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HPC Software - 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. [Mathematica 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)

9.0.1 (mathematica-9.0 or mathematica)

Default version available

9.0.1

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 loaded by default

Website

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

Matlab (21 Licenses Available)

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.  [Matlab Website - November 2012]

Available versions and module name

r2020a (matlab-r2020a)

r2019a (matlab-r2019a or matlab)

r2018b (matlab-r2018b)

r2018a (matlab-r2018a)

r2017b (matlab-r2017b)

r2017a (matlab-r2017a)

r2016b (matlab-r2016b)

r2015b (matlab-r2015b)

r2015a (matlab-r2015a)

r2014a (matlab-r2014a)

r2013b (matlab-r2013b)

r2012b (matlab-r2012b)

r2011b (matlab-r2011b)

r2009bSP1 (matlab-r2009b)

r2008SP1 (matlab-r2008SP1)

Default version available

r2019a

Official Website

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

Matlab-Simulink (16 Licenses Available)

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. [Matlab Simulink Website - November 2012]

Available versions and module name

r2019a(matlab-r2019a or matlab)

r2018b (matlab-r2018b)

r2018a (matlab-r2018a)

r2017b (matlab-r2017b)

r2017a (matlab-r2017a)

r2016b (matlab-r2016b)

r2015b (matlab-r2015b)

r2015a (matlab-r2015a)

r2014a (matlab-r2014a)

r2013b (matlab-r2013b)

r2012b (matlab-r2012b)

r2011b (matlab-r2011b)

r2009bSP1 (matlab-r2009b)

r2008SP1 (matlab-r2008SP1)

Default version available

2019a

Official Website

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

MatLab ToolBoxes

Available ToolBoxes and available Licences

(Available for all versions of Matlab)

Aerospace_Blockset            1
Aerospace_Toolbox             1
Bioinformatics_Toolbox        1
Communication_Blocks          5
Communication_Toolbox         5
Control_Toolbox               7
Distrib_Computing_Toolbox     5
Embedded_IDE_Link             5
Fixed-Point_Blocks            5
Fixed_Point_Toolbox           5
Fuzzy_Toolbox                 6
GADS_Toolbox                  1
Identification_Toolbox        1
Image_Toolbox                 1
MATLAB_Coder                  7
Neural_Network_Toolbox        12
Optimization_Toolbox          6
Power_System_Blocks           5
Real-Time_Workshop            7
Robust_Toolbox                1
RTW_Embedded_Coder            6
Signal_Blocks                 5
Signal_Toolbox                5
Simulink_Control_Design       6
SL_Verification_Validation    1
Stateflow_Coder               1
Statistics_Toolbox            9
Symbolic_Toolbox              10
Target_Support_Package        5
Vehicle_Network_Toolbox       5
Wavelet_Toolbox               5

 

Office Website for Toolboxes

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

Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.

Octave is distributed under the terms of the GNU General Public License. 

 [Octave Website - November 2013]

Available versions and module name

5.2.0 (octave-5.2.0 or octave)

3.6.4 (octave-3.6.4)

Default version available

35.2.0

Official Website

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

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. [Open Bugs 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. [R Website - November 2012]

Available versions and module name

3.5.3 (R-3.5.3)

3.2.3 (R-3.2.3)

3.1.1 (R-3.2.3)

3.0.2 (R-3.0.2 or R)

3.0.1 (R-3.0.1)

2.15.2  (R-2.15.2)

2.15.1  (R-2.15.2)

2.14.2  (R-2.14.2)

2.14.1  (R-2.14.1)

2.12.2 (R-2.12.2)

Default version available

3.5.3

Official Website

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

Documentation and Manuals

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

http://www.rdocumentation.org/

SPSS (by IBM)

The IBM SPSS Statistics Premium Edition helps data analysts, planners, forecasters, survey researchers, program evaluators and database marketers – among others – to easily accomplish tasks at every phase of the analytical process. It includes a broad array of fully integrated Statistics capabilities and related products for specialized analytical tasks across the enterprise. The software will improve productivity significantly and help achieve superior results for specific projects and business goals.   [SPSS Website - March 2014]

Available versions and module name

22 (spss or spss-22)

Default version available

22

Official Website

http://www-03.ibm.com/software/products/en/spss-stats-premium/

If, for whatever reason, you would like to use the older versions of the compilers, or other available software, you can simply "unload" the current module and load the older version. See Software Module Information webpage.

Software list

Bioinformatics
  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
Compilers
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
Data Mining and Analysis Applications
  • NCL (NCAR Command Language)
  • Ncview
  • NetCDF
  • NetCDF-Fortran
  • RapidMiner
  • STIR (Tomographic Imaging)
  • Weka
Development tools
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
Documentation Tools
  • Tex Live
  • Tex Info
Engineering Applications
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
Geospatial Tools
  • GDAL
  • GEOS
  • Panoply
Graphics Applications
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
Interpreters
  • Perl
  • Python (with many Modules Installed)
Mathematics and Statics
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
Run Time Environments
  • Java
Simulation Software
  • APSIM
Software Libraries
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS
Text Tools and Software
  • Flex