Walking Randomly

Version 3 of the Mozilla Foundation’s superb web browser, Firefox, has been released and is available for download. Firefox really is a massive improvement over Internet Explorer in my opinion and, most importantly of all, Firefox renders walkingrandomly.com properly! It looks hideous in Internet Explorer 6 and it simply isn’t my fault.

No matter what operating system you use – Windows, Linux or Mac OS X – there is a version of Firefox for you. So please…go get it now and experience this blog the way it’s creator intended.

Although Mathematica 6 has been out for quite a while now there are still some people at my university who refuse to upgrade from Mathematica 5.2 for one reason or another. Some don’t like the new help system, others don’t have the time to rewrite teaching notes and some find that their old Mathematica scripts simply don’t run properly in version 6 and they can’t figure out why.

Of course most users have embraced the new version as there is simply too much new functionality to do otherwise. Some people, however, have minor problems with version 6 that might not be show stoppers but are definitely annoying. One such problem was reported to me today by a user who was missing the “Evaluate Notebook” option that used to be present in the menu of version 5.2.

Fortunately things like this are easily fixed. Within a standard Mathematica install, there is a file called MenuSetup.tr which defines what appears on the menus. On my Windows system it appears in the following location

C:\Program Files\Wolfram Research\Mathematica\6.0\SystemFiles\FrontEnd\TextResources\Windows\MenuSetup.tr

To get “Evaluate Notebook” to appear in the “Evaluation” part of the menu just modify this file by adding the line

Item[“Evaluate &Notebook”, “EvaluateNotebook”],

after the part that reads

Menu[“E&valuation”,
{

Let me know if you find this useful.

Yesterday I wrote about Mathematica 6.0.2 not working properly on Ubuntu 8.04 and today I discover that Matlab 2007b doesn’t like it much either. When you run Matlab you might get nothing more than an empty gray window and Matlab will essentially be unusable. Apparently the problem stems from a bug with Java applications when using Compiz or Beryl effects so just turn them off and all will be well.

To fix the problem just click on System -> Preferences -> Appearance in the GNOME menu and select the Visual Effects tab. Set the effects to None and then click on close. Matlab 2007b should now work properly and you won’t be wasting any CPU cycles on eye candy.

Of course you might not want to disable all of the pretty visual effects. If so then try the workarounds detailed in The Mathwork’s article on this issue – I haven’t tried any of these extra tricks since they are unsupported and I am more insterested in a working Matlab than a pretty desktop.

Abaqus is an extremely powerful finite element analysis (FEA) package that is used by various departments at my university and it is an application that I provide some of the support for among our users. I am far from being an expert at using it but I do know a trick or two and am occasionally useful. Recently, someone emailed me because they were having trouble actually getting Abaqus 6.6 installed on a 64 bit CENTOS 5 machine. He was located on the other side of campus from me, but it was a nice day and I felt like a walk so, rather than giving the support via email, I popped over to see him face to face. I am glad I did too – because it was a tricky one!

I am aware that this is not the sort of thing my usual readers might be interested in so I will keep it as brief as possible – basically what I want to do is provide myself with a permanent record of what we discovered and how we fixed it in case I come across this problem again. In an ideal world it might also help a googler or two (do let me know in the comments if it does – it will make my day)

So…we log on as root, run the installation script and get the following error

Extracting temporary installation utilities to /opt/temp…
Executing the installation GUI…
Preparing to install…
Extracting the installation resources from the installer archive…
Configuring the installer for this system’s environment…
awk: error while loading shared libraries: libdl.so.2: cannot open shared object file: No such file or directory
dirname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
/bin/ls: error while loading shared libraries: librt.so.1: cannot open shared object file: No such file or directory
basename: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
dirname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
basename: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
hostname: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory

Launching installer…
grep: error while loading shared libraries: libc.so.6: cannot open shared object file: No such file or directory
/opt/temp/TEMP_ABAQUS_utils_root/jre/bin/java: error while loading shared libraries: libpthread.so.0: cannot open shared object file: No such file or directory

As far as I can tell the reason for this is that the installer cannot identify your shiny new kernel so it assumes that an old one is being used and THIS is where the problems start. The problem occurs in the script /cdrom/lnx86_64/product/UNIX/Disk1/InstData/NoVM/install.bin

Look inside this file and you will see 2 lines that contain

export LD_ASSUME_KERNEL

I commented these out by adding a # (after copying the installation cd to a writable filesystem of course):

#export LD_ASSUME_KERNEL

BIG mistake. I now had a shiny new error

Exception in thread "main" java.lang.NoClassDefFoundError: com/zerog/lax/LAX

After a bit of googling, I discovered this post which gave an explanation of the problem along with a solution. The important part is this:

“make sure any line you put a comment on, you either edit in overwrite mode, or you make sure you delete a character for every # sign you add”

I deleted the Tab character before each of the # I had added and the error went away but I could have saved myself the grief by NOT manually commenting out each instance of LD_ASSUME_KERNEL and just running the following sed command on install.bin instead

cat install.bin | sed “s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/” > /tmp/install.bin

Once this was taken care of, the installation proceeded without complaint and I was pretty confident that I was going to be out in time to meet my friend for coffee but, alas, it was not to be. When I tested the install by running the abaqus cae I received the following error message

/opt/abaqus/6.6-1/exec/ABQcaeK.exe: /opt/abaqus/6.6-1/External/libgcc_s.so.1: version `GCC_4.2.0′ not found (required by /usr/lib64/libstdc++.so.6)

I was starting to contemplate writing some FEA code for him rather than continue with this install as I felt that it might have been easier but it turned out that all we need to do is change the name of a couple of files (original source here). Do the following at your shell prompt (assuming the default installation location):

cd /opt/abaqus/6.6-1/External
mv libgcc_s.so libgcc_s.so.BACKUP
mv libgcc_s.so.1 libgcc_s.so.1.BACKUP

Job done! Finally! As always, if anyone finds this useful then please let me know.