Condor 7.1.1 supported ports

The development series for condor is dropping support for several platforms from 7.1.1 onwards:

1. Red Hat 9 (Suitable for openSUSE 10.x)
2. Solaris 5.8
3. Mac OS X PowerPC

RHEL 3 binaries should be fine for any Red Hat system (and presumably CentOS). Solaris 5.8 users can use the 5.9 binaries.

It should be noted they are continuing these ports for the current stable series (7.0.x).

Unfortunately the RHEL 3 binaries do not work on openSUSE 10.x (well they run but give Shadow exceptions if you try to do anything useful - like run a job!). Looks like a case to compile from source...

UPDATE: Condor 7.1.1 has been pulled due to numerous problems, look out for 7.1.2.

Perl on Eclipse 3.4 (Ganymede)

I use Eclipse everyday and the ability to use it for multiple languages is crucial. Perl is one of the languages I use and there is an excellent plugin for it: EPIC. However, after installing the recently released Ganymede (3.4) release I couldn't install it.

There are multiple versions of Eclipse available to download, typically I pick Classic. However, EPIC will not install on to this version. I found using Eclipse IDE for Java Developers worked fine. Hopefully any other plugins you use won't mind you using this version!

Display source code in MediaWiki

You have three options by default:

1. Display code inline like script.sh, by using <code>script.sh</code>.
2. Blocks of code can be wrapped with <pre>insert your code here</pre>. This works multi-line but doesn't allow formatting.
3. Indent your text to enable a <pre> like block, then apply standard '''bold''' and ''italic'' formatting.

The above options generally work quite well, but if you end up with lots of code from different languages and more than a few lines it would be handy to have syntax highlighting. Thankfully an extension to MediaWiki can do this. Use SyntaxHighlight_GeSHi to colour away; it is also used on Wikipedia.

You will need root access to your server and subversion installed, then follow the simple instructions on the extension website. Download the extension and GeSHi then add it to your LocalSettings.php.

Now you have a fourth option, wrap your code with <source lang="X">code here</source> where X is php, java, bash, ruby or one of the other nearly 50 supported langauges!

Thumbnails and TeX support for MediaWiki on Mac OS X

After you have setup a new MediaWiki installation you will likely want to enable some extra functionality which requires additional software.

First off to create thumbnails of images you need to install ImageMagick, which gives you the incredibly handy convert program.

Second you can add maths support, using TeX, for this you need ocaml, latex and dvipng. Grab the required programs from MacPorts, they are available from Fink as well.

• sudo port install ImageMagick
• sudo port install ocaml
• sudo port install tetex
• sudo port install ghostscript

Texvc will convert your TeX into whatever MediaWiki wants to display (HTML, MathML or PNG), but it needs to know where several programs are. Given you are probably running your webserver as the www user, who has no $PATH settings how do you tell Texvc where to find the files? In an unusal move, hardcode them! Edit <mediawiki>/math/render.ml, prefixing /opt/local/bin to the four commands

let cmd_dvips tmpprefix = "/opt/local/bin/dvips -R -E " ^ tmpprefix ^ ".dvi -f >" ^ tmpprefix ^ ".ps"
let cmd_latex tmpprefix = "/opt/local/bin/latex " ^ tmpprefix ^ ".tex >/dev/null"
let cmd_convert tmpprefix finalpath = "/usr/local/bin/convert -quality 100 -density 120 " ^ tmpprefix ^ ".ps " ^ finalpath ^ " >/dev/null 2>/dev/null"
let cmd_dvipng tmpprefix finalpath = "/opt/local/bin/dvipng -gamma 1.5 -D 120 -T tight --strict " ^ tmpprefix ^ ".dvi -o " ^ finalpath ^ " >/dev/null 2>/dev/null"

Them recompile texvc with make, ocaml will take over here.

Tell ImageMagick where gs is, by editing /opt/local/lib/ImageMagick-X.X.X/config/delegates.xml, where X.X.X is version number. Replaces every "gs" with "/opt/local/bin/gs", only edit "gs" entries, about half a dozen.

Finally tell MediaWiki to use TeX, by editing your LocalSettings.php with $wgUseTeX = true;

Now math support should be good to go. Thank to this compilation of advice for assistance.

So now this wikitext will produce the following:

== Magical latex in action ==
<math>\left \{ \frac{a}{b} \right \} \quad \left \lbrace \frac{a}{b} \right \rbrace</math>

<math>x \implies y</math> an AMS command

<math>f(n) =
\begin{cases}
n/2,  & \mbox{if }n\mbox{ is even} \\
3n+1, & \mbox{if }n\mbox{ is odd}
\end{cases}</math>

== Image thumbnail ==

[[Image:OpenSUSE.png|frame|Full size|center]]
[[Image:OpenSUSE.png|thumb|A thumbnail|center]]

Solubility Challenge

UCC has launched a competition in conjunction with JCIM. Essentially their article (DOI: 10.1021/ci800058v) which appeared on ASAP yesterday, details 132 druglike molecules. They report the solubility for 100 molecules and challenge you to predict the other 32 using whatever method you choose.

Submit your predictions by 15th September 2008 upon which the best submissions will be invited to detail their models as JCIM articles.

Full details are on the Goodman group website, including machine-readable files.

Subversion with CruiseControl

As we use subversion for our version control we need to do an extra step as CruiseControl only has limited subversion support (e.g. it can't checkout a project, I'm sure it should but has never worked for me).

To give it the power to do so you need to download SvnAnt. Copy the three jar's from the lib folder into the the lib folder in your installation: /cruisecontrol/apache-ant-1.7.0/lib. This way everything that keeps CruiseControl happy is in one place.Now you need to define a property file defining the location of SvnAnt, something like the file svn-build.props:

svnant.version=1.0.0

lib.dir=../apache-ant-1.7.0/lib

svnant.jar=${lib.dir}/svnant.jar
svnClientAdapter.jar=${lib.dir}/svnClientAdapter.jar
svnjavahl.jar=${lib.dir}/svnjavahl.jar

You need to ensure the lib.dir value is valid, depending where you call this file from (in this example /cruisecontrol/project). As you will see we make a wrapper script to grab the code from the repo, before launching the project ant script. The wrapper script may be in /cruisecontrol/project, but defines it basedir as /cruisecontrol/checkout.

A sample script can be found here (Blogger doesn't want to display it). To use it save to /cruisecontrol/project and edit the sample_project and subversion path. Your project will be checked out to /cruisecontrol/checkout, where it is built, tested, compiled etc. For the first time I had to checkout manually otherwise CruiseControl would kick a fuss up.

In your main config.xml call the new wrapper script (/cruisecontrol/project/sample_project.xml) in the schedule section. This way a fresh copy of the code is checked out before the CruiseControl commences the build.

Start condor on boot with Mac OS X

Once you have condor running on your clients you will want it to load by default when booting. The condor distribution includes linux-based startup scripts, however there are none for the mac. Looking through the mailing list there is a suggestion of scripts to use, but they use Panther (10.3) based technologies, not recommended in Tiger (10.4) and not available in Leopard (10.5).

Delving a bit further I found another way to start condor by using cron.

Create a script to start condor: sudo vim /usr/sbin/start_condor

Enter these contents, and customise to your installation:

#!/bin/bash
# Ensure network is all setup
sleep 100

# Ensure condor environment is loaded
source /opt/condor/condor.sh

# Start condor
/opt/condor/sbin/condor_master

Our condor installation is actually stored on an NFS drive, so the 100 second sleep is to ensure the NFS drives have mounted before the rest of this script runs. I handle the path settings for
$CONDOR_CONFIG, $PATH & $MANPATH in a separate script (condor.sh), alternatively you could specifiy $CONDOR_CONFIG in this script.

Tell cron about your script, and that it should be run on boot:
sudo echo "@reboot root /usr/sbin/start_condor" >> /etc/crontab
I have the condor daemons run as root, hence the root user mentioned in this crontab entry.

Test the script by running direct from the command-line first, if it runs then you should have trouble when rebooting.