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

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.

3/12/15

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

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

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

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

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

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

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).

7/28/15

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

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.

3/12/15

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

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

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

2/3/15

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

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

6/19/14

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

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.