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Tutorials

VPAC provides a range of practical guides leading VPAC users through key features and functions of various software applications installed on VPAC’s High Performance Computers.

Basic Tutorials

Linux Commands and File Structure

Knowledge of basic Linux commands and the file structure is necessary for any development on VPAC's high performance computers. The following summary provides a foundation for further research. For those unfamiliar with Linux, it should be printed out and kept as a 'crib sheet'. See More

Logging On and Transferring Files

To log on to a VPAC supercomputer, you will need a user account and password and a Secure Shell 2 (ssh) client. VPAC does not allow protocols such as Telnet, FTP or RSH as they insecurely send plain-text passwords over the network. Linux distributions almost always include SSH as part of the default installation as does Mac OS 10.x, although you may also wish to use the Fugu SSH client. For MS-Windows users, we recommend using the PuTTY SSH client. See More

Editing Files: nano, vim and emacs

There are three main text editors available on Linux systems. The first is nano, a very easy to use clone from the Pine email client that uses control keys with a the equivalent of a "shortcut bar". The hefty Emacs (Editor Macros) editor and environment is a feature-rich program that was first written in 1976 and is now up to version 22.1! Also deriving initially from 1976 is vim (Vi improved) which is a series of enhancements build on the "screen orientated" text editor vi. Vim is generally understood to be a modal editor, operating either in a insert mode (where typed text becomes part of the document) or command mode (where keystrokes are interpreted as commands that control the edit session). Vi or Vim are usually installed as the default text editor. See More

Modules

Modules are a set of commands that modify the system environment. Each module in is a file containing the information needed to initialise environment variables for a particular application. The advantage of the modules approach is that the user is not required to specify paths for different executable versions.See More

Intermediate Tutorials

Submitting and Running HPC Jobs

Submitting and running jobs on the cluster is a straight forward procedure with 3 basic steps: I) Setup and launch, II) Monitor progress and III) Retrieve and analyze the results. See More

NAMD

NAMD is a parallel, molecular dynamics simulation program used to model large biomolecular systems using high performance computing clusters which is freely available for academic work. If you are interested in running NAMD simulations you should also install a local copy of VMD on your own computer. VMD is a molecular viewer program that can be used to help set up NAMD simulation and to help analyze and visualize NAMD output. See More

Abaqus

Abaqus is a commercial software package for finite element analysis used in the automotive, aerospace, and industrial product industries. It is particularly popular with academic and research institutions due to the wide material modeling capability, and the program's ability to be customised. Abaqus provides a collection of multiphysics capabilities allowing for production-level simulations where multiple fields need to be coupled. Abaqus was initially designed to address non-linear physical behavior and comes with an extensive range of material models. See More

Advanced Tutorials

Compiling MPI Applications

MPI is a de facto standard, language-independent communications protocol used to program parallel computers with Language Independent Specifications (LIS) for the function calls and language bindings. Most MPI implementations are a combination of C, C++ and assembly language, and target C, C++, and Fortran programmers. This tutorial is a simple compilation example in C using GNU and Portland Group compilers. See More

Using Matlab DCS

MATLAB is a numerical computing environment and programming language used for computation, visualisation and programming for algorithm development, mathmatics (especially matrix and array computations with control flow), and engineering graphics. VPAC allows licensed users with a MATLAB parallel computing toolbox installed on their client machine to make use of the MATLAB Distributed Computing Server (DCS). See more.