Optimal configuration

2010 December 23

The miracle of life

Filed under: Uncategorized — Eric Fraga @ 20:49
Tags: , , ,

I recently ran into the following snippet of an interview with Craig Venter:

You know, I’ve asked two or three times, ‘Do you think you’re playing God?’ I mean, do you believe in God?
No. I believe the universe is far more wonderful than just assuming it was made by some higher power. I think the fact that these cells are software-driven machines and that software is DNA and that truly the secret of life is writing software, is pretty miraculous. Just seeing that process in the simplest forms that we’re just witnessing is pretty stunning.This comes from a 60 minutes interview.ORG-LIST-END


2010 October 21

Dual head with rotation with an nvidia graphics card on Debian Linux

Filed under: dualhead,linux,nouveau,nvidia,x11,xorg — Eric Fraga @ 16:16

I recently acquired a second display for my main system. I have been using a dual head system for a while but I now had two monitors which could change orientation. I decided it might be quite nice to have both of them in a portrait orientation as the majority of my work is either writing or coding. I would rather have more lines in my Emacs windows than more columns. I usually have auto-fill turned on and I also typically try to ensure that my coding limits itself to 80-100 columns at most.

However, when using the nv driver that is available in the Xorg system, I found that I could get dual head support but I could not manage to get xrandr to rotate the orientation for either screen. After a while searching, and trying a few of the options, it became clear to me that I was not going to manage to get nv to do what I wanted. At this point, I decided to explore the nouveau driver as I did not want to resort to the non-free nvidia driver that was also available.

nouveau seemed, from the documentation, to provide the features I wanted. However, this didn’t work at all out of the box, generating errors about drm cards, errors like this:

drmOpenDevice: node name is /dev/dri/card0
drmOpenByBusid: drmOpenMinor returns -1

After some searching on the web, I came across this page which pointed me in the right direction. It suggests updating libdrm but I already had the most up to date version. It also suggests, however, removing any traces of the proprietary nvidia driver. This did the trick! I did have to reboot after purging all evidence of that driver, and kernel modules etc, but I now have a dual rotated head system which is a joy to use!

2010 August 23

Sockets not quite working in Java

Filed under: debian,java — Eric Fraga @ 21:02

Recently, I had to revisit some code I had written in Java while back, as part of the Jacaranda system for process design and optimisation. This code provided a socket based interface for allowing Octave to communicate with Jacaranda. For some reason, the code which had worked for a very long time (years) now suddenly did not work. As it had been some months since I had used the code, I could not easily identify why.

Searching, using what I thought would be appropriate search terms, on the Web provided no hints as to what may have gone wrong. I gave up and found a different way to solve my problem, using the Octave Forge Java package. So I was happy.

Until today when I needed to install gPROMS from PSE Ltd, one of the few closed source packages I need to use every now and again. This package also makes use of sockets to communicate between different components of the system. So it was back to searching. This time I was more successful and found that the solution was related to Debian‘s recent changes with respect to IPV6 (Debian bug report #560056).

The solution was to turn off a particular system level configuration option:

sysctl net.ipv6.bindv6only=0

(as super-user, of course). This change can be made permanent by editing the file /etc/sysctl.d/bindv6only.conf.

2010-08-23 Mon 22:02

2010 April 4

New project on novel nano-catalysts for CO_2 conversion

Filed under: Research — Eric Fraga @ 00:33

2010-04-04 Sun

A new EPSRC funded project has just been announced, led by Professor Nora de Leeuw, UCL Chemistry. To quote from the grant proposal, we propose to use a robust combination of state-of-the-art computation and experiment in a grand challenge to design, synthesise, test, characterise, evaluate and produce for scale-up novel iron-nickel sulfide nano-catalysts for the activation and chemical modification of CO2. The design of the (Ni,Fe)S nano-particles is inspired by the active sites in modern biological systems, which are tailored to the complex redox processes in the conversion of CO2 to biomass. This is a completely new area for me so I am understandably quite excited!

2010 March 22

Installing Debian Linux on a Samsung N220

Filed under: linux — Eric Fraga @ 14:34

2010-03-22 Mon

Recently, I had to buy a new laptop for giving presentations. The laptop I ended up with is a Samsung N220, a netbook (although not a netbook as was as these latest netbooks are really the same size as some old laptops I’ve owned in the past…) with a very snazzy skin. I got the red one.

Anyway, this laptop came with an operating system I find no use for, even if it’s now in version 7, so the first thing I did was try the most recent Ubuntu release. I find that this is usually a good test of what is possible with new hardware. In this case, everything seemed to go quite nicely, including sound and being able to suspend to RAM.

However, I prefer having Debian on my systems. For new hardware, it’s usually best to go with the testing version as the drivers will be more up to date. The current testing version is known as squeeze. I downloaded the necessary files and prepared a USB disk using unetbootin. I booted the system after having setup the bios to allow booting from USB.

Almost everything worked out of the box. A few things did not work:

to get wireless working on my system, I noticed from dmesg that the card was being recognised. The card is a Realtek 8192 and the driver is r8192_pci. However, this driver needs firmware that is not distributed by Debian. I downloaded the firmware from links given in a thread on linuxquestions.org. Placed the files in /usr/local/lib/firmware/, rebooted and everything worked fine.

However, I believe that there may be some problems with the driver which make the wireless not function correctly after suspend to ram, although not always. I’m still investigating this.

screen brightness
the next problem was that the screen was quite dim and the keys for changing the brightness level (see next item) did not work. Some searching on the Web led me to the following magical incantation for setting the brightness:

     setpci -s 00:02.0 F4.B=xx

where xx is the level in hexadecimal with values between 00 (no backlighting) and ff (full light). I find that a value around 60 works quite well.

There is a script for making this easier to use.

hot keys
Most of the blue keys, meant to be used with Fn key, do not work out of the box. Two of them do: the suspend (top left on my keyboard) and the toggle for the touchpad (F10, again on my keyboard). The others do nothing at all. This page describes show to assign keycodes to these special function keys. Once keycodes have been assigned, you can then use whatever system your window or desktop manager of choice provides for binding these keys to desired commands. I use ratpoison which provides a very simple definekey command for this purpose.

2009 October 23

Running optimally

Filed under: Uncategorized — Eric Fraga @ 17:54

I loved this post comparing running a marathon to an optimisation problem! Although I do run a bit, I cannot even begin to imagine running a marathon. I can, however, imagine the goal of minimising misery.

2009 August 12

Crawley Down Pond

Filed under: Photos — Eric Fraga @ 13:26

In the middle of debugging some finite element code, I realised I was gettting nowhere (multi-dimensional problem with adaptive grids) so I decided to go for a bike ride to clear the mind. I went on the Worth Way which is part of the national cycle route 21 from London to Eastbourne. The bit I did was from Crawley to East Grinstead and back again, about 1.5 hours at my possibly leisurely pace!

2009 August 10

A Canadian abroad

Filed under: Uncategorized — Eric Fraga @ 17:40

As a Canadian living abroad, I don’t often get the chance to see the Canadian flag flying, unless I purposely go for a walk to Trafalgar Square in London, of course.  So it was a pleasant surprise to see the Canadian flag flying at Newhaven Fort in Sussex.

After visiting the fort, the reason for the flag is clear: the fort was used to station Canadian troops during the second World War.

The Canadians

2009 August 6


Filed under: Research — Eric Fraga @ 14:43
Tags: , ,

In early June, I attended the FutureSource exhibition at the ExCel exhibition centre in the docklands area of London. The exhibition was impressive. There were many companies demonstrating and presenting a very wide range of solutions in the renewable energy and waste to energy areas (amongst other things but these were the two areas that interested me).

I was primarily there, however, to attend a presentation by an Austrian delegation on the current state of the art in Austria in terms of renewable energy. Very impressive.


Filed under: Research — Eric Fraga @ 09:51
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In June, I went to the ESCAPE 19 conference in Krakow. I was only there for two short days and, therefore, photographic opportunities were rather limited.  I had to make best use of the time there to talk to colleagues from around the world. Also, the weather was not particularly good, at least this day.

The conference was excellent with good talks and posters and the city was lovely.  The first night I was there, I went out with some of the PhD students from our lab, as well as some colleagues from UCL and elsewhere, and we ran into Andrzej.  We convinced him to join us for a second dinner.  He took us to an absolutely wonderful restaurant on the main square (south side) of Krakow.

Dinner in Krakow

The photo shows, from left to right, Laureano, Eria, Songsong, Andrzej, Melanie, Giovanna, Adam and Suzie.

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