Missing Matlab menu’s with ubuntu

30 April, 2008

After installing matlab 7.4.0 on ubuntu hardy (8.04), I got the following stack trace on the gnome output console;

patrickd@battlestar:~$ Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb5ac0767]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_unlock+0x31) [0xb5ac08b1]
#2 /usr/lib/libX11.so.6(_XReply+0xfd) [0xb5e2c1bd]
#3 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa090826a]
#4 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa08ee352]
#5 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa08ee599]
#6 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so(Java_sun_awt_X11GraphicsEnvironment_initDisplay+0x24) [0xa08ee7a4]
#7 [0xadcbdb8b]
#8 [0xadcb7a7b]
#9 [0xadcb7a7b]
#10 [0xadcb5157]
#11 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb294f8ec]
#12 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb2a3e378]
#13 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb294f71f]
#14 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so(JVM_DoPrivileged+0x2db) [0xb29a7ebb]
#15 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/libjava.so(Java_java_security_AccessController_doPrivileged__Ljava_security_PrivilegedAction_2+0x3d) [0xb2f422cd]
#16 [0xadcbd43b]
#17 [0xadcb79a4]
#18 [0xadcb5157]
#19 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb294f8ec]
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb5ac0767]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0xb5ac081e]
#2 /usr/lib/libX11.so.6 [0xb5e2b518]
#3 /usr/lib/libX11.so.6(XGetVisualInfo+0x26) [0xb5e220a6]
#4 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa08ed227]
#5 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa08ed4b8]
#6 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so [0xa08ee6e0]
#7 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/xawt/libmawt.so(Java_sun_awt_X11GraphicsEnvironment_initDisplay+0x24) [0xa08ee7a4]
#8 [0xadcbdb8b]
#9 [0xadcb7a7b]
#10 [0xadcb7a7b]
#11 [0xadcb5157]
#12 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb294f8ec]
#13 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb2a3e378]
#14 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so [0xb294f71f]
#15 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/client/libjvm.so(JVM_DoPrivileged+0x2db) [0xb29a7ebb]
#16 /opt/matlab/sys/java/jre/glnx86/jre1.5.0/lib/i386/libjava.so(Java_java_security_AccessController_doPrivileged__Ljava_security_PrivilegedAction_2+0x3d) [0xb2f422cd]
#17 [0xadcbd43b]
#18 [0xadcb79a4]
#19 [0xadcb5157]

Which appears to be causing the standard menus in matlab not to display, after trying various solutions found around the great wide inter web, the one that finally worked for me was to edit the matlab startup script at <$matlab_home>/bin/matlab and insert the following at the top of the file;

export AWT_TOOLKIT=MToolkit

After editing the matlab startup script it now looks like;

patrickd@battlestar:~$ head /opt/matlab/bin/matlab
#!/bin/sh
export AWT_TOOLKIT=MToolkit
#
# Name:
# matlab script file for invoking MATLAB
#
# Usage:
# matlab [-h|-help] | [-n | -e]

Note: This doesn’t actually appear to stop the error message above from appearing in the terminal window, it does however allow the menus to display which for now is all I need to fix. If I later discover that the error message is causing something else not to work in Matlab then I ‘ll update this post.


Google toolbar bookmarks with Firefox-2 on Ubuntu Hardy (8.04)

30 April, 2008

After upgrading to ubuntu hardy (8.04) and trying to use Firefox 3b5 for a couple of days. I’ve decided to go back to using the Firefox 2.* series for browsing the web, as a lot of the extensions that I use day to day still aren’t supported in ff 3b5. So, I installed firefox 2 with the following command;

$ sudo apt-get install firefox-2

After installing firefox 2, I then tried to install google toolbar and got an error that the toolbar couldn’t be installed, after searching around the web. The solution that worked for me was to shutdown Firefox 2 and remove the preferences directory using;

$ rm -rf ~/.mozilla

When I restarted Firefox I was now able to install google toolbar. Unfortunately, after installing it and signing in using my gmail account, I was unable to access my bookmarks as I was just getting “downloading bookmarks” displayed when trying to access Bookmarks on the toolbar. No problem I thought I’ll just restart Firefox and hopefully that will fix it. Alas, this didn’t fix it. A little while later and a lot of forum searching and I finally happened upon a solution that worked for me, it involved installing the libstdc++5 library;

$sudo apt-get install libstdc++5

Then starting Firefox and disabling the google toolbar extension, restarting firefox and then enabling google toolbar extension and hey presto everything worked as expected.


Using Xilinx USB cable on LinuxMint / Ubuntu without windvr

8 April, 2008

This post is based on information found at the Xilinx JTAG information page . Using the Xilinx JTAG usb programmer without using the proprietary windvr.o (which no longer seems to work with modern kernel’s) kernel module requires that we use the open source libusb driver. There are a number of ways to obtain the driver but I prefer to install from source. The source can be obtained by using the command shown below and as the cable driver will be installed into the /opt/xilinx directory which my normal account (patrickd) doesn’t have write permissions to (/opt/xilinx must be written to using the sudo command or I could sudo to root and install from there, I could also allow write access to the /opt/xilinx but patrickd account but I prefer not to).

patrickd@patrickd-desktop:/opt/xilinx$ sudo git clone git://git.zerfleddert.de/usb-driver

Which generates the following error because git isn’t installed yet;

sudo: git: command not found

To install the Git source control system, run the following command;

patrickd@patrickd-desktop:/opt/xilinx$ sudo apt-get install gitk git-gui
Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages were automatically installed and are no longer required:
nautilus-actions
Use ‘apt-get autoremove’ to remove them.
The following extra packages will be installed:
git-core libdigest-sha1-perl liberror-perl tcl8.4 tk8.4
Suggested packages:
git-arch git-cvs git-svn git-email git-daemon-run gitweb cogito tclreadline
Recommended packages:
git-doc curl
The following NEW packages will be installed
git-core git-gui gitk libdigest-sha1-perl liberror-perl tcl8.4 tk8.4
0 upgraded, 7 newly installed, 0 to remove and 2 not upgraded.
Need to get 6206kB of archives.
After unpacking 14.6MB of additional disk space will be used.
Do you want to continue [Y/n]?

Once git is installed its time to try and reinstall the libusb driver, by running the previous command;

patrickd@patrickd-desktop:/opt/xilinx$ sudo git clone git://git.zerfleddert.de/usb-driver

Which will generate the following output although the actual values may differ;

Initialized empty Git repository in /opt/xilinx/usb-driver/.git/
remote: Counting objects: 551, done.
remote: Compressing objects: 100% (325/325), done.
Indexing 551 objects…
remote: Total 551 (delta 315), reused 417 (delta 226)
100% (551/551) done
Resolving 315 deltas…
100% (315/315) done

Change into the lib usb-driver directory then read the README file and attempt to ‘make’ or build the libusb driver;

patrickd@patrickd-desktop:/opt/xilinx$ cd usb-driver/
patrickd@patrickd-desktop:/opt/xilinx/usb-driver$ gedit README
patrickd@patrickd-desktop:/opt/xilinx/usb-driver$ sudo make

Unfortunately this will generate the following set of errors;

patrickd@patrickd-desktop:/opt/xilinx/usb-driver$ make
cc -Wall -fPIC -DUSB_DRIVER_VERSION=”\”2008-04-08 22:39:18\”” usb-driver.c parport.c config.c jtagmon.c -o libusb-driver.so -ldl -lusb -lpthread -shared
usb-driver.c:26:19: error: dlfcn.h: No such file or directory
usb-driver.c:28:20: error: stdlib.h: No such file or directory
usb-driver.c:29:20: error: string.h: No such file or directory
usb-driver.c:30:20: error: unistd.h: No such file or directory
usb-driver.c:31:19: error: fcntl.h: No such file or directory
usb-driver.c:32:23: error: sys/types.h: No such file or directory
usb-driver.c:33:22: error: sys/stat.h: No such file or directory
usb-driver.c:34:22: error: sys/time.h: No such file or directory
usb-driver.c:35:19: error: stdio.h: No such file or directory
usb-driver.c:36:17: error: usb.h: No such file or directory
usb-driver.c:37:20: error: signal.h: No such file or directory
usb-driver.c:38:21: error: pthread.h: No such file or directory
usb-driver.c:39:19: error: errno.h: No such file or directory
usb-driver.c:40:22: error: inttypes.h: No such file or directory
usb-driver.c:41:23: error: sys/ioctl.h: No such file or directory
usb-driver.c:42:25: error: sys/utsname.h: No such file or directory
usb-driver.c:43:27: error: bits/wordsize.h: No such file or directory
In file included from usb-driver.c:44:
usb-driver.h:253: error: expected specifier-qualifier-list before ‘uint32_t’
usb-driver.c:47: error: ‘NULL’ undeclared here (not in a function)
usb-driver.c:52: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
usb-driver.c:53: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
usb-driver.c:58: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
usb-driver.c:62: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int_wait’
usb-driver.c: In function ‘hexdump’:
usb-driver.c:70: warning: implicit declaration of function ‘fprintf’
usb-driver.c:70: warning: incompatible implicit declaration of built-in function ‘fprintf’
usb-driver.c:70: error: ‘stderr’ undeclared (first use in this function)
usb-driver.c:70: error: (Each undeclared identifier is reported only once
usb-driver.c:70: error: for each function it appears in.)
usb-driver.c:74: warning: incompatible implicit declaration of built-in function ‘fprintf’

In order to build the libusb driver, the libusb-dev files are required. Fortunately these files are currently available in the Debian archives and can be installed via the following command;

patrickd@patrickd-desktop:/opt/xilinx/usb-driver$ sudo apt-get install libusb-dev
Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages were automatically installed and are no longer required:
nautilus-actions
Use ‘apt-get autoremove’ to remove them.
The following extra packages will be installed:
libc6-dev linux-libc-dev
Suggested packages:
glibc-doc manpages-dev
The following NEW packages will be installed
libc6-dev libusb-dev linux-libc-dev
0 upgraded, 3 newly installed, 0 to remove and 2 not upgraded.
Need to get 3978kB of archives.
After unpacking 17.6MB of additional disk space will be used.
Do you want to continue [Y/n]?

Now to re-run the ‘make’ command;

patrickd@patrickd-desktop:/opt/xilinx/usb-driver$ sudo make
cc -Wall -fPIC -DUSB_DRIVER_VERSION=”\”2008-04-08 22:39:18\”” usb-driver.c parport.c config.c jtagmon.c -o libusb-driver.so -ldl -lusb -lpthread -shared
cc -DDEBUG -Wall -fPIC -DUSB_DRIVER_VERSION=”\”2008-04-08 22:39:18\”” usb-driver.c parport.c config.c jtagmon.c -o libusb-driver-DEBUG.so -ldl -lusb -lpthread -shared

Once the driver has been build it must be added to the environment variables, this is done by adding the following to .bashrc;

export LD_PRELOAD=/opt/xilinx/usb-driver/libusb-driver.so

Once this step has been completed the final step is to add the USB driver to the udev rules set, this is achieved by (taken from http://www.itee.uq.edu.au/~listarch/microblaze-uclinux/archive/2007/03/msg00101.html );

5) Make a new udev rule set file
$ sudo vi /etc/udev/rules.d/50-xilinx-usb-pav.rules # a new file with
arbitrary name (“50″ is recommended)
6) paste the following into this file, and save it
ACTION==”add”, BUS==”usb”, SYSFS{idVendor}==”03fd”, MODE=”666″
7) restart udev with:
$ /etc/init.d/udev restart


Installing ISE / EDK 8.2 on LinuxMint / Ubuntu

8 April, 2008

Once LinuxMint is installed its time to get down to actually using Linux for day to day tasks, but before I can do that I need to install Xilinx ISE and EDK v9.2. In this post I will detail all the steps required to install it within the LinuxMint environment, so here goes.

First copy the installation DVD to a temp folder and change the files so that they are all executable this is required as on most distributions the setup file isn’t executable. I could have just changed the execution bit for the “setup” file but as this file calls into other scripts in the directory tree it was just easier change the whole tree.

patrickd@patrickd-desktop:~/temp$ cp -R /mnt/cdrom ~/temp/ise

patrickd@patrickd-desktop:~/temp$ chmod -R u+x *

As I typically prefer not to install applications in my home directory, preferring instead to install custom applications (non-distro packaged) under the /opt tree, I need to start the setup script using the sudo command.

patrickd@patrickd-desktop:~/temp$ sudo ./setup

[sudo] password for patrickd:

And finally we have installed ISE as can be seen from the output of in the terminal window where the installation was started from.

************ setup done! ***************

At this stage the ISE environment is installed but before project navigator can be used so environment variables need to be configured fortunately xilinx provides a script to do this.

patrickd@patrickd-desktop:~/temp$ . /opt/xilinx/ise82/settings.sh
patrickd@patrickd-desktop:~/temp$ ise

In order to make things a little easier I’ve decided to add this script to my .bashrc, to edit the .bashrc script using gedit type the following;

patrickd@patrickd-desktop:~/temp$ gedit ~/.bashrc

and then add this to the bottom of the file

# Added the ISE settings script to the environment
. /opt/xilinx/ise82/settings.sh

EDK Installation

The procedure for installing the EDK is the same as that outlined above except instead of installing EDK into /opt/xilinx/ise82 the EDK software is installed into /opt/xilinx/edk82. In order to added the correct environment variables for EDK into the environment shell .bashrc should be edited as below,

# Added the EDK settings script to the environment
. /opt/xilinx/edk82/settings.sh


Getting started with LinuxMint

8 April, 2008

After distro hopping for a number of years around most of the available popular Linux distributions including fedora, centos, redhat, kubuntu, ubuntu, archlinux, mandriva, ulteo, gentoo and even some flavours of *bsd. I’ve finally decided to settle (at least for a while 🙂 ) on LinuxMint 4.0 which is based on ubuntu but just to me appears to be a *lot* prettier 🙂

I intend to use at least part of this blog to keep track of how things progress and to document any issues that I encounter with my day to day usage.

Stay tuned.


Hello world!

8 April, 2008

Hi everyone,

This is my first foray into the world of blogging, this site will probably just be used as a place to brain dump some of the things that I’m currently working on.

Feel free to look around and leave comments.

😉