The following list of software is available on the nyx cluster. To access any of these packages, use the module load modulename command; for more information on the module command see our module documentation page.

Many of these packages have multiple versions, to see available versions, type module avail.

 

Module Name	Versions	Description	Additional Information
R	2.9.1	R is a software environment for statistical computing	Vendor Website
abaqus	6.8	abaqus is set of general purpose nonlinear finite element analysis (FEA) tools	CAC Documentation Vendor Website
abinit	5.8.4-intel	ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis.	Vendor Website
aces2	2005	ACES II (= Advanced Concepts in Electronic Structure) is a series of programs for performing high-level quantum chemical ab initio calculations. Its major strength is the accurate calculation of atomic and molecular energies as well as properties using "many-body" techniques such as many-body perturbation theory (MBPT) and, in particular coupled-cluster techniques to treat electron correlation.	Vendor Website
acml	4.0.1-gcc 4.0.1-gcc-mp 4.1.1-pgi 4.2.0-pgi-i8	ACML is the AMD Core Math Library, which contains functions from BLAS and LAPACK, among other things, optimized for the AMD CPUs	Vendor Website
adina	8.5.2	ADINA System for the analysis of solids, structures, fluids and fluid flow with structural interactions.	Vendor Website
amber	8.0	Amber a set of molecular mechanical force fields for the simulation of biomolecules	CAC Documentation Vendor Website
ampl	2008	AMPL is a comprehensive, powerful and flexible algebraic modeling language	CAEN Documentation Vendor Website
ansys	11.0	ANSYS, produced by ANSYS, Inc., is a finite element simulation tool that incorporates multiphysics to simulate real world conditions. This allows users to analyze parts for behavior under multiple physical forces simultaneously	CAEN Documentation Vendor Website
autodock	4.0.1	AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.	Vendor Website
blat	34	Blat is a tool which performs rapid mRNA/DNA and cross-species protein alignments.	Vendor Website
boost	1.39.0	Boost provides free peer-reviewed portable C++ source libraries.	Vendor Website
cfour	beta	CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum mechanical calculations on atoms and molecules.	Vendor Website
charmm	c32b2 c35b2	CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. You must possess a license to use this software.	CAC Documentation Vendor Website
chemkin	4.1	CHEMKIN software enables the simulation of complex chemical reactions	Vendor Website
cmake	2.6.4	CMake is a family of tools designed to build, test and package software.	Vendor Website
comsol	3.4 3.5a	COMSOL Multiphysics is a modeling package for the simulation of any physical process you can describe with partial differential equations	CAC Documentation CAEN Documentation Vendor Website
cplex	11.0	CPLEX is a high-performance optimizer for linear programming	CAC Documentation CAEN Documentation Vendor Website
cplex-threaded	11.0	CPLEX is a high-performance optimizer for linear programming	CAC Documentation CAEN Documentation Vendor Website
cubit	11.1	loads the CUBIT Mesh Generation Kit	Vendor Website
cuda	2.2	CUDA is the development environment for using nVidia's graphics cards for processing	CAC Documentation Vendor Website
ddt	2.4.1	Distributed Debugging Tool is a comprehensive graphical debugger designed for the complex task of debugging parallel code.	CAC Documentation Vendor Website
espresso	4.1-pgi	Espresso: Electronic Structure Computation Software	Vendor Website
fftw	2.1.5-gcc 2.1.5-intel 2.1.5-pgi 3.2.1-gcc 3.2.1-intel 3.2.1-pgi	FFTW is a C/Fortran subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions	Vendor Website
flomerics	72	FLOTHERM is a powerful 3D computational fluid dynamics software that predicts airflow and heat transfer in and around electronic equipment, including the coupled effects of conduction, convection and radiation.	Vendor Website
fluent	12.0 6.3	fluent - a comprehensive CFD (computational fluid dynamics) analysis tool. The FLUENT solver can be used to model turbulence, combustion, and multiphase applications.	CAC Documentation CAEN Documentation Vendor Website
gaussian	03-32bit 03-64bit 03-64bit-linda	Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.	CAC Documentation CAEN Documentation Vendor Website
grads	2.0.a7.1	The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.	Vendor Website
gromacs	3.3.1-gcc 4.0.2-gcc 4.0.5-gcc	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.	CAC Documentation Vendor Website
gti	6.2	GT-SUITE offers the only true virtual engine/powertrain tool, capable of integrated simulations of the total engine and powertrain system	Vendor Website
hdf5	1.6.9-gcc 1.6.9-pgi 1.8.3-gcc 1.8.3-intel 1.8.3-pgi 1.8.3-pgi-par	HDF5 is a set of file formats and libraries designed to store and organize large amounts of numerical data.	Vendor Website
helios	1.10	loads the HELIOS Generalized Geometry Lattice Analysis package	Vendor Website
hfss	10.1 11.1	loads the hfss environment for Full-Wave Sprice extraction and electromagnetic field simulation	CAC Documentation Vendor Website
hspice	2006.09-sp1	HSPICE is used for circuit simulation	Vendor Website
idl	7.0	IDL is software for data analysis, visualization, and cross-platform application development	CAEN Documentation Vendor Website
intel-comp	10.0 11.0 9.1 c-10.0.025 c-11.0.074 c-9.1.043 fortran-10.0.025 fortran-11.0.074 fortran-9.1.037	This loads both the Intel C and Fortran compilers	Vendor Website
java	1.6.0_01	loads the Java development and runtime environment	Vendor Website
lammps	1Jul09	A classical molecular dynamics code LAMMPS, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator	Vendor Website
lsdyna	971-R421	LS-DYNA is a general purpose transient dynamic finite element program; we support a parallel version	Vendor Website
marc	2007r1	MARC is a non-linear FEA program	CAEN Documentation Vendor Website
mathematica	6.0	Mathematica is a compuer algebra system	CAC Documentation CAEN Documentation Vendor Website
matlab	2009a	Matlab is interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design	CAC Documentation CAEN Documentation Vendor Website
mcnp5	1.4 1.51	loads the mcnp5 environment	Vendor Website
metis	4.0.1-pgi	METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering	Vendor Website
mkl	10.1	This loads the Intel Math Kernel Library (MKL) runtime.	Vendor Website
moab
modules		loads the modules environment
molpro	2008.1-intel	Molpro is a complete system of ab initio programs for molecular electronic structure calculations	Vendor Website
mpiexec	0.83	Mpiexec is a replacement program for the script mpirun, which is part of the mpich package.	Vendor Website
msmodel	4.4	Material Studio -- a software environment that brings the world's most advanced and validated materials simulation technology to the CAC	CAC Documentation CAEN Documentation Vendor Website
nag	5.1 5.2	NAGWARE - f95/f90 fortran compiler	CAC Documentation CAEN Documentation Vendor Website
naglib	7.0-gcc 7.0-pgi 7.0-pgi-mp	NAG has over 1,450 tried and tested routines that are both flexible and portable	Vendor Website
namd	2.7b1	NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.	Vendor Website
nastran	r3	Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies	CAC Documentation CAEN Documentation Vendor Website
ncbi	200908	Provides Blast. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.	Vendor Website
nco	3.9.9	The netCDF Operators, or NCO, are a suite of programs known as operators. Each operator is a standalone, command line program which is executed at the UNIX shell-level like, e.g., ls or mkdir. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output.	Vendor Website
netcdf	4.0-gcc 4.0-pgi	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data	Vendor Website
ocean	6.1-32bit 6.1-64bit	loads the Open Command Environment OCEAN part of Cadence IC	Vendor Website
octave	2.1.57	GNU Octave is a high-level language, primarily intended for numerical computations.	Vendor Website
openfoam	1.5	OpenFOAM CFD Toolbox	Vendor Website
openmpi	1.2.6-intel 1.3.2-gcc 1.3.2-intel 1.3.2-nag 1.3.2-pgi 1.3.2-pgi62	loads the OpenMPI/GCC compiler environment	Vendor Website
optistruct	9.0	Optistruct finite element based software program for both structural analysis and design optimisation. OptiStruct is used to design, evaluate and improve performance of mechanical structures.	CAC Documentation CAEN Documentation Vendor Website
parmetis	3.1.1-intel 3.1.1-pgi	ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations.	Vendor Website
petsc	3.0.0-p7-intel-debug 3.0.0-p7-intel-opt 3.0.0-p7-pgi-debug 3.0.0-p7-pgi-opt	PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism.	Vendor Website
pgi	6.2 7.2 8.0 9.0	loads the PGI compiler environment	CAC Documentation Vendor Website
polimi	1.2.5	loads the polimi environment	Vendor Website
samtools	0.1.4	SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.	Vendor Website
scipy	0.7.0	Scipy is open-source software for mathematics, science, and engineering.	Vendor Website
sentaurus	2007.03	Loads the Synopsys TCAD programs	Vendor Website
starccm	4.04	Star-ccm+ is a CFD application that supports parallel processing	Vendor Website
stata	10	Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics.	CAC Documentation Vendor Website Manuals
subversion	1.6.3
torque		loads the Torque and Maui batch computing environment	CAC Documentation Vendor Website
vasp	4.6.36 5.2.2	VASP is a licensed package for performing ab-initio quantum-mechanical molecular dynamics (MD)	CAC Documentation Vendor Website
vcs	2006.06	loads the VCS simulation environment	Vendor Website
verilog	5.8	loads the Verilog part of Cadence IC	Vendor Website
visit	1.11.2	loads the Visit serial and parallel engine for visualization of large data	Vendor Website
xpressmp	2007a	Xpress-MP is a suite of mathematical modeling and optimization tools used to solve linear, integer, quadratic, non-linear, and stochastic programming problems.	Vendor Website

Automatically generated list of 78 packages at Wed Oct 21 16:10:58 2009.