Here you will find information about scientific applications and libraries, and code development tools available on the Matrix and Jazz clusters, in the default (current) environment. Once logged in, use the module avail command to list all available software. For further information about our environment modules, please refer to the Matrix or Jazz guide.
It is worth having a look at this page before installing things on your own.

Compilers and parallel environment

• Gnu C/C++ and Fortran
• Intel C/C++ and Fortran
• PGI C/C++, Fortran
• OpenMPI

Development Tools

• Python along with ipython /IDLE IDE and scipy/numpy packages
• PERL
• Totalview: Source code and memory debugger for C, C++ and Fortran applications
• QTCreator: Cross-platform IDE application and GUI framework
• Vampir: Parallel code analysis framework

Numerical Libraries

• ACML: AMD Core Math Library
• BLACS: Basic Linear Algebra Communication Subprograms
• Boost: Boost C++ Libraries
• FFTW: A fast, free C FFT library!
• MKL: Math Kernel Library from Intel
• ScaLAPACK: Scalable Linear Algebra PACKage

Data Management Libraries

• CGNS: CFD General Notation System
• HDF5: library for machine-independent data formats
• NETCDF: library for machine-independent data formats

Applications

• Amber: Molecular Dynamics Package
• Avogadro: Free cross-platform molecule editor
• CP2K: Atomistic and molecular simulations program
• CPMD: Ab initio molecular dynamics
• DL_POLY: Classical Molecular Dynamics Simulation Software
• Gromacs: Molecular dynamics package primarily designed for biomolecular systems
• LAMMPS: Molecular Dynamics Simulator
• MATLAB
• NAMD: Scalable molecular dynamics code for large biomolecular systems
• R: Software environment for statistical computing and graphics

Data visualization and analysis

• Tecplot: Data visualization, Simulation Analytics, CFD analysis
• Visit: Visualization Tool
• VMD: Visual Molecular Dynamics
• AtomEye: Atomistic configuration viewer
• Chimera: Molecular structures interactive visualization and analysis

Only on Matrix

Numerical Libraries

• GSL Scientific Library

Applications

• Autodock: Software for automated docking calculations
• DOVIS: Autodock tool for virtual screening
• Gauss: Statistical package
• Gaussian: Quantum chemistry package
• MXAN: Tool for a quantitative analysis of the XANES region of the spectrum
• Nwchem: Quantum chemistry package
• OpenFOAM: Computational Fluids Dynamics package
• Quantum Espresso: Electronic structure calculation suite
• Rosetta: Tool for predicting and designing protein structures
• Stata: Data analysis and statistical software
• VASP: Ab Initio Simulation Package

Only on Jazz

Compilers and Development Tools

• CUDA Toolkit: GPU compiler, math libraries and tools for debugging
• CUDA Fortran extension provided by PGI

Numerical Libraries

• Cusp: Generic Parallel Algorithms for Sparse Matrix and Graph Computations
• MAGMA: Matrix Algebra on GPU and Multicore Architectures

GPU-enabled applications: AMBER, DL_POLY, Gromacs, LAMMPS, NAMD