Available Software at the RCC Group

ABAQUS

ABAQUS is a finite element solver used for stress, heat transfer, and other types of analysis in mechanical, structural, civil, biomedical, and related engineering applications.

Abinit

Abinit finds the total energy, charge density, and electronic structure of systems made of electrons and nuclei, using pseudopotentials and a plane-wave basis.

AFNI

AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.

Amber

Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids.

AMD Core Math Library (ACML)

AMD Core Math Library (ACML) is an optimized math library that contains BLAS and LAPACK functionality.

AMPL

AMPL is a modeling language and system for formulating, solving and analyzing large-scale optimization (mathematical programming) problems.

ANSYS

ANSYS is a finite element design and analysis software that allows a user to model problems in structures, thermal/fluid flow and electromagnetics.

Avizo

Avizo is a powerful, multifaceted tool for visualizing, manipulating, and understanding scientific and industrial data.

BEAGLE

BEAGLE is a GPU accelerated library for evaluating likelihood of sequence evolution in trees.

BigDFT

BigDFT is a massively parallel electronic structure code using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation).

BLAST

BLAST finds regions of local similarity between nucleotide or protein sequences.

BLAST+

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications.

BLAT

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.

Boost

Boost is a set of peer-reviewed C++ development source libraries.

CMake

CMake is a cross-platform, open-source build system.

COMSOL

COMSOL Multiphysics is an engineering, design, and finite element analysis software environment for the modeling and simulation of any physics-based system.

CPLEX

CPLEX solves linear and convex quadratic programs by simplex or interior-point methods, and linear and convex quadratic integer programs by a branch-and-bound procedure.

CUDA

CUDA is a C-programming language environment for computing on NVIDIA GPU processors.

CUDA SDK

The CUDA SDK is code to support development on NVIDIA series GPUs.

CUDA Toolkit

The CUDA Toolkit is a compiler, profiler and libraries for development on NVIDIA GPUs.

DDT

DDT, the Distributed Debugging Tool is a comprehensive graphical debugger for scalar, multi-threaded and large-scale parallel applications that are written in C, C++ and Fortran.

Desmond

Desmond is a high-performance molecular dynamics code designed for use on conventional commodity clusters. Desmond's speed is attributable to novel parallel algorithms and numerical techniques developed by D.E. Shaw Research

Distributed Matlab (dmatlab)

Distributed Matlab (dmatlab) allows Matlab jobs to be run in parallel.

DL_POLY

DL_POLY is a general purpose serial and parallel molecular dynamics simulation package.

Doxygen

Doxygen is a documentation system.

Eclipse

Eclipse is an open-source IDE for C, C++, Java, and other languages.

EEGLAB

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data.

EMAN2/Sparx

EMAN2/Sparx are GPU accelerated routines for transmission electron microscopy image processing.

Ferret

Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

FFmpeg

FFmpeg is a set of tools and libraries for manipulating audio and video streams.

FFTW

FFTW is a fast, free C FFT library that includes real-complex, multidimensional, and parallel transforms.

FLUENT

FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications.

FreeSurfer

FreeSurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Gambit

Gambit is a grid-generator and a geometry modeler.

GAMS

The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization.

Gaussian 03

Gaussian 03 provides state-of-the-art capabilities for electronic structure modeling.

Gaussian 09

Gaussian 09 provides state-of-the-art capabilities for electronic structure modeling.

GaussView

GaussView supports all Gaussian features and includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types.

GMP

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

GotoBLAS2

GotoBLAS2 is an optimized version of the standard BLAS libraries.

GPAW

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method.

Grace

Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif.

GROMACS

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.

GSL

The GNU Scientific Library (GSL) is a numerical library containing a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

IDL

IDL is a software package for data visualization and image processing and analysis.

Impute

Impute is a program for estimating (imputing) unobserved genotypes in SNP association studies.

IMSL

The IMSL Libraries are a comprehensive set of mathematical and statistical functions that programmers can embed into their software applications.

Intel Compilers

The Intel Compilers consist of C/C++ and Fortran compilers that create highly optimized executables for the Intel architecture.

Intel Math Kernel Library (MKL)

The Intel Math Kernel Library (MKL) is an optimized math library that contains BLAS, LAPACK, FFTs, and other functions.

Jaguar

Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory.

LAMMPS

LAMMPS is a classical molecular dynamics code. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAPACK

LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

LS-DYNA

LS-DYNA is a general purpose transient dynamic finite element program capable of simulating complex real world problems.

Maestro

Maestro is the unified graphical user interface to the Schrödinger Suite of applications.

Maple

Maple contains extensive functionality for solving mathematical problems.

Materials Studio

Materials Studio by Accelrys is a comprehensive materials modeling and simulation application designed for scientists in chemicals and materials R&D as well as pharmaceuticals development.

Mathematica

Mathematica is a fully integrated software environment for technical and scientific computing. Mathematica combines numerical and symbolic computation, visualization, and programming in a single, flexible interactive software system.

MATLAB

MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation.

Molden

Molden is a package for displaying molecular density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac. It also supports a number of other programs via the Molden Format.

MRIcro

MRIcro is an application that allows you to view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images).

MRIcron

MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest.

NAMD

NAMD is a parallel molecular dynamics code for large biomolecular systems.

Nastran

Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies, providing capabilities in linear statics, dynamics, nonlinear analysis, heat transfer, acoustics and more.

NCL

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

NCO

NCO is a suite of standalone, command-line programs takes netCDF files as input, then operates (e.g., derives new data, averages, hyperslabs, manipulates metadata) and produces a netCDF output file. NCO primarily aids manipulation and analysis of gridded scientific data.

NetCDF

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

NetLogo

NetLogo is a programmable modeling environment for simulating natural and social phenomena.

NWChem

NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.

OpenCV

OpenCV is a GPU accelerated library of routines for real time computer vision.

OpenDX

OpenDX is a uniquely powerful, full-featured software package for the visualization of scientific, engineering and analytical data.

OpenFOAM

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

OpenMPI

OpenMPI is a MPI-1 and MPI-2 compliant MPI (Message Passing Interface) library. MPI is a standard API used for distributed memory parallel computing.

PAPI

The Performance API (PAPI) specifies a standard application programming interface (API) for accessing hardware performance counters available on most modern microprocessors.

ParaView

ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large.

Patran

Patran is pre/post-processing software for Finite Element Analysis (FEA), providing solid modeling, meshing, and analysis setup for MSC Nastran, Marc, Abaqus, LS-DYNA, ANSYS, and Pam-Crash.

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

PLINK

PLINK will generate a number of standard summary statistics that are useful for quality control (e.g., missing genotype rate, minor allele frequency, Hardy-Weinberg equilibrium failures and non-Mendelian transmission rates).

Pointwise

Pointwise allows mesh generation for computational fluid dynamics (CFD).

Portland Group (PGI) Compilers

The Portland Group (PGI) Compilers include C, C++, and Fortran compilers to create highly optimized executables for the Intel and AMD architectures.

povray

povray is a high-quality, totally free tool for creating stunning three-dimensional graphics.

PWGui

PWGui a user interface for editing Quantum Espresso files.

PyMOL

PyMOL is a molecular viewer, render tool, and 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures.

Q-Chem

Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods.

Quantum Espresso

Quantum Espresso performs Electronic structure calculations using Density Functional Theory, Pseudo-Potentials and plane waves.

R

R is a free software environment for statistical computing and graphics.

RNAMotif

RNAMotif is a RNA sequence database search software.

SAS

SAS is a powerful data analysis and statistical analysis tool providing users with insights that are often hidden in data in order to provde evidence-based decisions.

ScaLAPACK

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. It is currently written in a Single-Program-Multiple-Data style using explicit message passing for interprocessor communication. It assumes matrices are laid out in a two-dimensional block cyclic decomposition.

Schrodinger

The Schrodinger software suite provides a range of products from general molecular modeling programs to a full-featured suite of drug design software including both ligand and structure based methods.

SCIRun

SCIRun is a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems.

SeDuMi

SeDuMi is a software package to solve optimization problems over symmetric cones. This includes linear, quadratic, second order conic and semidefinite optimization, and any combination of these.

SPM5

SPM5 is a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data.

SPM8

SPM8 is a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data.

SPSS

SPSS is a statistical package that contains a full range of analytical techniques plus structural equation modeling (SEM) as well as in-depth sampling assessment and testing.

Stata

Stata is a statistical package designed for researchers of all disciplines.

Structure

Structure is a free software package for using multi-locus genotype data to investigate population structure.

Tecplot

Tecplot is complete CFD visualization tool that helps analyze, explore and understand complex simulation data.

TeraChem

TeraChem is a GPU accelerated quantum chemistry code.

Thrust

Thrust is STL-like C++ header libraries for development on the NVIDIA GPUs.

TotalView

TotalView is a dynamic source code and memory debugger for C, C++ and Fortran applications. It supports both MPI and threaded codes.

Valgrind

Valgrind is a code analysis tool. It currently includes six production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache profiler, and a heap profiler. It also includes two experimental tools: a heap/stack/global array overrun detector, and a SimPoint basic block vector generator.

VASP 4

VASP 4 is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.

VASP 5

VASP 5 is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.

VisIt

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms.

VMD

VMD is a free program for visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies.

wxDragon

wxDragon is a visualization program that can work with output files from programs such as VASP, ADF, Gamess, etc.

XCrySDen

XCrySDen is a visualization tool for Quantum Espresso files.

XFdtd

XFdtd is a 3D EM simulation software package that provides engineers with powerful and innovative tools for modeling and EM simulation.