When developing a website, and in particular an intranet, for an organisation there is often a debate on what should be on the frontpage.

Different departments and different individuals all seem to have "strong opinions" on the matter.

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is used to model atoms or as a parallel particle simulator at the atomic, meso, or continuum scale. It has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. You may remember a difficult install from the past.

MVAPICH and MVAPICH2 is an implementation of MPI for computing systems and servers using InfiniBand, 10GigE/iWARP and RoCE & etc networking technologies.

Installation consists of downloading the tarball into an appropriate directory, extracting it, loading the enviroment variable modules, using of some previously established configuration files, runnig make and make install, and establishing the symbolic links. Note that MVAPICH and MVAPICH2 are entirely different products.


cd /usr/local/src/MVAPICH2

Tuning and Analysis Utilities (TAU) is a program and performance analysis tool for high-performance parallel and distributed computing with a suite of tools for static and dynamic analysis of programs written in C, C++, FORTRAN 77/90, Python, High Performance FORTRAN, and Java.

You'll also need the Program Database Toolkit (PDT), also available from the same location. Let's install that first. You'll need to set your environment variables. You use modules, right?


module load gcc/4.4.4
modulel load openmpi-gcc/1.3.4

R is a language and environment for statistical computing and graphics. To install R download the tarball to an appropriate place and extract e.g.,

cd /usr/local/SRC/R
wget http://cran.r-project.org/src/base/R-2/R-2.11.1.tar.gz
tar xvf R-2.11.1.tar.gz

Let the home page describe what it is about (in the worst possible English): "MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem.

Anyone who does even a modicum of web developments finds themselves taking tabled text, sometimes in the most horrid format, and having to introduce it into some sort of clean html.