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Schrödinger, Maestro and Remote Connections

The installation of the chemical simulation suite, Schrödinger on high performance computer systems is hardly unusual. What is problematic is when users wish to access the GUI package, maestro, remotely using x-windows forwarding. Except when a user is extremely close to the system it is extremely likely that the graphic representation will be frustratingly slow for manipulation. There is, however, some ways around this.

JAGS (Just Another Gibbs Sampler) Installation.

For those fascinated by the world of analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation (and let's face it, who isn't?), there is a delightful program called JAGS. Unfortunately it is a little stubborn to install.

Download the latest version from our friends at Sourceforge and extract in a sensible place (e.g., /usr/local/src/JAGS.

Now witness some example failures to install, which a reasonable person would assume would be sufficient.

Rmpi and INLA: A couple of different R packages

Some R libraries and packages are easier to install than others. The typical method is to download the tarball and run R CMD INSTALL -l /path/to/library pkg1 pkg2 from the Linux command line or install.packages(c("pkg1", "pkg2")) from the R command-line after selecting from chooseCRANmirror(). But not every R package follows this contention.

The Worst of English

Presentation to the Unitarian School of Languages, Friday December 14, 2012

1. Phonemic representation

Can "ghoti" be pronounced "fish"?

gh is pronounced "f", like "enough".
o is pronounced "i", like "women".
ti is pronounced "sh", like "nation".

The first published reference is in 1874, citing an 1855 letter that credits ghoti to one William Ollier Jr.

Replace Latin Swedish with Unicode in PhpMyAdmin

When establishing a website database (e.g., Drupal, Wordpress etc) with PhpMyAdmin (e.g., through CPanel) one may be surprised to discover that the default character collation order is in latin1_swedish_ci. For most "plain text" ASCII-style posts this isn't a problem. It becomes a problem however when an article is supposed to display characters which require a different character set. A personal discovery of this nature was with Esperanto diacritical characters. Characters which latin1_swedish_ci cannot display will be replaced with "?", one per character.

The Story of Mel, A Real Programmer

This was posted to USENET by its author, Ed Nather (utastro!nather), on May 21, 1983.

A recent article devoted to the *macho* side of programming made the bald and unvarnished statement:

GAMESS Parallel Installation

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. Before installation you must agree to the license. A link will be provided from which the source can be downloaded.

Grafic++ Install with Environment Modules

Grafic++ MPI/C++ code to generate initial conditions for cosmological simulations using multiscale gaussian random fields, based on Edmund Bertschinger's GRAFIC-2 package. Provides a replacement for both grafic1 and grafic2.

Download from sourceforge http://sourceforge.net/projects/grafic/

Extract in a sensible place, change to that directory


cd /usr/local/src/GRAFIC
wget
tar xvf grafic++-1.1.3.tar.gz

Load requisite modules and export FFTW variables (as they won't be found). Seriously, it will drive you nuts if you don't do this.

Espresso Installation with Environment Modules

Espresso (Extensible Simulation Package for Research on Soft matter) is a "highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology."

Download the tarball and extract in a sensible place.


mkdir /usr/local/src/ESPRESSO
cd /usr/local/src/ESPRESSO
wget http://download.savannah.gnu.org/releases/espressomd/espresso-3.1.0.tar.gz

Software Freedom Day, 2012

SFD Melbourne 2012

Software Freedom Day: Saturday September 15

Linux Users of Victoria and Free Software Melbourne is hosting Software Freedom Day in Melbourne!

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