Glenn

SPRNG

Computational stochastic approaches (Monte Carlo methods) based on random sampling are becoming extremely important research tools not only in their "traditional" fields such as physics, chemistry or applied mathematics but also in social sciences and, recently, in various branches of industry. An indication of importance is, for example, the fact that Monte Carlo calculations consume about one half of the supercomputer cycles. One of the indispensable and important ingredients for reliable and statistically sound calculations is the source of pseudo random numbers. SPRNG provides a scalable package for parallel pseudo random number generation which will be easy to use on a variety of architectures, especially in large-scale parallel Monte Carlo applications.

SPRNG 1.0 provides the user the various SPRNG random number generators each in its own library. For most users this is acceptable, as one rarely uses more than one type of generator in a single program. However, if the user desires this added flexibility, SPRNG 2.0 provides it. In all other respects, SPRNG 1.0 and SPRNG 2.0 are identical.

R

R is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques, and is highly extensible.

PAUP

PAUP is a leading program for performing phylogenetic analysis for bioinformatics sequences. PAUP currently runs as a single processor program. No further enhancements are suggested.

Octave

Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.

MrBayes

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. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

LS-DYNA

LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).

LAMMPS

The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems.  LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.

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