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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.
9/22/14
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.
6/19/14
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.
6/19/14
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.
6/19/14
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).
9/4/14
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).
9/24/14
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.
9/4/14
MPICH2 is an implementation of MPI (v2.x) that runs over Ethernet.
6/19/14
mpiP is a lightweight, scalable interface for MPI profiling.
6/19/14
MrBayes is a parallel program for the Bayesian estimation of phylogeny.
9/4/14
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.
9/8/14
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.