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Software Resources

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

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1/5/16
ABAQUS is a finite element analysis and multiphysics suite for simulation.
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AMBER (Assisted Model Building and Energy Refinement) is a suite of programs designed to carry out molecular dynamics simulations, particularly on biomolecules.
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ANSYS/CFX (Computational Fluid Dynamics) is a comprehensive suite for the simulation and prediction of fluid behavior.
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BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences.
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CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics.
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COMSOL is a multiphysics simulation suite.
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CUDA is a parallel computing platform and programming model invented by NVIDIA for GPUs (graphic processing unit).
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Dalton is a molecular electronic structure program.
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DDT is a distributed debugging tool with an intuitive GUI and support for MPI, OpenMP, and CUDA.
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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.
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FFmpeg is a software suite for recording, converting and streaming audio and video.
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FFTW (Fastest Fourier Transform in the West) is library for computing the discrete Fourier transform (DFT) in one or more dimensions.
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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.
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The entire GNU compiler suite is available, with the usual invocations, gcc, g++, and g77.
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Hadoop is available on the general computing partition.  
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IDL (Interactive Data Language) is a popular commercial package for data visualization and analysis.
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The Intel compiler suite is available, including C/C++ (icc/icpc) and Fortran 77/95 (ifort).
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Intel Cluster MKL (Math Kernel Library) provides highly tuned BLAS, LAPACK and DFTs (discrete fourier transforms).
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Intel implementation of the Message Passing Interface (v2.x).
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The Java Execution and Development Environments.
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LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics program that models particles in a liquid, solid, or gaseous state.
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LS-DYNA is a general-purpose finite element program for highly nonlinear, transient dynamic analysis using explicit time integration.
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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).
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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.
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A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
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MVAPICH2 is an implementation of MPI (v2.x) for Infiniband.
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NAMD is a molecular dynamics program for the simulation of large biomolecular systems.
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NWChem is a massively parallel software package with a wide array of computational chemistry functionality, for both QM, QM/MM calculations.
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Open MPI is an open source implementation of MPI (v2.x).
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OpenMP is an application programming interface (API) intended for directing multi-threaded shared memory parallelism.
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OpenSees (Open System for Earthquake Engineering Simulation) is a software package for simulating the seismic response of structural and geotechnical systems.
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ParaView is a CFD and numerical simulation visualization package for large data sets.
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Perl is a high-level interpreted programming language.
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PETSc is the Portable Extensible Toolkit for Scientific Computation.
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The Portland Group compilers, a suite of high performance compilers and associated tools.
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Python is an interpretive programming language.
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Q-Chem is a ab initio quantum chemistry package.
R
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R is a software environment for statistical computing and graphics.
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Rosetta Commons is a protein sequence analysis suite.
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STAR-CD and STAR-CCM+ are computational fluid dynamics packages.
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Tecplot is a CFD and numerical simulation visualization package.
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VMD ia a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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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.
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WebMO is a web-based interface to computational chemistry packages.