the disadvantage that mailservers may be alarmed from this attachment and drop the mail.

Since I usually write ASCII mails without attachments I sign them inline. Such a signed mail that reaches your inbox may look like:

Depending on the used mail-client I usually also attach my public key, so if you’re using a mail-client that is able to handle GPG signed/encrypted mails it should parse the crypto stuff and verify whether the signature is correct or not. In this case the mail will be collapsed so that you’ll see something like this (with an indication whether the signature was valid or not):

But if you’re using a client that doesn’t ever heard about GPG it won’t recognize the cryptographic parts and you’ll only see lot’s of clutter. In this case I recommend to change the mail-client! ;-)

web content anlayzer

Just developed a small crawler to check my online content at binfalse.de in terms of W3C validity and the availability of external links. Here is the code and some statistics…

The new year just started and I wanted to check what I produced the last year in my blog. Mainly I wanted to ensure more quality, my aim was to make sure all my blog content is W3C valid and all external resources I’m linking to are still available. First I thought about parsing the database-content, but at least I decided to check the real content as it is available to all of you. The easiest way to do something like this is doing it with Perl, at least for me. The following task were to do for each site of my blog:

• Check if W3C likes the site
• For each link to external resources: Check if they respond with 200 OK
• For each internal link: Check this site too if not already checked

While I’m checking each site I also saved the number of leaving links to a file to get an overview. Here is the code:

You need to install LWP::UserAgent , XML::TreeBuilder and WebService::Validator::HTML::W3C . Sitting in front of a Debian based distribution just execute:

The script checks all sites that it can find and that match to

So adjust the $domain variable at the start of the script to fit your needs. It writes all W3C results to /tmp/check-links.val , the following line-types may be found within that file: So it should be easy to parse if you are searching for invalids. Each external link that doesn’t answer with 200 OK produces an entry to /tmp/check-links.fail with the form Additionally it writes for each website the number of internal links and the number of external links to /tmp/check-links.log . If you want to try it on your site keep in mind to change the content of $domain and take care of the pattern in line 65:

Because I don’t want to check internal links to files like .png or .tgz the URL has to end with / . All my sites containing parseable XML end with / , if your sites doesn’t, try to find a similar expression.

As I said I’ve looked to the results a bit. Here are some statistics (as at 2011/Jan/06):

 Processed sites 481 Sites containing W3C errors 38 Number of errors 63 Mean error per site 0.1309771 Mean of internal/external links per site 230.9833 / 15.39875 Median of internal/external links per site 216 / 15 Dead external links 82 Dead external links w/o Twitter 5

Most of the errors are now repaired, the other ones are in progress. The high number of links that aren’t working anymore comes from the little twitter buttons at the end of each article. My crawler is of course not authorized to tweet, so twitter responds with 401 Unauthorized . One of the other five fails because of a cert problem, all administrators of the other dead links are informed.

I also analyzed the outgoing links per site. I’ve clustered them with K-Means, the result can be seen in figure 1. How did I produce this graphic? Here is some R code:

You’re right, there is a lot stuff in the image that is not essential, but use it as example to show R beginners what is possible. Maybe you want to produce similar graphics!?

Pre- and Post-suspend

Today I got another complaint in a row of complaints of my Jabber contacts, arguing that they can’t send me messages although my account seems to be online in their buddy list. That happens when I put my notebook to sleep, this time I got informed by Micha.

Here are 3 steps to patch this problem, dealing with gajim-remote, PowerManagement-Utils and DBus.

This annoying events happens when I was online with my notebook and close the lid so the notebook goes sleeping. Unfortunately my Jabber client Gajim doesn’t notice that I’m going to disconnect and so the Jabber server isn’t informed about my absence. Due to connection instabilities the server waits some time of inactivity until it recognizes that there is really no more client before it tells all my friends I’m gone. During this time I appear online but messages are not able to reach my client, so they are lost in hell. That sucks, I know, and now I’ve reacted.

First of all I checked how to tell Gajim to disconnect via command line and found the tool gajim-remote , it comes with Gajim itself. Here are some examples of using it:

Ok, so far, next task is to understand what is done when the lid is closed. The task to suspend or hilbernate is, at least in my case, done by pm-utils (PowerManagement-Utils). It comes with some tools like pm-suspend or pm-hibernate and so on. To tell these tools to do something before respectively after suspending there is a directory in /etc/pm/sleep.d . Here You can leave some script that look like those in /etc/init.d/* . Here is a smart example now located in /etc/pm/sleep.d/01users on my notebook, you can use it as skeleton:

Make it executable and give it a try. It checks for each logged-in user whether there is a .suspend or .awake in its $HOME to execute it before suspending respectively after resuming. Next step is telling Gajim to change its status. Unfortunately the gajim-remote script is speaking to the running Gajim-instance via DBus. You may have heard about DBus, there are two main options of DBus buses: system- and session-bus. To speak to Gajim you use the session DBus and need the bus address. That is a problem, this address is acquired while your X-login, and you don’t know it from a remote session or if the system executes scripts while suspending. So if you just try to execute gajim-remote change_status offline in your .suspend you’ll get an error like D-Bus is not present on this machine or python module is missing or Failed to open connection to "session" message bus . Your DBus session address within an X-session is set in your environment in $DBUS_SESSION_BUS_ADDRESS ( echo $DBUS_SESSION_BUS_ADDRESS ). So what are your options to get this address for your .suspend script? • You can export your env to a file when you login (maybe automatically via .xinitrc ) to parse it • All addresses are saved in $HOME/.dbus/session-bus/ , so try to find the right one..
• Get it from a process environment

The last possibility is of course the nicest one. So check if Gajim is running and extract the DBUS_SESSION_BUS_ADDRESS from /proc/GAJIM_PID/environ ! Here is how it can be done:

That’s it, great work! Save this file in $HOME/.suspend and give it the right for execution. You can also write a similar script for $HOME/.awake to reconnect to your Jabber server, but you eventually don’t want to reconnect each time you open the lid..

So the next time I close my laptops lid Gajim disconnects immediately! No annoyed friends anymore :P

ShortCut[image]: ScreenShooting a JPanel

This is about taking a screenshot of a JPanel to save the visible stuff as an image to disk.

Sometimes it may happen that you create a swing GUI with a panel to draw cool stuff. Here you can learn how to let the user take a screenshot of this graphic with a single click on a button.

First of all create such a JPanel and fill it with crazy graphics, then create a BufferedImage with the size of the panel and tell the panel to draw its content to this image instead of printing the content to the screen and, last but not least, save this image:

You see it’s very simple. Of course it’s also possible to create other types of image with ImageIO, like JPEG or GIF, but for more information take a look in the documentation. In a project that will be published you should think about using a JFileChooser instead of hard coding the name of the new image ;-)

Just dealt with an annoying topic: How to add a link to a Java swing frame. It’s not that hard to create some blue labels, but it’s a bit tricky to call a browser browsing a specific website…

As I mentioned the problem is to call the users web browser. Since Java SE 6 they’ve added a new class called Desktop. With it you may interact with the users specific desktop. The call for a browser is more than simple, just tell the desktop to browse to an URL:

Unfortunately there isn’t support for every OS, before you could use it you should check if it is supported instead of falling into runtime errors..

So far.. But what if this technique isn’t supported!? Yeah, thats crappy ;) You have to check which OS is being used, and decide what’s to do! I searched a little bit through the Internet and developed the following solutions:

Combining these solutions, one could create a browse function. Extending the javax.swing.JLabel class, implementing java.awt.event.MouseListener and adding some more features (such as blue text, overloading some functions…) I developed a new class Link, see attachment.

Of course it is also attached, so feel free to use it on your own ;)

Unfortunately I’m one of these guys that don’t have a Mac, shame on me! So I just could test these technique for Win and Linux. If you are a proud owner of a different OS please test it and let me know whether it works or not. If you have improvements please tell me also.

Revived iso2l

Someone informed me about a serious bug, so I spent the last few days with rebuilding the iso2l.

This tool was a project in 2007, the beginning of my programming experiences. Not bad I think, but nowadays a pharmacist told me that there is a serious bug. It works very well on small compounds, but the result is wrong for bigger molecules.. Publishing software known to fail is not that nice and may cause serious problems, so I took some time to look into our old code…

Let me explain the problem on a little example. Let’s denote the atom Carbon $\text{C}$ has two isotopes. The first one $\text{C}^{12}$ with a mass of 12 and an abundance of 0.9 and another one $\text{C}^{13}$ with a mass of 13 and an abundance of 0.1 (these numbers are only for demonstration). Let’s further assume a molecule $\text{C}_{30}$ consisting of 30 Carbon atoms. Since we can choose from two isotopes for each position in this molecule and each position is independent from the others there are many many possibilities to create this molecule from these two isotopes, exactly $2^{30}=1073741824$. Let’s for example say we are only using 15 isotopes of $\text{C}^{12}$ and 15 isotopes of $\text{C}^{13}$, there still exists $\frac{30!}{15!\cdot 2} = 155117520$ combinations of these elements. Each combination has an abundance of $0.9^{15} \cdot 0.1^{15} \approx 2.058911 \cdot 10^{-16}$.

Unfortunately in the first version we created a tree to calculate the isotopic distribution (here it would be a binary tree with a depth of 10). If a branch has an abundance smaller than a threshold it’s cut to decrease the number of calculations and the number of numeric instabilities. If this thresh is here $10^{-10}$ none of these combinations would give us a peak, but if you add them all together (they all have the same mass of $15 \cdot 12 + 15 \cdot 13 = 375$) there would be a peak with this mass and an abundance of $\frac{30!}{15!\cdot 2} \cdot 0.9^{15} \cdot 0.1^{15} \approx 3.193732 \cdot 10^{-8} > 10^{-10}$ above the threshold. Not only the threshold is killing peaks. This problem is only shifted if you decrease the thresh or remove it, because you’ll run in abundances that aren’t representable for your machine, especially in larger compounds (number of carbons > 100). So I had to improve this and rejected this tree-approach.

And while I’m touching the code, I translated the tool to English, increased the isotopic accuracy and added some more features. In figure 1 you can see the output of version 1 for $\text{C}_{150}$. As I told this version loses many peaks. I contrast you can see the output of version 2 for the same compound in figure 2. Here the real isotopic cluster is visible.

Please try it out and tell me if you find further bugs or space for improvements or extensions!

FM-Contest: Mappings

As you know, I took part in the programming contest organized by freiesMagazin. I still presented the tactics of my bot, here is how I parse the maps.

The maps are very simple, there are just two types of fields: wall and floor. Walls aren’t accessible and block views. Bots can just move through floor-fields, but these fields are toxic, so they’ll decrease the health of a bot. This toxicity should be kept in mind while programming an AI, but shouldn’t play any role in this article. Here is an example how a map is presented to the bot (sample map provided by the organizers):

The number sign (#) identifies walls, spaces are floor fields. The task is to get the bot understanding the maps topology. It’s a big goal if you can split the map to areas or rooms to know whether you’re in the same room as an opponent and what’s the best possibility to change the room. I’ll explain my statements on a very simple example:

You’ll immediately see there are two rooms, one major one and a small lumber room at the bottom right corner of the map. But how should the bot see it!?

My first attempt was to build rooms based on horizontal and vertical histograms of wall-fields. Something like image processing.. This attempt was fast rejected, inefficient and not rely good working.

The second idea was to sample way-points to the map and building rooms based on visibility between these points. I’ve read that autonomous vacuum cleaners are working based on this technique ;-)

One night later I found a much better solution, it’s based on divisive clustering. Starting with the whole map repeat the following steps recursively:

• Is this part of the map intersected by a wall-field?
• YES: If this part is larger than a threshold split this part of the map in four parts with ideally same size and repeat this algorithm with each part, otherwise stop
• NO: We found a room! Label all its fields and try to connect it to the left, right, bottom and top if there are no walls intersecting

If this is done, we’ve found the main parts of each room. After wards I try to expand each room to neighbor fields that are unlabeled and doesn’t have neighbors with different labels. Fields that are connected to more than one room are doors.

To explain the idea of the algorithm I’ll present the procedure on my small example. At the beginning there are of course intersecting wall-fields, so it is split into four parts. Three of them aren’t intersected anymore, so they are labeled:

Since the rooms with label 1, 2 and 3 are connected and not intersected by a wall-field, they are merged together:

But the fourth part contains wall fields, so it is split into four more parts. Three of them are still intersected, but one gets labeled:

Splitting the remaining parts give to small rooms, so they are rejected by the size-threshold. So we try to expand the found rooms and end in the following situation:

Here D represents a door. Doors are saved separately to remember how rooms are connected and know the possibilities of fleeing out of a room if a predator comes in to catch you…

All this parsing is done in a separate thread, so the bot is able to do it’s work even if the maps are large and take a long time to parse… Of course here is a lot of space for improvements, but for this contest it is enough I think.

Unfortunately I cant recommend further readings, I don’t know any previous work like this.