Search Documentation


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.


NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.


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 Library

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.


MINPACK is a library of Fortran routines for the solution of non-linear, multivariate minimization problems.

Getting Started

Welcome to OSC! If you are new to supercomputing, new to OSC, or simply interested in getting an account (if you don't already have one), we have some resources to help you.

Available File Systems

Home Directories

Each user ID has a home directory on one of the NFS shared file systems. You have the same home directory regardless of what system you’re on, including all login nodes and all compute nodes, so your files are accessible everywhere. Most of your work in the login environment will be done in your home directory.

File System Usage

OSC has several different file systems where you can create files and directories. The characteristics of those systems and the policies associated with them determine their suitability for any particular purpose. This section describes the characteristics and policies that you should take into consideration in selecting a file system to use.

The various file systems are described in subsequent sections.