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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.

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

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.

Storage Hardware

The storage at OSC consists of servers, data storage subsystems, and networks providing a number of storage services to OSC HPC systems. The current configuration consists of:

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 molecular systems.  LAMMPS generally scales well on OSC platforms, offers a variety of modelling techniques, and offers GPU enhanced computation.

Jmol

Jmol is a simple molecular visualization program. It can read many file formats and can write various formats. Animations of normal modes and simulations are implemented. Jmol is an OpenScience Java application.

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