lev_lafayette's blog

Our era has been defined by the ever-increasing scale and performance of information technology and its impact on many facets of society. Information technology has been made possible by the rapid, and continuing, development of semiconductor technology which enables high speed electronic processing and storage of data. These advances have continued unabated over more than six decades, enabling the realisation of computers with increasing speeds, sophistication and capability to facilitate the solution of complex problems of larger scale, more rapidly and with increased detail.

There has been a lot of social media and even mainstream media attention to the various problems people are encountering with the Nexus 7 (2012. 2013) tablets especially after upgrading to "lolipop" (5.1).

Parallel programming is the implementation of simultaneous computation typically applied through either tasks or data. In this introduction the need, core concepts, potential problems, and implementations will be described and illustrated with multiple examples in R, Python, C, and Fortran.

Presentation to Linux Users of Victoria, November 2015

High performance computing is a necessity for scientific research and increasingly so; however initial steps are also being made in vocational engineering at RMIT. Applying the andragogical principles in the education sector with free and open source content encourages educational connectivism which improves learning and relevance.

Presentation to the Open Source Developers Conference, Hobart, October 2015

Julia is a high-level, high-performance dynamic language for technical computing. With a "just in time" compiler, it is very fast, especially compared to languages like MATLAB, Octave, R etc. However it is relatively new and a cluster installation and package deployment has a few quirks.

Download the source from github. By default you will be building the latest unstable version of Julia from the git checkout. However, we want to run 0.4.0 (or rather, 0.4rc4) which is the last stable release.


# cd /usr/local/src/JULIA

Many Android devices come with storage configurations that are surprising to end-users. A product that is advertised as having 32 gigabytes of memory may in fact turn out to have much less available in terms of installing applications.

There are some excellent packages for GNU Octave, the free and open-source numerical computation language that is "highly compatible" with the proprietary and closed-source MATLAB (tm).

A researcher uses an HPC system to analyse DNA methylation data. However when they try to install some related libraries, the installation fails.

Mr. Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Download, extract. Note that the developers have produced a tarbomb which will require a separate directory created before download. This has been raised as a bug.

Note that more recent versions of MrBayes make much better use of autoconfiguration tools.


cd /usr/local/src/MRBAYES
mkdir mrbayes-3.2.5
cd mrbayes-3.2.5

GAMESS (General Atomic and Molecular Electronic Structure System (GAMESS)) is a general ab initio quantum chemistry package. You will need to agree to the license prior to download, which will provide a link to gamess-current.tar.gz

Download and extract, load the environment variables for atlas and gcc.


cd /usr/local/src/
tar gamess-current.tar.gz
cd gamess
module load atlas/3.10.2
module load gcc/4.9.1