Skeptics’ Guide to the Universe transcripts project

Posted on April 11, 2012 by rwh

I’m a huge fan of the Skeptics’ Guide to the Universe, a podcast of science and skepticism, and I’ve been thinking for a while that it’d be really good to have transcripts of the episodes to facilitate linking and searching. But I couldn’t find any other project, other than a thread on the SGU forums. So I decided to put my time where my mouth is, and just do some transcribing.

It takes me about three times the amount of time to do a transcript as the podcast’s length (which is about 80 minutes), so generally a couple of nights’ work for a single SGU podcast. I guess I might be able to manage about two podcasts a week, and given that there are currently a bit over 350 podcasts in the archive, and a new one released each week, it’ll probably take me about seven years to finish them all! So… I created a wiki, sgutranscripts.org. Now we’ll just have to see if the community gets behind it, otherwise I could be here for a long time.

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RDP VirtualBox without the proprietary Oracle extension pack

Posted on April 9, 2012 by rwh

These days, virtualisation is all the rage. The various competing virtualisation products have reached a level of maturity where they can be reliably used for server consolidation. VirtualBox is one of the easiest to use, most featureful programs available in this space and with the ability to run on many different OSes on hardware with or without VM extensions, it is also one of the most popular. However, there is one wrinkle when it comes to using it for server consolidation: the proprietary RDP/USB2 extension pack.

The conventional wisdom when running a headless server with VirtualBox is that you need to install this proprietary extension pack from Oracle. This is fine until you want to use the server in production: as the PUEL only covers you for personal use and evaluation, you must purchase licenses. You can either pay £34 per user or £670 per “socket” (which has quite a convoluted definition). This gets you USB2 and RDP support.

However, there is another way, at least when it comes to RDP support. Continue reading →

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How to build MySQL Workbench on Ubuntu Precise (pre-release)

Posted on April 4, 2012 by rwh

Update 2012-04-25: mysql has appeared in the universe package archive. You should be able to install it with a simple:

sudo apt-get install mysql-workbench

Read on if you still want to compile from source.

Right now (2012-04-04), Ubuntu 12.04 hasn’t been released yet, and so there is no binary package from Oracle of MySQL Workbench for Precise. I managed to get the MySQL Workbench binaries for Oneiric to run, by manually installing libzip1_0.9.3-1_amd64.deb from Oneiric, but this wasn’t stable (crashed as soon as I tried to run a SQL Query).

So I decided to build from source. Here’s how I did it Continue reading →

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Ubuntu on Amazon ec2 from scratch

Posted on July 7, 2011 by rwh

Update: I’ve now rolled this blog post into the Ubuntu wiki’s: EC2 Starters Guide page. Hopefully this helps out the Ubuntu community!

The informatics team here at MalariaGEN have been working with ec2 since before I joined them. So naturally, it’s one technology with which I’ve had to come to grips in the course of doing my job. For me, EC2 had a fairly steep learning curve, and after spending a while trying to learn it through doing, I decided that I would just have to spend some time getting properly to grips with how things worked. As part of that I decided to document it in a way that I’d not yet seen on the web: logically, comprehensively, explaining all the strange concepts and quirks that were clouding my understanding and stopping me from getting my job done efficiently. Continue reading →

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Lentil soup

Posted on July 6, 2011 by rwh

Tablespoon olive oil
2 Onions, diced
2 Carrots, diced
Some celery, diced
1 cup of red lentils
1L of veg stock
1-2 tsp curry powder
1 small tin of tomatoes
4 cloves of garlic, diced
salt and pepper

Fry the onions, carrots and celery until the onions are translucent. Add the curry powder and fry a bit more. Add the stock, lentils, tomatoes and garlic. Bring to a boil then reduce heat and simmer for 25 mins or until lentils are cooked. Salt and pepper to taste AND CHILLI. Eat with buttered toast.

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Ubuntu’s Ambiance: selected items in unfocused windows are invisible

Posted on June 6, 2011 by rwh

I have a confession to make: I really like Ubuntu’s design, its look and feel, and its colour scheme.  And it seems to get better with each release.  The new Natty theme is really beautiful, and the dark window decorations of the Ambiance theme are great (especially now that they’ve chased down the odd dark text on dark background problems).

Having said that, there’s one thing that I really don’t like: the way that it’s virtually impossible to tell what you have selected in windows other than the one that happens to be focused.  This is because the focused elements get completely desaturated, like this:

Which items are selected? It's anyone's guess!

Continue reading →

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Installing Ubuntu on the lenovo ideapad S205

Posted on June 5, 2011 by rwh

My girlfriend’s laptop died recently, and as her birthday was coming up I thought I’d buy her a new netbook to get her up and running again (well, really, to get my mac back).  For £300 from Amazon, we had a machine that was much like her old laptop; it’s amazing what you can get for so little money these days.  However, there were two things I didn’t realise: one, the ideapad-S205 lacks an optical drive (whoops).  The second was that it’d take me basically a whole day of dicking around to get Ubuntu to dual boot with Windows 7.  I hope this guide will help people out with the second problem (and I solved the first one by buying a USB DVD drive for another £30). Continue reading →

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Gridengine the Ubuntu/Debian way

Posted on June 1, 2011 by rwh

I’ve had Sun GridEngine running on our cluster of 12-core HP blades from its earliest days. What has not been working is the the inter-host communication (the ability of the system to schedule and distribute jobs across the nodes). I therefore set out to fix this situation. It turns out that the problems that prevented this from working are mainly caused by quirks in the way that the Debian (and by inheritance, Ubuntu) packaging was done. Continue reading →

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Scripting class, answers 1

Posted on March 31, 2011 by rwh

1. In firefox, right click on an image and do Copy link location. Then use that link in your script. {1..21} is shorthand for the space separated list from 1 to 21, i.e.: “1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21″.

[ $ii -le 21 ] is shorthand for “test $ii -le 21″

# using a for loop
for ii in {1..21}
do
        wget "http://helms-deep.cable.nu/~rwh/blog/wp-content/uploads/2011/03/img${ii}.jpg"
done
 
# using a while loop
ii=1
while [ $ii -le 21 ] # spaces are required
do
        wget "http://helms-deep.cable.nu/~rwh/blog/wp-content/uploads/2011/03/img${ii}.jpg"
        ii=`expr $ii + 1` # spaces are required
done

For an interesting discussion: why did I use ii for my incrementer instead of i?

2. Note the double quotes, which are required to escape the filenames which contain special characters (spaces and parentheses). It is always good practice to wrap variables that contain filenames in double quotes for this reason.

for file in img*.jpg
do
        mv "$file" "`basename "$file" .jpg` (modified).jpg"
done

3. First, make sure imagemagick is installed:

sudo apt-get install imagemagick
for file in img*\ \(modified\).jpg 
do 
        convert -resize 50% "$file" "`basename "$file" .jpg` (small).jpg" 
done

4. First, we install the software we need:

sudo apt-get install vorbis-tools
sudo apt-get install lame

Then we convert the files:

wget http://helms-deep.cable.nu/~rwh/files/lara_st_john.tar.gz
tar xvzf lara_st_john.tar.gz
cd lara_st_john/bach_violin_concertos
for file in *.ogg
do
        oggdec "$file"
        lame --vbr-new `basename "$file" .ogg`.wav `basename "$file" .ogg`.mp3
done

5. First, we extract the track information from the ogg file using the vorbiscomment command and save it in a temporary file. Then we use grep and sed to select each datum and save it in a shell variable. Once we have all this info ready, we can decode the ogg file to wav, then encode the wav to mp3, passing in the shell variables which contain the track information.

for file in *.ogg
do
        base=`basename "$file" .ogg`
        vorbiscomment "$file" > "$base.comment"
        tt=`grep -e "^title"  "$base.comment" | sed -e 's/title=\(.*\)$/\1/'`
        ta=`grep -e "^artist" "$base.comment" | sed -e 's/artist=\(.*\)$/\1/'`
        tg=`grep -e "^genre"  "$base.comment" | sed -e 's/genre=\(.*\)$/\1/'`
        ty=`grep -e "^date"   "$base.comment" | sed -e 's/date=\(.*\)$/\1/'`
        tl=`grep -e "^album"  "$base.comment" | sed -e 's/album=\(.*\)$/\1/'`
        oggdec "$file"
        lame --vbr-new --tt "$tt" --ta "$ta" --tg "$tg" --ty "$ty" --tl "$tl" "$base.wav" "$base.mp3"
        rm -f "$base.comment"
        rm -f "$base.wav"
done
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Scripting class questions 1

Posted on March 29, 2011 by rwh

Loops

1. using wget or curl, and a for loop, download all of the following images:

2. using a loop, backticks (`) and the basename command, rename all of the images, adding “(modified)” to their filenames

3. using a loop, backticks, basename, and the convert command (part of the imagemagick image processing suite), resize all of the images to 50% of their original size

4. using wget or curl,tar, a loop, oggdec and lame, convert the following files into mp3s:

http://helms-deep.cable.nu/~rwh/files/lara_st_john.tar.gz

5. (hard) repeat question 4, but retain all ID3 tag information.

6. Use a loop and the “uptime” and “free” commands to record the system load once a minute for the duration of the class. Store the information in CSV format. Use a spreadsheet to draw graphs of this information.

File management

1. Download the following tar.gz, and extract it using the tar command. In the resulting directory, find the newest file that matches name-asdf*.

System commands

1. Write a cron job that will email you the free space on your hard disk once per hour. Its output should be:

Hello, your hard disk has X% of hard drive space remaining!

2. Using the “du” command, find out which of the directories in the root directory of your hard drive is using the most hard disk space. Suggest some files you might delete if you were running out of space.

3. Use the find command to return a list of the files in your home directory that you have modified in the last week. Exclude anything that is not a regular file.

Regular expressions

VIM

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