Software packages that are available on the CCR cluster.
These packages are installed and maintained by CCR
ABAQUS is a finite element analysis and multiphysics suite for simulation.
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.
AMBER (Assisted Model Building and Energy Refinement) is a suite of programs designed to carry out molecular dynamics simulations, particularly on biomolecules.
ATLAS (Automatically Tuned Linear Algebra Subroutines) provides C and Fortran interfaces to an efficient implementation of BLAS and LAPACK.
Babel is a toolbox for the format conversion of data from molecular modeling, chemistry, solid-state materials, and biochemistry.
BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences.
CFX (Computational Fluid Dynamics) is a comprehensive suite for the simulation and prediction of fluid behavior.
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics.
CNS (CNSsolve) is a crystallography and NMR analysis package.
COMSOL is a multiphysics simulation suite.
CPMD (Car-Parrinello Molecular Dynamics) is an ab initio electronic structure and molecular dynamics package.
CS-Rosetta is a suite for chemical shifts based protein structure prediction using ROSETTA.
CUDA is a parallel computing platform and programming model invented by NVIDIA for GPUs (graphic processing unit).
Dalton is a molecular electronic structure program.
DDT is a distributed debugging tool with an intuitive GUI and support for MPI, OpenMP, and CUDA.
Drops is a simulator for phase separation structures in block copolymer melts and blends, based on the density functional theory.
EIGENSOFT is a software suite for population genetics methods and the EIGENSTRAT stratification method.
Quantum ESPRESSO is a PWscf electric structure package.
FFmpeg is a software suite for recording, converting and streaming audio and video.
FFTW (Fastest Fourier Transform in the West) is library for computing the discrete Fourier transform (DFT) in one or more dimensions.
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.
The entire GNU compiler suite is available, with the usual invocations, gcc, g++, and g77.
Hand tuned Levels 1-3 BLAS routines from Kazushige Goto.
Hadoop is available on the general computing partition.
HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
IDL (Interactive Data Language) is a popular commercial package for data visualization and analysis.
IGV (Integrative Genomics Viewer) is visualization tool for the exploration of large genomic datasets.
The Intel compiler suite is available, including C/C++ (icc/icpc) and Fortran 77/95 (ifort).
Intel Cluster MKL (Math Kernel Library) provides highly tuned BLAS, LAPACK and DFTs (discrete fourier transforms).
Intel implementation of the Message Passing Interface (v2.x).
The Java Execution and Development Environments.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics program that models particles in a liquid, solid, or gaseous state.
LS-DYNA is a general-purpose finite element program for highly nonlinear, transient dynamic analysis using explicit time integration.
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).
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.
A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
Molekel is a molecular visualization package.
Parallel implementation of NCBI BLAST.
MPI-HMMER is a parallel version of HMMER.
MPICH2 is an implementation of MPI (v2.x) that runs over Ethernet.
mpiP is a lightweight, scalable interface for MPI profiling.
MrBayes is a parallel program for the Bayesian estimation of phylogeny.
MVAPICH2 is an implementation of MPI (v2.x) for Infiniband.
NAMD is a molecular dynamics program for the simulation of large biomolecular systems.
NetCDF (Network Common Data Form) is a set libraries and machine independent data formats.
NWChem is a massively parallel software package with a wide array of computational chemistry functionality, for both QM, QM/MM calculations.
Open MPI is an open source implementation of MPI (v2.x).
OpenMP is an application programming interface (API) intended for directing multi-threaded shared memory parallelism.
OpenSees (Open System for Earthquake Engineering Simulation) is a software package for simulating the seismic response of structural and geotechnical systems.
ParaView is a CFD and numerical simulation visualization package for large data sets.
Perl is a high-level interpreted programming language.
PETSc is the Portable Extensible Toolkit for Scientific Computation.
The Portland Group compilers, a suite of high performance compilers and associated tools.
Phenix is a suite for the automated determination of macromolecular structures using X-ray crystallography.
Python is an interpretive programming language.
Q-Chem is a ab initio quantum chemistry package.
R is a software environment for statistical computing and graphics.
Rosetta Commons is a protein sequence analysis suite.
STAR-CD and STAR-CCM+ are computational fluid dynamics packages.
Tecplot is a CFD and numerical simulation visualization package.
TotalView is a commerical parallel debugging tool for complex applications using MPI and OpenMP APIs.
Towhee is a Monte Carlo molecular simulation package.
VMD ia a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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.
WebMO is a web-based interface to computational chemistry packages.