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

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

1/5/16

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

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

1/5/16

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

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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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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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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).

1/5/16

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

1/5/16

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.

1/5/16

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

1/5/16

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

1/5/16

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.