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Software Resources

Software packages that are available on the CCR cluster.  These packages are installed and maintained by CCR staff. 

6/19/14

ABAQUS is a finite element analysis and multiphysics suite for simulation.

6/19/14

ADF (Amsterdam Density Functional) is software for first-principles electronic structure calculations (molecules and solids), based on Density Functional Theory (DFT).  Runs in parallel under MPI.

6/19/14

AMBER (Assisted Model Building and Energy Refinement) is a suite of programs designed to carry out molecular dynamics simulations, particularly on biomolecules.

6/19/14

ATLAS (Automatically Tuned Linear Algebra Subroutines) provides C and Fortran interfaces to an efficient implementation of BLAS and LAPACK.

6/19/14

Babel is a toolbox for the format conversion of data from molecular modeling, chemistry, solid-state materials, and biochemistry.

6/19/14

BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences.

6/19/14

CFX (Computational Fluid Dynamics) is a comprehensive suite for the simulation and prediction of fluid behavior.

6/19/14

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics.

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CNS (CNSsolve) is a crystallography and NMR analysis package.

6/19/14

COMSOL is a multiphysics simulation suite.

6/19/14

CPMD (Car-Parrinello Molecular Dynamics) is an ab initio electronic structure and molecular dynamics package.

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CS-Rosetta is a suite for chemical shifts based protein structure prediction using ROSETTA.

6/19/14

CUDA is a parallel computing platform and programming model invented by NVIDIA for GPUs (graphic processing unit).

6/19/14

Dalton is a molecular electronic structure program.

6/19/14

DDT is a distributed debugging tool with an intuitive GUI and support for MPI, OpenMP, and CUDA.

6/19/14

Drops is a simulator for phase separation structures in block copolymer melts and blends, based on the density functional theory.

6/19/14

EIGENSOFT is a software suite for population genetics methods and the EIGENSTRAT stratification method.

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Quantum ESPRESSO is a PWscf electric structure package.

6/19/14

FFmpeg is a software suite for recording, converting and streaming audio and video.

6/19/14

FFTW (Fastest Fourier Transform in the West) is library for computing the discrete Fourier transform (DFT) in one or more dimensions.

6/19/14

GAMESS (General Atomic and Molecular Electronic Structure System) is an ab initio quantum chemistry package, distributed and maintained by the Gordon group at Iowa State University.

6/19/14

The entire GNU compiler suite is available, with the usual invocations, gcc, g++, and g77.

6/19/14

Hand tuned Levels 1-3 BLAS routines from Kazushige Goto.

6/19/14

Hadoop is available on the general computing partition.  

6/19/14

HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.

6/19/14

IDL (Interactive Data Language) is a popular commercial package for data visualization and analysis.

6/19/14

IGV (Integrative Genomics Viewer) is visualization tool for the exploration of large genomic datasets.

6/19/14

The Intel compiler suite is available, including C/C++ (icc/icpc) and Fortran 77/95 (ifort).

6/19/14

Intel Cluster MKL (Math Kernel Library) provides highly tuned BLAS, LAPACK and DFTs (discrete fourier transforms).

6/19/14

Intel implementation of the Message Passing Interface (v2.x).

6/19/14

The Java Execution and Development Environments.

6/19/14

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics program that models particles in a liquid, solid, or gaseous state.

6/19/14

LS-DYNA is a general-purpose finite element program for highly nonlinear, transient dynamic analysis using explicit time integration.

6/19/14

MAP is graphical interface for profiling serial and MPI codes. It is licensed from Allinea, who are also the developers of DDT (Distributed Debugging Tool).

6/19/14

MATLAB is a high-performance language for technical computing.  It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notations.

6/19/14

A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

6/19/14

Molekel is a molecular visualization package.

6/19/14

Parallel implementation of NCBI BLAST.

6/19/14

MPI-HMMER is a parallel version of HMMER.

6/19/14

MPICH2 is an implementation of MPI (v2.x) that runs over Ethernet.

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mpiP is a lightweight, scalable interface for MPI profiling.

6/19/14

MrBayes is a parallel program for the Bayesian estimation of phylogeny.

6/19/14

MVAPICH2 is an implementation of MPI (v2.x) for Infiniband.

6/19/14

NAMD is a molecular dynamics program for the simulation of large biomolecular systems.

6/19/14

NetCDF (Network Common Data Form) is a set libraries and machine independent data formats.

6/19/14

NWChem is a massively parallel software package with a wide array of computational chemistry functionality, for both QM, QM/MM calculations.

6/19/14

Open MPI is an open source implementation of MPI (v2.x).

6/19/14

OpenMP is an application programming interface (API) intended for directing multi-threaded shared memory parallelism.

6/19/14

OpenSees (Open System for Earthquake Engineering Simulation) is a software package for simulating the seismic response of structural and geotechnical systems.

6/19/14

ParaView is a CFD and numerical simulation visualization package for large data sets.

6/19/14

Perl is a high-level interpreted programming language.

6/19/14

PETSc is the Portable Extensible Toolkit for Scientific Computation.

6/19/14

The Portland Group compilers, a suite of high performance compilers and associated tools.

6/19/14

Phenix is a suite for the automated determination of macromolecular structures using X-ray crystallography.

6/19/14

Python is an interpretive programming language.

6/19/14

Q-Chem is a ab initio quantum chemistry package.

R
6/19/14

R is a software environment for statistical computing and graphics.

6/19/14

Rosetta Commons is a protein sequence analysis suite.

6/19/14

STAR-CD and STAR-CCM+ are computational fluid dynamics packages.

6/19/14

Tecplot is a CFD and numerical simulation visualization package.

6/19/14

TotalView is a commerical parallel debugging tool for complex applications using MPI and OpenMP APIs.

6/19/14

Towhee is a Monte Carlo molecular simulation package.

6/19/14

VMD ia a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

6/19/14

VMTK is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

6/19/14

WebMO is a web-based interface to computational chemistry packages.