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Installation of MVAPICH2 for Different Compilers

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

PDT/TAU Installation on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

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

Installing R and Updating Packages (with sed and Perl fun)

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.,

Installing MrBayes for MPI and 64-bit

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.

Sed, AWK and Creating HTML Tables

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.

Installing a GUI for EGSnrc Usercodes

A previous installation of EGSnrc was based around a command-line option. There is also a GUI interface for EGSnrc usercodes which is quite trivial to install and run.

Ensure that your environment variables for EGSnrc are loaded (e.g., module load egs). For example

set	HEN_HOUSE	/usr/local/EGSnrc/$version/
set	my_machine	x86_64-unknown-linux-gnu-pgf77
setenv  EGS_HOME	/home/$USER/egsnrc/

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

Underworld is a 3D-parallel geodynamic modelling framework capable of deriving viscous / viscoplastic thermal, chemical and thermochemical models consistent with tectonic processes, such as mantle convection and lithospheric deformation over long time scales.

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

Desmond is a software package developed at D.E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on parallel systems. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions.

Installing LAMMPS (and MEAM) on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

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.

I'm surprised I haven't documented this in the past, because I've installed it plenty of times. Nevertheless here's how it goes.

Replicating Packages on a new Debian/Ubuntu install

For a variety of reasons, you may wish to upgrade your Debian/Ubuntu or similar system without going through the normal process of a distribution update. Perhaps you are, for example, moving to entirely new hardware. Obviously you want to keep the data in your home directory; but you may also wish to keep the various packages you have previously downloaded. The following is some simple steps to make your life easier.

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