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The New Government Supports Religious Bigotry

The new Victorian Premier, Ted Ballieu, has recently announced intention to change the Victoria's Equal Opportunity Act 2010 which ensured that religious organisations could not discriminate in the field of non-religious employment.

Installing Demon with Intel and OpenMPI

DeMon (Density of Montréal) "is a software package for density functional theory (DFT) calculations. It uses the linear combination of Gaussian-type orbital (LCGTO) approach for the self-consistent solution of the Kohn-Sham (KS) DFT equations. The calculation of the four-center electron repulsion integrals is avoided by introducing an auxiliary function basis for the variational fitting of the Coulomb potential."

The Future is GPGPU

Since the early 1990s the x86 line of CPUs has dominated the computer world. Although it has hardly entered popular consciousness that is all changing. A revolution is afoot, as significant as the change from mainframes to clustered or networked systems some twenty years ago. It is time to welcome our new GPU overlords who, in the November 2010 list of the world's supercomputers, have taken 1st, 3rd and 4th position.

Ignorant, Dangerous and Organised

Recently a PEW study surprised many by its announcement that most atheists know more about religion that those of strong belief, despite the fact that a majority consider religion to be "very important" to their lives. In other surprise figures, a sizeable minority of Protestants cannot name the gospels and a similar figure of Catholics are unaware of the sacrament of transubstantiation.

Upgrading Drupal Core and Modules

The following is a "sufficiently paranoid" approach to upgrading Drupal core and modules. As always, when one is going down this path the first thing to do is put the site in offline mode from admin/settings/site-maintenance.

Then make a back-up of your site, existing modules and themes, and database.


cp -r drupal-site drupalsite-bak
mysqldump drupal6-site > drupal6-site.sql

Download the core modules, based on the suggested updates from admin/reports/updates. You might even want to turn this into a script;

Installing BEAST on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

BEAST (Bayesian Evolutionary Analysis Sampling Trees ) "is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology".

Installing GROMACS on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

The GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics simulation package that is very fast and has support for different force fields. It is notable for being used for protein folding at Folding@Home.

Installation and Issues With Environment Modules Compiled Under 64 Bit

The Modules Package is a set of commands and information files that provides a simple command interface for modifying the environment. Each module in The Modules Package is a file containing the information needed to initialize the environment for a particular application (or any environment information). It's awesome, and installation is easy. But there is a bug...

Parallel NETCDF Installation

Parallel NETCDF is an implementation of the Network Common Data Form which supports parallel I/O. An excellent summary of the advantages are described by Choudhary, Liao, Gao, and Li.

Installation is fairly trivial. Download the tarball from the site, extract, load some modules, configure for the appropriate site, make and make install, and create modules. For example;


wget http://ftp.mcs.anl.gov/pub/parallel-netcdf/parallel-netcdf-1.2.0.tar.bz2

Installing and Testing Valgrind on Linux

Valgrind is an instrumentation framework for building dynamic analysis tools. Which is a fancy way of saying that it's a debugging suite that automatically detects many memory management and threading bugs, which is a very good thing. Valgrind can handle dynamically generated code, so long as none of the generated code is later overwritten by other generated code. It can also perform detailed profiling to help speed up your programs. It comes with extensive documentation.

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