HPC Software

Compilers

Intel C and C++ Compiler

Intel compilers include advanced optimization and multithreading capabilities along with excellent compatibility with popular development environments.

"Quote from Official Website - November 2012" 

Available versions and module name

13.0.1 (intel-ics or intel-ics-2013)

10.1.018 (intel-cc-10.1.018)

9.1 20070215 (intel-cc-9.1.047)

Default version available

13.0.1

Website

http://software.intel.com/en-us/c-compilers/

Intel Fortran Compiler

Intel Fortran Compiling Suites include advanced optimization and multithreading capabilities, highly optimized performance libraries and analysis tools for creating fast reliable multithreaded applications.

"Quote from Official Website - November 2012" 

Available versions and module name

13.0.1 (intel-ics or intel-ics-2013)

10.1.018 (intel-fc-10.1.018 or intel-fc)

9.1.043 (intel-fc-9.1.043)

Default version available

13.0.1

Website

http://software.intel.com/en-us/fortran-compilers/

GNU Compiler

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system.

"Quote from Official Website - November 2012" 

Available versions and module name

gcc 4.3 (compiler/gcc-4.3

gcc-fortran 4.3 ( gcc-fortran-43 or gcc-fortran)

Default version available

gcc 4.3

gcc-fortran 4.3

Official Website

http://gcc.gnu.org/

Data Mining and Analysis Applications

NetCDF

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

"Quote from Official Website - December 2012" 

Available versions and module name

4.1.1 (netcdf-4.1.1 or netcdf)

Default version available

4.1.1

Official Website

http://www.unidata.ucar.edu/software/netcdf/

NCL
NCAR Command Language

NCL is an interpreted language designed specifically for scientific data analysis and visualization. 

"Quote from Official Website - December2012" 

Available versions and module name

5.1.1 (ncl-5.1.1 or ncl)

Default version available

5.1.1

Official Website

http://www.ncl.ucar.edu/

STIR

(Tomographic Imaging)

STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET, but other application areas and imaging modalities can and might be added.

STIR is the successor of the PARAPET software library which was the result of a (European Union funded) collaboration between 6 different partners (see Credits).

"Quote from Official Website - January 2013" 

Available versions and module name

  2.2 (STIR-2.2 or STIR)

Default version available

2.2

Official Website

http://stir.sourceforge.net/

Weka

Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes. 

"Quote from Official Website - November 2012" 

Available versions and module name

3.6.4 (weka-3-6-4 or weka)

3.6.1 (weka-3-6-1)

Default version available

3.6.4

Official Website

http://www.cs.waikato.ac.nz/ml/weka/

Development tools

GNU Emacs

GNU Emacs is an extensible, customizable text editor - and more.

"Quote from Official Website - November 2012" 

Available versions and module name

22.3.1

Official Website

http://www.gnu.org/software/emacs/

Engineering Applications

ANSYS (Fluent)

ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

"Quote from Official Website - November 2012" 

Available versions and module name

13.0 (ansys-10.3 or ansys)

Default version available

13.0 

Official Website

http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+Fluent

Comsol Multiphysics

The COMSOL Multiphysics simulation environment facilitates all the steps in the modeling process – defining your geometry, meshing, specifying your physics, solving, and then visualizing your results.

"Quote from Official Website - November 2012"

Available versions and module name

4.2a (comsol-4.2a)

4.1 (comsol-4.1) 

4.0 (comsol-4.0) 

3.4 (comsol-3.4) 

Default version available

Software not load by default 

Official Website

http://www.comsol.com/

Graphics Applications

ImageMagick

ImageMagick  is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.

"Quote from Official Website - December 2012" 

Available versions and module name

6.8.0-8 (imagemagick-6.8.0-8 or imagemagick)

Default version available

6.8.0-8

Official Website

http://www.imagemagick.org/script/index.php

Comsol Multiphysics

PLplot is a cross-platform software package for creating scientific plots. To help accomplish that task it is organized as a core C library, language bindings for that library, and device drivers which control how the plots are presented in non-interactive and interactive plotting contexts.

The PLplot core library can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs (of the same or different sizes) may be placed on a single page, and multiple pages are allowed for those device formats that support them.

"Quote from Official Website - December 2012"

Available versions and module name

5.9.9 (plplot-5.9.9 or plplot)

Default version available

5.9.9

Official Website

http://plplot.sourceforge.net/

Interpreters

Python

Available versions and module name

2.7.3 (python-2.7.3)

2.6.2 (python-2.6.2 or python)

Python Modules

A number of python modules are available

Available versions and module name

numpy -  1.3.0

ScientificPython - 2.9.0

psyco - 1.6

gmpy - 1.04

ScientificPython - 2.9.0

psyco - 1.6

Website

http://numpy.scipy.org/

http://www.scipy.org/

http://psyco.sourceforge.net/

http://gmpy.sourceforge.net/

Mathematics and Statics

Mathematica

Almost any workflow involves computing results, and that's what Mathematica does—from building a hedge-fund trading website or publishing interactive engineering textbooks, to developing embedded image-recognition algorithms or teaching calculus.

Mathematica is renowned as the world's ultimate application for computations. But it's much more—it's the only development platform fully integrating computation into complete workflows, moving you seamlessly from initial ideas all the way to deployed individual or enterprise solutions. 

"Quote from Official Website - November 2012"

Available versions and module name

6.0.3 (mathematica-6.0.3)

7.0 (mathematica-7.0)

8.0 (mathematica-8.0 or mathematica)

Official Website

http://www.wolfram.com/mathematica/

Documentation and Tutorials http://www.wolfram.com/mathematica/resources/

Grid Mathematica

Available versions and module name

2.1 (gridmathematica)

Default version available

Not installed by default 

Matlab

MATLAB^® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java^™.

"Quote from Official Website - November 2012"

Available versions and module name

r2012b (matlab-r20012b or matlab)

r2011b (matlab-r2011b)

r2009bSP1 (matlab-r2009b)

r2008SP1 (matlab-r2008SP1)

Default version available

2012b

Official Website

http://www.mathworks.com.au/products/matlab/

Matlab-Simulink

Simulink^® is a block diagram environment for multidomain simulation and Model-Based Design. It supports system-level design, simulation, automatic code generation, and continuous test and verification of embedded systems.

Simulink provides a graphical editor, customizable block libraries, and solvers for modeling and simulating dynamic systems. It is integrated with MATLAB^®, enabling you to incorporate MATLAB algorithms into models and export simulation results to MATLAB for further analysis.

"Quote from Official Website - December 2012"

Available versions and module name

r2012b (matlab-r20012b or matlab)

r2011b (matlab-r2011b)

r2009bSP1 (matlab-r2009b)

r2008SP1 (matlab-r2008SP1)

Default version available

2012b

Official Website

http://www.mathworks.com.au/products/simulink/

OpenBUGS

BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an ‘expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types.

"Quote from Official Website - December 2012"

Available versions and module name

3.2.2 (openbugs-3.2.2 or openbugs)

Default version available

3.2.2

Official Website

http://www.openbugs.info/w.cgi/FrontPage

R

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

Available versions and module name

2.14.2  (R-2.14.2 or R)

2.12.0 (R-2.12.0)

2.11.1 (R-2.11.1)

Default version available

2.14.2

Official Website

http://www.r-project.org/

Documentation and Manuals

http://cran.r-project.org/manuals.html

Run Time Environments

Software Libraries

"Quote from Official Website - December 2012"

Available versions and module name

  3.3.3 (fftw-3.3.3 or fftw)

Default version available

3.3.3

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

"Quote from Official Website - November 2012"

Available versions and module name

1.15 (gsl-1.15 or gsl)

Default version available

1.15

http://www.gnu.org/software/gsl/

Message Passing Interface (MPI) is a standardized and portable message-passing system designed by a group of researchers from academia and industry to function on a wide variety of parallel computers. The standard defines the syntax and semantics of a core of library routines useful to a wide range of users writing portable message-passing programs in ForTran or the C Programming Language". 

"Quote taken from http://en.wikipedia.org/wiki/Message_Passing_Interface  November 2012"

Available versions and module name

SGI Message Passing Toolkit  - 2.06 (mpt/2.06)

Intel MPI - 4.0 (mpi/intel-4.0)

Default version available

mpt - 2.06

Website

http://en.wikipedia.org/wiki/Message_Passing_Interface

http://techpubs.sgi.com/library/manuals/3000/007-3773-004/pdf/007-3773-004.pdf

http://software.intel.com/en-us/intel-mpi-library