OpenFOAM is a suite of computational fluid dynamics applications. It contains myriad solvers, both compressible and incompressible, as well as many utilities and libraries.
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.
MATLAB is a technical computing environment for high-performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use envionment where problems and solutions are expressed just as they are written mathematically--without traditional programming.
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 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.
MPI is a standard library for performing parallel processing using a distributed-memory model. The Glenn and Oakley clusters at OSC use the MVAPICH implementation of the Message Passing Interface (MPI), which is based on MPICH and optimized for the high-speed Infiniband interconnects.
MVAPICH2, based on the MPI-2 standard, is installed on both Oakley and Glenn. The older MVAPICH, based on the MPI-1 standard, is installed on Glenn only.
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).
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large molecular systems. LAMMPS generally scales well on OSC platforms, offers a variety of modelling techniques, and offers GPU enhanced computation.
The Intel compilers for both C/C++ and FORTRAN.
Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:
- if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
- the top hits in a BLAST search are hypothetical sequences from genome projects.
- your protein consists of several domains which are of different types.
HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.
HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.