Boot messages to service console

You may have heard about management consoles!? If a server is dead you can revive it via service console without driving the long way to the data center (often miles away).

While logged into the service console you of course have the chance to reboot the machine itself. To get to know what it is doing while booting you may want to see all the messages that are usually prompted to the terminal at the attached monitor. Unfortunately you aren’t next to the machine, and so there is no monitor attached to it, but you can force grub to prompt all messages both to terminal and to service console.

First of all you have to setup the serial console:

serial --unit=0 --speed=57600 --word=8 --parity=no --stop=1

The --unit parameter determines the COM port, here it’s COM1, if you need COM2 you should use --unit=1 . --speed defines a baud rate of 57600 bps, see your manual. To learn more about the other parameter you are referred to the Grub manual for serial. Next you have to tell Grub where to write the output:

terminal --timeout=5 console serial

This line tells grub that there are two devices, the typical console on the attached screen and our previous defined serial console. With this directive Grub waits 5 seconds for any input from serial console or the attached keyboard and will print its menu to that device where the input was generated. That means if you’re at home and press any key, Grub will show you all outputs to your serial connection, but your student assistant (who had to go to the server, by bike while raining!!) isn’t able to see whats happening. But if your assistance is faster than you and hits a key on the physically attached keyboard, he’ll see anything and you’ll look through a black window… If nobody produces any input the output is written to that device that is listed first.

Last but not least you have to modify the kernel sections of the boot menu and append something like that at the end of every kernel line:

console=tty0 console=ttyS0

That tells grub that all kernel messages should be printed to both the real console of the attached screen and the serial console. Keep in mind to modify ttyS0 to match your serial port (here it is COM1). Grub decides for the device that is listed last to also send all stdin/stdout/stderr of the init process, that means only the last device will act as interactive terminal. E.g. checks of fsck are only printed to the last device, so stay calm if nothing happen for a long time on the other one ;-)

Here is a valid example for copy and paste:

# init serial console
serial --unit=0 --speed=57600 --word=8 --parity=no --stop=1
# what device to use for grub menu!?
terminal --timeout=5 console serial
# ....
title           Debian GNU/Linux, LOCAL CONSOLE
root            (hd0,0)
kernel          /vmlinuz-SOMEWHAT-openvz-amd64 root=UUID=AAAAAAAA-BBBB-CCCC-DDDD-EEEEEEEEEEEE ro console=ttyS0 console=tty0
initrd          /initrd.img-SOMEWHAT-openvz-amd64

title           Debian GNU/Linux, LOCAL CONSOLE
root            (hd0,0)
kernel          /vmlinuz-SOMEWHAT-openvz-amd64 root=UUID=AAAAAAAA-BBBB-CCCC-DDDD-EEEEEEEEEEEE ro console=tty0 console=ttyS0
initrd          /initrd.img-SOMEWHAT-openvz-amd64

Here both Grub entries are booting the same kernel, but the first one will use the local console as interactive terminal whether the other entry takes the serial console for interactions.

ShortCut[xtrlock]: Avoid Xscreensaver

By default Xfce provides screen-locking via Xscreensaver. Here is how you change it.

Xfce runs a script called xflock4 to lock the screen, to change the default behavior just foist another script on Xfce! The default path settings for searching for this executable shows, that /usr/local/bin has higher priority than /usr/bin (here is the original xflock4 located). The rest should be clear!

E.g. to use xtrlock instead of Xscreensaver you just have to link to the binary:

% ln /usr/bin/xtrlock /usr/local/bin/xflock4

On a multiuser system you may allow each user to use it’s own locking-solution. So just write a script that checks if $HOME/.screenlock is executable and runs it or falls back to a default screensaver:


# default

# does user want smth else??
[ -x $HOME/.screenlock ] && DO=$HOME/.screenlock


Save it executable as /usr/local/bin/xflock4 - done…

Homage to floating points

I recently got very close to the floating point trap, again, so here is a little tribute with some small examples!

Because Gnu R is very nice in suppressing these errors, all examples are presented in R.

Those of you that are ignorant like me, might think that 0.1 equals 0.1 and expect 0.1==0.1 to be true, it isn’t! Just see the following:

> a=0.1
> b=0.3/3
> a
[1] 0.1
> b
[1] 0.1
> a==b

You might think it comes from the division, so you might expect seq(0, 1, by=0.1) == 0.3 contains exactly one vale that is TRUE !? Harrharr, nothing like that!

> seq(0, 1, by=0.1) == 0.3

Furthermore, what do you think is the size of unique(c(0.3, 0.4 - 0.1, 0.5 - 0.2, 0.6 - 0.3, 0.7 - 0.4)) !? Is it one? Not even close to it:

> unique(c(0.3, 0.4 - 0.1, 0.5 - 0.2, 0.6 - 0.3, 0.7 - 0.4))
[1] 0.3 0.3 0.3

Your machine is that stupid, that it isn’t able to save such simple numbers ;) And another example should show you how these errors sum up:

> sum=0
> for (i in 1:100) sum = sum + 0.01
> sum
[1] 1
> print(sum, digits=16)
[1] 1.000000000000001

As you can see, R tells you that you summed up to exactly one, suppressing the small numerical error. This error will increase with larger calculations! So be careful with any comparisons. To not fail the next time, for example use the R build-in function all.equal for comparison:

> unique(c(0.3, 0.4 - 0.1, 0.5 - 0.2, 0.6 - 0.3, 0.7 - 0.4))
[1] 0.3 0.3 0.3
> all.equal(0.3, 0.4 - 0.1, 0.5 - 0.2, 0.6 - 0.3, 0.7 - 0.4)
[1] TRUE

Or, if you’re dealing with integers, you should use round or as.integer to make sure they really are integers.

I hope I could prevent some of you falling into this floating point trap! So stop arguing about numerical errors and start caring for logical fails ;-)

Those of you interested in further wondering are referred to [Mon08].


David Monniaux. The pitfalls of verifying floating-point computations. ACM Trans. Program. Lang. Syst., 30(3):1–41, 2008.

ShortCut[R]: locator

Welcome to my new category: ShortCut! Here I’ll shortly explain some smart features, unknown extensions or uncommon pathways of going for gold. Today it’s about the Gnu R tool locator.

With locator you are able to detect the mouse position inside you plot. Just run locator() and click some points, when you’re finished click the right button and locator will print the x - and y -values of the clicked positions. With this tool it’s possible to visually validate some numerical calculation.

With a little bit more code, you can output the coordinates right into you plot:

> x<-seq (0, 10, .01)
> plot (x, dgamma (x, rnorm (1, 2, 0.5), rnorm (1, 1, 0.5)), t='l', main='any curve', ylab='y')
> text (p<-locator (1), paste (p, collapse="\\n"), adj=0)

With a click into the plot you’ll be able to create a result like figure 1.

RNA-Seq - introducing Galaxy

I’m actually attending a lecture with the great name RNA-Seq, dealing with next generation sequencing (NGS). I think the lecture is more or less addressed to biological scientist and people who are working with genome analyzers, but I think there is no harm in visiting this lecture and to get to know the biologists point of view.

These scientists are using different sequencing platforms. Some popular examples are Roche 454, Illumina/Solexa, ABI SOLiD, Pacific Biosciences PacBio RS, Helicos HeliScope™ Single Molecule Sequencer or Polonator, but there are much of more such platforms. If you are interested in these different techniques, you are referred to [Met09]. There is no standard, so all these machines produce output in different formats and quality. In general you’ll get a fastq file as result of sequencing. This file contains roughly more or less small reads of sequences and a quality score of each recognized nucleotide. The quality score is encoded in ASCII characters and contains four line types. Here is an example of such a file:

@SRR039651.1 HWUSI-EAS291:8:1:1:356
@SRR039651.2 HWUSI-EAS291:8:1:1:410
@SRR039651.3 HWUSI-EAS291:8:1:1:1018

As you can see, in general the file contains an identifier line, starting with @ , the recognized sequence, a comment, starting with + , followed by the quality score for each base. It’s a big problem that there is no common standard for these quality scores, they differ in domain depending on the sequencing platform. So the original Sanger format uses PHRED scores ([EG98] and [EHWG98]) in an ASCII range 33-126 ( ! - ~ ), Solexa uses Solexa scores encoded in ASCII range 59-126 ( ; - ~ ) and with Illumina 1.3+ they introdused PHRED scores in an ASCII range 64-126 ( @ - ~ ). So you sometimes won’t be able to determine which format your fastq file comes from, the Illumina scores can be observed by all of this three example. If you want to learn more about fastq files and formats you are referred to [CFGHR10]. Interested readers are free to translate the ASCII coded quality scores of my small example to numerical quality scores and post the solution to the comment!

There is a great tool established to work with these resulting fastq files (this is just a small field of application): Galaxy. It is completely open source and written in Python. Those who already worked with it told me that you can easily extend it with plug-ins. You can choose wheter to run your own copy of this tool or to use the web platform of the Penn State. There’s a very huge ensemble of tools, I just worked with a small set of it, but I like it. It seems that you are able to upload unlimited size of data and it will never get deleted!? Not bad guys! You can share your data and working history and you can create workflows to automatize some jobs. Of course I’m excited to write an en- and decoder for other data like videos or music to and from fastq - let’s see if there’s some time ;-)

But this platform also has some inelegance’s. So there is often raw data presented in an raw format. Have a look at figure 1, you can see there is a table, columns are separated by tabs, but if one word in a column is much smaller/shorter as another one in this column this table looses the human readability! Here I’ve colorized the columns, but if the background is completely white, you have no chance to read it.

So instead of getting angry I immediately wrote a user-script. It adds a button on the top of pages with raw data and if it is clicked, it creates an HTML table of this data. You can see a resulting table in figure 2. If you think it is nice, just download it at the end of this article.

All in all I just can estimate what’s coming next!


Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, and Peter M. Rice. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6):1767–1771, April 2010.
Brent Ewing and Phil Green. Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research, 8(3):186–194, March 1998.
Brent Ewing, LaDeana Hillier, Michael C. Wendl, and Phil Green. Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Research, 8(3):175–185, March 1998.
Michael L. Metzker. Sequencing technologies — the next generation. Nature Reviews Genetics, 11(1):31–46, December 2009.
Download: JavaScript: galaxydatasetimprover.user.js (Please take a look at the man-page. Browse bugs and feature requests.)

Martin Scharm

stuff. just for the records.

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