Category Archives: Programming

braidlab 3.0 is out!

The latest full release of braidlab is out! Braidlab is a MATLAB toolbox which incorporates algorithms for analyzing braid groups of punctured disks in both theoretical and applied contexts. It was primarily written by Jean-Luc Thiffeault, but Michael Allshouse and I have contributed code to it as well. Feel free to direct your questions either at JLT or at me.

You can find a good summary of release updates on the main release-3.0 announcement, but here’s my list of favorites:

  • We moved the repository to GitHub. This means that you can (and should) use our Issue Tracker to let us know what went wrong or what you would like to see included in future releases. We are also present on MATLAB Central.
  • Installation from source should now work on Matlab 2014b without any special configuration. There are two known installation issues which are out of our reach: conflict of “mex” command with a LaTeX command, and lack of GMP libraries on your system. Make sure you read the installation guidelines in the manual first to see how to resolve these (and other) known problems.
  • “Data braids” now have a broader support. This type of braids is useful if you are trying to represent physical trajectories, which have an independent variable, e.g., time, attached to them.
  • More functions are implemented as MEX C++ code, which means that they ultimately run faster (some of them have even been parallelized!)

To install, go to the release page, scroll down, download the pre-packaged binaries. If you want to build from source, you can either download the source or even clone our git repository to stay up to date with the latest developments.

In all cases: let us know if braidlab works on your end and if you find it useful.

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Installing ATLAS with full LAPACK on 64 bit Linux

This is a walkthrough guide to installing ATLAS 3.8.3 with full LAPACK on 64 bit Linux. Hope you’ll find it useful. Continue reading

Holding it all!

If you ever used the “hold” command in Matlab and were annoyed by having to manage colors manually if you wanted to change colors for your data, there is hope! This link

http://blogs.mathworks.com/loren/2009/06/03/hold-everything/

shows you how you can harness Matlab plot’s color cycling mechanism across “hold”s!

Monitoring from afar

A test run of remotespy on fly

A test run of remotespy on fly

Let’s just assume that you have some important stuff being done on your server. A computation running, like I do, something getting compiled for a long time, or whatever else you might need. You don’t want to be sitting all the time, sshed in and running tail -f dump.log. So you think to yourself: “If only I could have this file posted to a website so I could just check it here and there from my cellphone”. That’s your wish (believe me — I can read minds). Well, I had the same wish a while back and this little script came out of it. Continue reading

Learning Python and Fortran

I have decided to invest some time into learning Python and Fortran (95) as I believe both may be useful in my future research. I’m usinPython Scripting for Computational Science by Langtangen for Python. I still haven’t decided on tutorial for F95, but it will most probably be Fortran 90/95 for Scientists and Engineers by Chapman.