Judson's Notes

So I decided to upgrade from Ubuntu 11.10 to 12.04. Since apparently the upgrade is not released to the masses until 12.04.1, I had to force the upgrade via:

do-release-upgrade

The upgrade went fine. I'm still not enthusiastic about Unity. Although the new HUD seems potentially useful, there are too many other things that turn me off from Unity:

1. Searching for programs via the Super key and typing does not automatically return recently used documents like Gnome 3 does.
2. The launcher is inflexible and incompatible with lots of my programs, like Matlab and JabRef. If I add an entry to the launcher, then launch the application, another entry is added to the launcher at the bottom.
3. The Unity launcher can't support folders of items and it is really inflexible and uncustomizable.
4. I really don't like the way that the menu items of a program appear at the top of the screen.
5. Hate the application-centric task switching
6. The workspace appears in the launcher instead of the system tray

So I am going back to Gnome 3, except this time on Ubuntu instead of Fedora. That should solve a lot of the problems I had with wireless connectivity and SE Linux.

To start in Gnome 3, I just chose it from the available desktops when I logged in to Ubuntu.  There are several things I had to fix/tweak. Most of them are so obvious I can't believe Gnome 3 doesn't come like that already:

First, open install and open the gnome tweak tool:

sudo apt-get install gnome-tweak-tool

Open it up by looking for Advanced Settings in the menu. Here are the things I tweak:

1. Desktop -> Have file manager handle the desktop -> On
2. Desktop -> Computer icon visible -> On
3. Desktop -> Home icon visible -> On
4. Shell -> Show date -> On
5. Shell -> Arrangement of buttons on the titlebar -> All

Those are the major items, along with the intallation of some shell extensions from here:

1. Remove accessibility icon
2. Alternate status menu (with Power off button)
3. User themes ( !!! this one caused gnome-tweak-tool to stop working and return the error "Trace/breakpoint trap (core dumped)". I had to uninstall it)
4. Dock
5. Places Status Indicator
6. Removable Drive Menu
7. Native Window Placement
8. Windows Alt Tab (switches to window centric!)
9. Calculator
10. system-monitor

There is very little documentation out there on how to alter gsettings to move the dock extension to the left side of the screen. However, I found that this worked for me:

cd ~/.local/share/gnome-shell/extensions/dock\@gnome-shell-extensions.gcampax.github.com
gsettings --schemadir ./schemas set org.gnome.shell.extensions.dock position left

I started looking around for a way to save my terminal layouts on the screen (typically 3 terminals or a specific size/location). I could immediately find something to do it with, but did find terminator:

sudo apt-get install terminator

Then redirected my terminal shortcut (Ctrl+Shift+N) to the command "terminator". After launching terminator, I split it up and arranged the terminals like I wanted, then right-click -> Preferences and saved the layout. Now that layout starts by default. Perfect!

I also found another incredible tool called guake:

sudo apt-get install guake

It creates a hidden terminal that will pop-up or go away via a keyboard shortcut (F12). New tabs can be opened/closed via easily customized keyboard shortcuts, making it an extremely useful way to quickly run commands.

Things I want to be able to do:

1. Adjust sensitivity of the trackpoint pointing stick. This can be done by putting new values in the appropriate files like this (values can range from 0 to 255):

echo 200 > /sys/devices/platform/i8042/serio1/serio2/sensitivity
echo 200 > /sys/devices/platform/i8042/serio1/serio2/speed 

Using sudo did not work with these commands, so I had to login to a terminal as root by typing "su". I played with values until I found something that I liked, which was 200 for both sensitivity and speed. Now the trick is to get these values to initialize at startup. Following this, I created a udev rule in /etc/udev/rules.d/. I created a file called "trackpoint.rules" and put this inside:

SUBSYSTEM=="serio", DRIVERS=="psmouse", ATTR{description}=="Synaptics pass-through", WAIT_FOR="/sys/devices/platform/i8042/serio1/serio2/sensitivity" ATTR{sensitivity}="200", ATTR{speed}="200"

update: this is still working after many reboots and a couple weeks of use.

2. switch from using the discrete Nvidia NVS 4200m graphics card to the integrated Intel Graphics

At first I was using the discrete graphics and I used the nvidia-xconfig utility to get a working xorg.conf. Now I want to switch to the integrated graphics and see how my battery life changes. To do this, I removed the xorg.conf file like this:

sudo mv /etc/X11/xorg.conf /etc/X11/xorg.conf.nvidia

and restarted my system. When it restarted, i went into the BIOS and switched to integrated graphics with OS detection disabled. Then Ubuntu started up fine using the integrated graphics.

The key here is to save your xorg.conf, and if you want to go back to using the nvidia graphics card, you will probably just have to move the xorg.conf.nvidia back to xorg.conf and restart, switching to discrete graphics in the BIOS.

My battery life went from 3.5 hours with discrete graphics to 5.5 hours with integrated graphics.

I'm encountering several bugs with my Thinkpad T520 and Ubuntu 11.10.

LCD backlight keys don't work. The notification comes up shown the brightness being adjusted, but nothing changes. The solution for this was to add the line

 Option   "RegistryDwords" "EnableBrightnessControl=1"

 Section "Device"
Identifier  "Device0"
Driver  "nvidia"
VendorName  "NVIDIA Corporation"
BoardName "NVS 4200M"
Option  "RegistryDwords" "EnableBrightnessControl=1"
EndSection 

The trackpad stops working sometimes. I'm still working on this one.

Problems coming out of a suspended state: I notice several problems when coming out of sleep, like the touchpad stops working and my wireless connection keeps dropping.

I got my new Thinkpad T520 and am working on setting it up. I am using a second hard drive in the DVD bay (aka Ultrabay). My hard drives are configured as:

/dev/sda -- 128GB SSD in the primary hard drive slot
partition 1 - 200MB Fat 32 - for UEFI if I decide to use it
partition 2 - 4GB swap
partition 3 - 45GB ext4 - primary Ubuntu partition
partition 4 - 72GB ntfs - storage for my truecrypt volumes so they can be accessed from windows or ubuntu

/dev/sdb -- 640GB hard drive in the DVD bay adaptor
partition 1 - 80GB ntfs - primary windows 7 partition
partition 2 - 510GB ext4 - all subdirectories of my home directory

First I installed 64-bit windows on the second hard drive using a USB memory stick. Then I installed Ubuntu in its partition. After this, I made sure that the first hard drive was selected as the first boot device in the BIOS. I also made sure that the BIOS was set to UEFI and Legacy Boot and that the discrete graphics card was enabled by default instead of Optimus. I don't care about battery life at this point.

I want to install Windows 7 on a separation partition but I don't have a DVD drive in my computer. How do I mak a boot thumb drive? It's actually pretty easy:

1. Insert a thumb drive with at least 3GB space
2. Format it as NTFS or Fat32
3. Copy the Windows 7 DVD contents or iso file contents onto the thumb drive
4. Open a command prompt
5. change directories to the thumb drive, for example, type E:\
6. change directories to the boot directory: type cd boot
7. At the command prompt, type: bootsect.exe /NT60 E:

Where the drive letter E is where my USB drive was mounted.

The only caveat is that the final command to write the boot sector to the thumb drive must be done from a machine of the same architecture. So if you are trying to make a thumb drive with 64-bit windows on it, you have to run that command from 64-bit windows.

I'm creating a presentation in Beamer and using Tikz to make some transparent overlays using the opacity option. For instance, here's a piece of code:

\begin{frame}
\frametitle{Title}
\begin{tikzpicture}
\node at (0,1) {test};
\end{tikzpicture}
\end{frame}
\begin{frame}
\frametitle{Title}
\begin{tikzpicture}
\node at (0,1) {test};
\filldraw[fill=green!20!white, draw=green!40!black,thick,opacity=0.3] (0,1) circle (1);
\end{tikzpicture}
\end{frame}

The color of the Beamer template and font rendering seriously changes between slides 1 and 2. If I remove the opacity option, the rendering of slide 2 goes back to normal.

This problem only occurs in Adobe Reader. Evince or Okular can view the pdf without a problem. However, I am using animations, and so need Adobe Reader for my animations. This means that I just can't do fancy transparent overlays. Apparently the rendering that Adobe uses changes based on whether there is transparent stuff present, and it just doesn't look right in this case.

A while ago, when I got fed up with KDE, I started using XFCE. So far I like it's simple interface. It's clean and fast. But some extra features would be nice, like easy access to recently used documents. This and more can be obtained by through XFCE goodies:

sudo apt-get install xfce4-goodies

Add the places item to a panel to view recently used items.

I was getting this Matlab error after I put a perfectly good bit of code inside a function:

Error: File: MAIN.m Line: 70 Column: 12
Functions cannot be indexed using {} or . indexing.

There was a problem with the indexing in a piece of code that looked like this:

A = trim(i).alpha;

The fix was to initialize the "trim" variable at the start of the function like this:

trim(1).alpha=[];

Problem solved. I have no idea why it happened, but don't care right now.