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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!

President's and Secretary's Combined Report to the Linux Users of Victoria, Inc, Annual General Meeting, 2012

To begin with it is necessary to say that circumstances has meant that this will be a report that combines the duties of President and Secretary, a matter that will be discussed further. Overall however, looking back over the past year, it can said that this has been another successful for Linux Users of Victoria. Starting from September last year, we hosted a very successful Software Freedom Day, which was extremely well-attended by relevant members of the community, providing an excellent opportunity for networking and planning.

OpenMPI 1.6.1 with PGI compilers installation issue

When installing the latest version of Open MPI (Version 1.6.1) with PGI compilers (specifically 12.5), the installation fails.

The following configure option are set:


CC=pgcc CXX=pgcpp F77=pgf77 FC=pgf90 ./configure --prefix=/usr/local/${BASE}-pgi --with-openib --with-tm=/usr/local/torque/latest --enable-static --enable-share

For Torque "latest" in this context is only 2.4.17, however that shouldn't be the issue. The make fails as follows:


make[6]: Leaving directory `/usr/local/src/OPENMPI/openmpi-1.6.1/ompi/contrib/vt/vt/tools/vtunify'

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