Fuzzy Logic

I got home today and booted up my Ubuntu Linux (8.04) server that had been down most of the semester and got some fun errors.  Now, the reason it was down in the first place was because the CMOS battery was out which caused hell with the system’s security features and I hadn’t bothered to get a new CMOS battery.  So I boot it up and walk upstairs to set up my desktop.  I come back downstairs and get this ever friendly message:

* An automatic file system check (fsck) of the root filesystem failed.  A manual fsck must be performed, then the system restarted. The fsck should be performed in maintenance mode with the root filesystem mounted in read-only mode.

So, basically, my main filesystem was broken somehow.  Adding insult to injury, of course, was the fact that the thing that was shown as causing the problem was S01E02 of Firefly, which I was considering watching soon.  Great. On a strange note, the other place that was giving me trouble was on /etc/acpi/suspend.d/10-thinkpad-standby-led.sh. As for the problem itself,  I know why it happened, of course–this server only goes down when the power goes out and I would imagine that the file reference didn’t get correctly written to the journal before the server crashed. So, after multiple “Multiply-claimed block(s) in inode: x: xxxx xxx” errors, it finally told me to reboot.  After doing so, it fscked the disk again and then had me reboot AGAIN.  Awesome.  That finally let it work though, so I can’t complain.  Now to get a new CMOS battery…

Adobe announced on December 17th that AIR 1.5 is now available for Linux!  This is a pretty big deal for Linux users because the previous version we were using was a buggy version that didn’t have all of the newest features (and was unreliable at that).  With this new release comes the new version for both x86 and x64 processors!  Read on for the whole explanation!

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In my research I work with the Physics simulation software GEANT4.  It’s an incredibly detailed and realistic package, but it’s an absolute beast to get working.  A while ago one of my coworkers found this site and it makes it incredibly easy.  It went down a while ago, but you can find it at http://aix1.uottawa.ca/~skirkwoo/GEANT4-Kubuntu.html now.  I believe the old link is up as well, but the newer link is Dr. Kirkwood’s official site.  It’s a really great install and very valuable because it works on 8.04 (Hardy Heron), which is a Long-Term Service release.  The guide is for Kubuntu, but it works great on Ubuntu as well.

A quick note about using newer version of Ubuntu: From 8.10 (Intrepid Ibex) on, Ubuntu doesn’t come with a g77 package. g77 is not used for GEANT4 specifically, but with CERN’s ROOT, which is an amazing statistical analysis package. You won’t NEED this for GEANT4, but it allows you to do some cool stuff.  Anyhow, instead of g77, Intrepid (8.10) comes with ‘gfortran’ which is not the same code, it seems.  Now, there are two ways on handling it.  I, personally, advise sticking to 8.04 and the g77 it comes with.  However, you can use a newer version of Ubuntu (or its variants) and either use Hardy packages or install from source.  Either way, it’s nice to have ROOT installed for statistical analysis.

As a side note, I’m hoping to (eventually) post a complete walkthrough of the process I go through when compiling CLHEP, GEANT4, and ROOT on a 8.04 machine.  It’ll probably be a while before I manage to get it written up, but it sure would be nice…

As anyone who has ever listened to Security Now knows, backing up your data is incredibly important.  It’s that one thing that seems completely unneccessary almost all of the time, especially if you never delete anything.  Whenever your hard drive dies, however, you need a good solution to recover your data.  Linux users love using rsync to sync to an external server but there doesn’t seem to have a great way to backup with a GUI to a local drive.  When I found the program Flyback, I thought I had found my solution.  However, I found it had a tendency to lock up at times for me.  It also hadn’t been updated when I wanted to switch.  Evidently someone forked it into a program called “Warpback”, but I haven’t seen any real work on that front.

After a bit of searching, though, I’ve found a nice updated program called Back in Time.  I really like a lot of the features it supports.  It’s written in python and uses rsync and diff to do its magic.  One of the nice features of Back in Time is that it only updates files that have been updated since the last backup.  This doesn’t seem like that huge of a thing, but it does it well.  The only problem I’ve found is that the it won’t accept symlinks that link to outside of its directories–you’ll have to manually include that directory to be included.  Other than that, it’s great!  Check it out.

Just a quick fix for this problem–I’m more posting this for myself than anyone else.  Anyhow, if you have at one point installed the non-official Java package and then installed the sun-java6-jre package set, you may be missing some things.  The error I was getting was

Exception in thread "main" java.lang.UnsatisfiedLinkError:
Can't load library: /usr/lib/jvm/java-6-openjdk/jre/lib/i386/xawt/libmawt.so

The exact error being:

Exception in thread "main" java.lang.UnsatisfiedLinkError: Can't load library: /usr/lib/jvm/java-6-openjdk/jre/lib/i386/xawt/libmawt.so
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1666)
at java.lang.Runtime.load0(Runtime.java:787)
at java.lang.System.load(System.java:1022)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1767)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1684)
at java.lang.Runtime.loadLibrary0(Runtime.java:840)
at java.lang.System.loadLibrary(System.java:1047)
at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:67)
at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:47)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.loadLibraries(Toolkit.java:1610)
at java.awt.Toolkit.<clinit>(Toolkit.java:1632)
at java.awt.Component.<clinit>(Component.java:568)
at CreditSystem.main(CreditSystem.java:17)

The solution I found was to issue the following command

sudo update-java-alternatives -s java-6-sun

That will update your files and fix it. Fun fun…