Back Again

created: 18 Sep 2010 18:18
tags: chemmcom
After a looong pause, I'm back updating Chembytes. I was busy with papers, debugging and other problems, so Chembytes was not my first priority. Now everything is back to normal, so I have start to write again and new topics are on the way.

The first great news, is that I have start to collect all the scrapnotes i have in Evernote notebooks. The first notebook with 10 tips is already available here, both in evernote and html format.

The choice of Evernote is due to the fact that is free and is a powerful software to store, manage and search notes, while this is difficult to do in a wiki. Let me know if you like this experiment
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Gpu Computing

created: 12 Jul 2010 14:57
tags: geeky
Back to blogging, before the summer break. A friend of mine send me an interesting mail about GPU computing. Yes, GPU (as for Graphical Processing Unit) and not CPU. The mail is below:

On Thursday I went to London to learn about GPU (graphics processing
unit) accelerated calculations. GPUs seem to be the future in high
performance computing they can provide computing power (per gigaflop)
10 times cheaper and using 20 times less energy than conventional CPUs
(=> less electricity and air conditioning running costs). This is
achieved through a highly parallel architecture; each graphics card
can have up to 512 cores and one can put up to 4 GPUs in a single
desktop. Connecting 2000 CPUs together and achieving good scaling
would require huge investments in special high speed interconnects
(e.g. infiniband) that are far too expensive for most universities and
thus only used in supercomputing centres. This is why on Lucky (where
the nodes are connected with gigabit Ethernet) you can only hope for
good scaling using the cores in a single node, so max 8 cores. Using a
desktop with 4 GPUs, you have 2000 GPU cores in one machine using
shared memory, so you can run parallel jobs on 2000 cores without the
need for expensive high speed interconnects.

While not all applications have been rewritten to work on GPUs, there
is a lot of work going on and progress being made. See for details.

MD codes which now support GPU acceleration include:

NAMD 2.7 Beta 2 including CUDA Acceleration
HOOMD: Highly Optimized Object Oriented Molecular Dynamics
GROMACS using OpenMM
ACEMD Bio-molecular Dynamics Package

For quantum chemistry there is a Terachem, written especially for GPUs
which offers up to 1000 x speed up using a GPU compared to using a
single CPU using the GAMESS QC package. Unfortunately, the
functionality is limited at the moment; it can only handle S and P
orbitals and can only do basic single point calculations,
optimisations, transition state searches and molecular dynamics. No TD
or CI for the moment see

However, GAMESS (US) is currently working on a GPU implementation
which should be able to do CI and TD calculations, but it may be some
time before it is ready.

For those of you who use Matlab, there is also a GPU accelerated
version of Matlab see to get
an idea of the speedups which can be achieved.

If anyone wants to buy a GPU personal supercomputer, you can find them
at Once you put a
reasonable amount of RAM on the machine and add a 2050 GPU, it's about
5000 euros for one machine. But remember this can do an AMBER MD
simulation at the same speed as 64 cores on a supercomputer, which
would cost ~ 50000 euros. And you don't need a special air-conditioned
room, you can put it under your desk.

Not bad eh?
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Leeenux V3

created: 06 Apr 2010 17:36
tags: eeepc leeenux
Few days ago the new version of leeenux was released. Despite the fact I was really happy with the old version (2.0), I have decided to spend part of the belgian rainy easter testing the new version on my 701.

With respect version 2.0, the main differences are:

New kernel, new UNR menu, splitting up from EasyPeasy and switching to Ubuntu Minimal as base, new applications. Leeenux usplash, xsplash, gdm login. New eee-control modes. For eee 701g (2G, 4G, 4G surf - with Intel Celeron): 450MHz, 540MHz, 630MHz, 765MHz, 900MHz, and overclocking to 945MHz. Corrected modes for netbooks with Intel Atom processor.

I've downloaded the standard edition (extended and game editions are also available): the iso is of 450MB and once installed takes 1.3GB of space on the hard disk. Not bad.
The installation is fast and dummy proof, not a single problem. About the installation I can only say to do manually the HD partitioning, so to get rid of the swap partition of 256MB. With 1GB of ram is almost useless, it take a lot of space (I have 4GB…) and increase the number of read/write cycles for my little SSD HD.

First impressions
The boot, once leeenux is installed, is fast: I would say about 30 sec to arrive at the login screen. The new graphical interface loose a bit of appeal with respect the old one, but I have to admit is more clean

The new gui (the background is mine…)

The top bar can be customized with some applets, which allows to use multiple workspaces.

Navigation through the menus and screens is smooth even with the cpu underclocked at 450MHz (by default the clock is set to 630MHz). The new settings for the cpu clock seems to work flawlessly and allows to manage heat (the cpu temperature while I write this page increase from 48-50 @450MHz to 53 degrees Celsius at 900MHz. Also, the frame gets noticeable hotter) and the duration of the battery (1h30 and I'm still 40%… btw, the battery is almost dead) Also, the Eee icons let us turn on and off wifi and card reader, but not the camera (pity).

All the function keys are working, as well as resume/suspend, wi-fi, brightness, external screen and mute/volume with relative OSD. Microphone is also working, while the camera is, for me, in black and white only, both in cheese and skype. Yes, I have tried to change the size/resolution of the camera. Well, not a big deal for me.

As usual, the pre-installed software is a good selection, and can make happy the majority of the users. What is missing, can be easily installed via synaptic.
Since I need a scientific distro, I had to remove some software I was not going to use, in order to install what I needed. in particular I have removed:

  • all the games and emulators
  • thunderbird
  • sunbird
  • prism facebook
  • rhythmbox
  • gnasm video player
  • abiword
  • gnumeric
  • paint

and some other minor packages

What I have installed is:
for work:

  • latex
  • openoffice (I needed for impress)
  • gfortran
  • java
  • gnuplot
  • xmgrace
  • imagemagick
  • povray
  • tachyon
  • pyton-numpy
  • gromacs
  • tinker
  • vmd
  • marvin beans
  • ekee
  • openbabel
  • skype
  • chrome
  • prism google-mail

for fun:

  • gphoto2
  • babelgps

and something more.
This leave me with 909 MB free on 3.7GB (25% free), more than enough to work, considering I have a 8GB SD always in my card reader.

Now, many people find the screen of the 701 too small to work, and that is true, but with leeenux… is a bit less true. Every window is maximized by default so there is plenty of space. Let's see some examples:

From the repository, we can install the version 3.1. Openoffice has a quite messy GUI: lots of icons, menus and sections. I have set the view options to scale the interface to 90% and to use the small icons. The result is below:


Not bad.

The terminal is simply perfect:


Browser: Chrome
Already Chrome has a clean interface, that makes it perfect for the small screens like that of the 701, plus it can be used fullscreen (F11):


xmgrace is not well displayed by default, but it is enough to add the option -free to the command used to fire it up (also via the menu), and you will get:


Marvin Beans
Marvin Beans is one of the best suite to work with chemical structures: it has a 2D editor with 3D clean up capabilities, a converter and a 3D viewer. It runs wonderfully in Leeenux:


VMD is a bit tricky: I would suggest you to unmaximize at least the main gui. in the picture, a caffeine molecules is displayed and the tk console is also active. All in unmaximized mode. Hint: use the option -size 400 400 to start vmd, so that when unmaximized you will have a manageable windows.


I use gThumb to create screenshows of images of plots or VMD renderings. Also, it can be used to perform basic photo editing.


You cannot use a computer in the lab if it cannot visualize pdf files. In Leeenux evince is installed by default. Here in action in full screen mode with a paper of mine:


In few words, leeenux is the uber distro for the 701 and, probably for all the netbooks out there.
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