Category: English

How to set up a good partition scheme in Linux

May 9, 2010 / / 2 Comments

It’s always a good idea to have at least two partitions, one for your O.S. and one for your data. There are a lot of programs which you can use to part your harddrive  (e.g.: [ gparted | qparted ]).

I’m pretty happy with my current schema, which I developed long time ago, when my harddrive was only 40 Gb. I wrote about this in this old post, which I’m translating from Italian to English.

This is a schema for an old laptop of 40 Gb, but you can extend the concept.

Harddisk: 40 Gb

/ 10 Gb (root, where you will install the operative system)

swap 1Gb (should be the same amount of RAM you’ve got if you want to suspend)

/home 29 Gb

The main idea is to create a 10Gb for your O.S., the swap for the RAM and then everything left should go as space for the home.

This is pretty good way to part your disk because:

  1. Your data are detached from the O.S., so you can clean your partition very quickly and put a shiny new one in no time.
  2. 10 Gb is maybe too many for the O.S., but I tend to install a huge amount of stuff and sometimes when writing big file you need space in tmp.

So far it works for me.

With my new (3 years old…) laptop I have this figures:

 

18.4 Gb for the root (/)

4 Gb for the swap

87.7 Gb for the /home

It’s made of gold

April 27, 2010 / / 0 Comments

nexus_one

From the 26th of April is possible to preorder the Nexus One from Vodaphone U.K.
The funny part is they are asking 35£ per month with only 1Gb of data on a 24 months contract.

This is hilarious.

O2 is selling the iphone at 15£ per month, with unlimited amount of Data for a contract of 12 months.

Or you can have for 15£ per month as a tariff for a smart phone.

What exactly are they thinking in vodaphone?

I’m thinking to get a google phone just from google page and run it on O2 network…

We don’t talk about GIL

April 17, 2010 / / 0 Comments

GIL is the Global Interprer Lock for python

This video makes some really cool points.

Especially around the 3 minute. You can have a proper laugh 🙂

Interesting article about python parallelization

The first rule is we don’t talk about GIL.
The second rule is we don’t talk about GIL…

Github project support soon?

April 16, 2010 / / 1 Comment

It seems github will be supporting project accounts soon:

This would be very cool. Right now Neuronvisio is hosted under my account name, something not personal, but project centric make a lot of sense. Especially when you have more than one developer.

On top of this there is this amazing plugin for mercurial, which will make git user very easy if they want to collaborate with those.

Maybe Sumatra is going in this direction, maybe not. Back on this soon.

Sumatra and git support

April 7, 2010 / / 2 Comments

Sumatra is very cool idea which I felt the need from a long time. Andrew started the development of it and released the version 0.1 few days ago. The idea was great: record all the details about your simulation, storing the parameters, why you have launched it, what was the outcome. Tagging on top for categorization as well.

There was only one problem: Sumatra was not supporting git so I was unable to use it. Therefore, giving the fact was opensource I just baked a series of patches which were integrated in the tool and now sumatra has a git support 🙂

If you want to have a feel about it and want to try with git there is an example repository on github which you can use.

This is the results of the webinterface (sumatra stores everything in the django ORM system) showing the tables of the simulations:

If you click on the single record you can access the details of the simulation:

Using sumatra you will be able to:

  • search your simulations’ results
  • describe the results of the simulation on the simulation record itself, keeping everything very compact and ordered.
  • retrieve all the tiny details when you will need (papers hopefully..)

Storing all this informations is done automatically for you (except the analysis’ results of course), so you can focus more on your science, without worrrying on loosing your results.

Soon I’ll integrate sumatra in Neuronvisio.

P.S.: The patch for git integration (second part) is on its own way and it should be integrated soon in the tree, so you will need to run the bleeding edge and integrate the patch yourself if it’s not yet there (and you can’t wait 🙂 )

Have Fun

Neuronvisio 0.4.4 in the wild

April 1, 2010 / / 0 Comments

Today I released Neuronvisio 0.4.4 .

This release fix quite a lot of the doc and change the API to load the sqlite database. There are a lot of changes under the hood.

There is a lot of work going on on the plotting, and if you are interested to have a modularity (so you can plot anykind of variables and integrate is with Neuronvisio just let me know.

Have a look at the plot_vector() method in the Control class

I think it will be possible to refactor the code, creating a Plotter obj where the x and y are for the plot and how to create the legend. Then just pass this object to the plot routine, which will have no idea what is plotting, but is able to extract this info from the plot obj. This need a bit of thinking and use cases
What’s next:

There is an ongoing process to integrate Neuronvisio with sumatra. Sumatra is very handy software however it supports only hg and subversion for now, while I’m really based on git. For this reason there is a patch sent to Andrew to start to work on this. Hopefully Sumatra will support git soon and then I will start to see how to integrate that on Neuronvisio and TimeScale.
One problem I need to solve is how to save the geomtery of the model when I save the results of a simulation.

Using the NEURON ability to export the model in NeuroML and to reload it would be the way to go, but more investigation on this are required.

In the mean time..

.. enjoy Neuronvisio

Making patch with mercurial

March 30, 2010 / / 0 Comments

Just mirroring the solution I found here to find it later on.

How to make patch with git and with mercurial

git log
git log HEAD^ -p
git format-patch HEAD^
git send-email 001-patchname.patch
git send-email HEAD^ # alternatively

Doing the same w/ HG:

hg log # note this isn't paginated, a feature git has over hg imo
hg log -r tip -p
hg email -r tip

Who owns science?

March 17, 2010 / / 0 Comments

Who owns science

Patents, research driven by the market, blue sky research and other issues will be touched at the EMBL-EBI symposium this incoming Friday (19th).

I think the debate will be very interesting and the level of speakers is very high. Will be streamed on ustream so you can follow from home if you’re not in Cambridge.