All posts by Mick

C, fortran, Linux, programming, Ubuntu

Compiling EIGENSOFT on Ubuntu Januty

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These are rough notes on how to compile Eigensoft 3 on Ubuntu Jaunty.

Update, Eigensoft 4 is available and should compile on more recent versions of Ubuntu:
http://www.hsph.harvard.edu/faculty/alkes-price/software/

Create a location to build the code:

Warning: /tmp is for temporary files, and any files & directories you create there will be remove upon some subsequent reboot.

cd /tmp;
mkdir EIGEN;
cd  EIGEN;

Get the Eigensoft source code:

wget  http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG3.0.tar.gz;
tar xzvf EIG3.0.tar.gz;

Install required dependences: Continue reading Compiling EIGENSOFT on Ubuntu Januty →

Cplusplus, Linux, Ubuntu

Compiling Osra on Ubuntu Jaunty

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This is a brief HOWTO on compiling OSRA, (Optical Structure Recognition) on Ubuntu Jaunty. To quote the OSRA home page, OSRA is

… is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification – see http://en.wikipedia.org/wiki/SMILES) or SD file – a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick – including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF representation of the molecular structure images encountered within that document …

Update: I’ve a newer document that shows how to install Osra on Ubuntu 11.10 (Oneiric):

Make a directory to compile the source:

mkdir /tmp/OSRA; cd /tmp/OSRA;

Be careful doing this in /tmp is cleaned upon reboot the directory may be removed.

Install dependencies needed by the OS:

sudo apt-get install libgraphicsmagick1-dev libmagick++-dev libgraphicsmagick++1-dev potrace gocr  libtclap-dev libopenbabel-dev libopenbabel3 openbabel libnetpbm10 libnetpbm10-dev

Don’t install ocrad and remove it if it’s on your system (you can probably reinstall if you need to after you get Osra to compile):
sudo apt-get remove –purge ocrad;

Source Code:

Instead of manually getting the source packages download the sources used to build the packages for Ubuntu if available.  Make sure the src lines are commented in, in your /etc/apt/sources.list . This will automatically download and extract the code into the current directory:

cd /tmp/OSRA; apt-get source gocr ocrad potrace;

This downloads Gocr 0.46 which the OSRA docs say may not work:

– GOCR/JOCR, optical character recognition library, version 0.43 or later (version 0.45 recommended, do not use 0.46! See special instructions for 0.47 compilation below) Continue reading Compiling Osra on Ubuntu Jaunty →

adriondack, Boston, Cambridge, flickr, photo

4th of July Fireworks!

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I won’t be in Boston for the fireworks show on July 4th. But if you show up at the last minute to see the fireworks, they start at 10.30pm, you can head onto to Harvard Bridge, commonly know as Mass Ave Bridge and get some decent view of the fireworks.

The last time I watched the fireworks from the bridge was in 2007, and I was near the middle at the 200 smoot mark:
200 Smoots!

The views of the fireworks was quite good, not as good as being on the river banks. Considering you could show up 5 minutes before the start of the display instead of 12 hours before is a good tradeoff in viewing quality. 🙂 Continue reading 4th of July Fireworks! →

Debian, Ireland, Linux, picture, travel, Ubuntu

Killing X

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On Ubuntu it used to be that ctrl-alt-backspace would kill X (the backend of the various graphical user interfaces on Linux). In an aim to be user friendly this is now disabled by default. This can be a real pain if X locks up, you can’t kill it nor change to a console.

On Debian and Ubuntu you can install the dontzap command which will allow you to kill X:

sudo apt-get install dontzap

Then run dontzap:

sudo dontzap -d

Or you can the following section to your /etc/X11/xorg.conf file (which is what the dontxzap command does):

Section "ServerFlags"
        Option  "DontZap"       "False"
EndSection

See Alberto Milone’s blog for more info:
http://albertomilone.com/wordpress/?p=335

Firefox, internet, Linux, Ubuntu

(2.0.0.16 > 3.0.8) == true ?

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I use Kayak.com whenever I’m planning a trip any where, it’s a good source to determine who flies to what destination and whose got the lowest price. Today, there’s a wee bug on their website where they tell me I should upgrade to Firefox 2.0.0.16, this would be sound advise except for the fact that I’m using a newer version of Firefox:

Kayak.com Firefox versioning bug

So I think someone needs to look at the math used here, because 3.0.8 is greater than 2.0.0.16. This is using Firefox on Ubuntu Linux.

Update: This may not be a Kayak.com problem and may be a problem with how Ubuntu build Firefox. In the Firefox “about:” page (type about: in the URL bar). It reports the following:

Firefox "about:" page.

There is a Ubuntu bug that may be related to this, and I’ve added a comment and the screen-shot that’s immediately above.

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Kaboom is cool!

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Great tool for converting KDE3 settings to KDE4 on Debian. Also, it’s works well to merge KDE4 settings from .kde4 with KDE3 settings in .kde. This is useful as KDE4 1st used .kde4 to save personal KDE configuration data. KDE4 is now using .kde for config data, which mean early KDE4 users will have problems with new KDE4 apps. Fear not, Kaboom will help!

http://pkg-kde.alioth.debian.org/kaboom.html

I’d advise saving back-up copies of both .kde and .kde4 .

BU Linux, Linux, Red Hat, Ubuntu

Red Hat 9

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I have a Red Hat 9 server that I have to support for a wee while longer. I needed to install some packages and I didn’t have the original install CD’s nor access to Red Hat’s repositories.

After lot’s and lot’s of searching I found the ISO images at:
ftp://archive.download.redhat.com/pub/redhat/linux/9/en/iso/i386/

But, there’s too many users on Red Hat’s FTP server and I can’t get access … thankfully rpmfind.net have a mirror:
http://fr.rpmfind.net/linux/redhat/9/en/iso/i386/

So now I can download the ISO images, and mount them on the Linux box using the loop-back interface and install the packages I need.

I expect to have new hardware within a month or so, and I’ll probably be using BU Linux or Ubuntu 8.04.

Hardware, Laptop, Linux, Tech, Ubuntu

Ubuntu Jaunty & ATI

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This is quick’n’dirty writeup to help others who might have the same problem. I’ll clean this up later in the week …

Ubuntu Jaunty is the new beta version of Ubuntu. It comes with a new version of X.Org and the ATI drivers have been incompatible with this version of X.Org. ATI recently released drivers that support X.Org 1.6. If you have problems with X not starting follow the instructions here:
https://wiki.ubuntu.com/X/Troubleshooting/FglrxInteferesWithRadeonDriver

For me what happened is that X wouldn’t start properly and cause my Lenovo T400 to freeze and lock up. The laptop would boot but when X would start (when the login screen appears) I’d get a black screen with red lines at the top. To solve this I booted to runlevel 1, also known as failsafe mode. If your using a laptop with wireless, I suggest you connect directly to your router using a network cable, otherwise you may have to configure wireless manually (it’s not that hard).

When your system starts, select failsafe mode, on the next screen to appear choose the option to go to a “root shell with networking”.

Next remove the install ATI drivers and install from scratch the ones you need:

sudo apt-get remove –purge xorg-driver-fglrx xserver-xorg-video-ati xserver-xorg-video-radeon
sudo apt-get install xserver-xorg-video-ati
sudo apt-get install –reinstall libgl1-mesa-glx libgl1-mesa-dri
dpkg-reconfigure -phigh xserver-xorg

If this doens’t work for you see the Ubuntu page mentioned above.