Available Applications

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This is a partial list of applications available on POD.  To see a complete list please log in to POD and query the module system.

$ module avail

If there are applications you don't see here, please let us know and we'll be happy to work with you to get them installed and configured.

FEA, CFD and FDTD Modeling

LS-DYNA / LS-PrePostLS-DYNA is an advanced general-purpose multiphysics simulation software package. Its core-competency lie in highly nonlinear transient dynamic finite element analysis (FEA) using explicit time integration. LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.
LS-OPTLS-OPT is an optimization and probabilistic analysis program that can interface with LS-DYNA.
OpenFoamOpenFOAM (Open source Field Operation And Manipulation) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems, including computational fluid dynamics (CFD).
ANSYS HFSSANSYS HFSS software is the industry standard for simulating 3-D full-wave electromagnetic fields. Its gold-standard accuracy, advanced solver and compute technology have made it an essential tool for engineers designing high-frequency and high-speed electronic components.
ANSYS FluentANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications.
Star-CD and Star-CCM+STAR-CCM+ is CD-adapco´s newest CFD software product. It uses the well established CFD solver technologies available in STAR-CD, and it employs a new client-server architecture and object oriented user interface to provide a highly integrated and powerful CFD analysis environment to users.
ConvergentCONVERGE is a Computational Fluid Dynamics (CFD) code that completely eliminates the user time needed to generate a mesh through an innovative run-time mesh generation technique.
LumericalSimulation tools that implement FDTD algorithms.
SU2The SU2 suite is an open-source collection of C++ based software tools for performing Partial Differential Equation (PDE) analysis and solving PDE constrained optimization problems.
AVL FIREAVL FIRE is a powerful multi-purpose thermo-fluid software representing the latest generation of 3D CFD.
AbaqusDSS SIMULIA Abaqus Unified FEA product suite offers powerful and complete solutions for both routine and sophisticated engineering problems covering a vast spectrum of industrial applications.

Weather Modeling and Cartographic Projections

WRFWeather Research and Forecasting model is a numerical weather prediction system.
COAMPSThe Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS®), developed and run by the Naval Research Laboratory in Monterey, CA, is the numerical model used for wind nowcasts and forecasts.
GRIB2GRIB (GRIdded Binary or General Regularly-distributed Information in Binary form)
PROJA Cartographic Projections library

Life Sciences, BioTech and Genomics

LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program that makes use of MPI for parallel communication.
SOAPdenovo Short Oligonucleotide Analysis Package (SOAP) is a bioinformatics package used for the assembly and analysis of DNA sequences.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler that is designed for short reads.
LifeTech LifeScope Life Technology's genomic analysis software for SOLiD next-generation sequencing
BioPerl BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
Bowtie Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences.
Burrows-Wheeler Aligner BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Celera Assembler Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.
GATK The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.
HMMR HMMR is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
BLAST In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
mpiBLAST mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
Picard Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
SAMtools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
Velvet Sequence assembler for very short reads.
VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

General Science Applications & Libraries

CLHEP (Physics) CLHEP (short for A Class Library for High Energy Physics) is a C++ library that provides utility classes for general numerical programming, vector arithmetic, geometry, pseudorandom number generation, and linear algebra, specifically targeted for high energy physics simulation and analysis software.
FDS-SMV (Fire Dynamics Simulator) Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.
Geant4 (Physics) Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
GSL (GNU Scientific Library) The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
SciPy SciPy (pronounced “Sigh Pie”) is a Python-based ecosystem of open-source software for mathematics, science, and engineering.
NCAR NCAR Graphics is a Fortran and C based software package for scientific visualization.
netCDF and NCO NCO (netCDF Operators) is a suite of programs designed to facilitate manipulation and analysis of self-describing data stored in the netCDF format.
OpenCV OpenCV (Open Source Computer Vision Library) is a library of programming functions mainly aimed at real-time computer vision.
PETSc The Portable, Extensible Toolkit for Scientific Computation (PETSc, pronounced PET-see; the S is silent), is a suite of data structures and routines developed by Argonne National Laboratory for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
HDF5 Hierarchical Data Format (HDF, HDF4, or HDF5) is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data.
TrilinosTrilinos is a collection of open source software libraries intended to be used as building blocks for the development of scientific applications
NWChemOpen-Source High-Performance Computational Chemistry package
GAMESSThe General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package
PSI4PSI4 is an open-source suite of ab initio quantum chemistry programs

Mathematics and Statistics Applications & Libraries

R and RmpiR is a language and environment for statistical computing and graphics.
MATLABMATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming.
NumPy NumPy is the fundamental package for scientific computing with Python.
ANN An artificial neural network (ANN) based software package for classification of remotely sensed data.
ATLAS ATLAS (Automatically Tuned Linear Algebra Software) provides C and Fortran interfaces to an efficient BLAS implementation, as well as a few routines from LAPACK.
BLAS Basic Linear Algebra Subroutine (BLAS) is a de facto application programming interface standard for publishing libraries to perform basic linear algebra operations such as vector and matrix multiplication.
Boost Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.
Intel Math
Kernel Libraries
Intel® Math Kernel Library includes a wealth of routines to accelerate application performance and reduce development time.
FFTW The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms (DFTs).
ParMETIS ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
SPBLASTK For solving large sparse system of linear equations.
UDUNITS UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

Rendering, Remote Visualization and Image Manipulation

RealityServer RealityServer is a software platform for the development and deployment of 3D Web Services and 3D applications.
JasPer The JasPer project creates a reference implementation of the codec specified in the JPEG-2000 Part-1 standard (i.e. ISO/IEC 15444-1). It consists of a C library and some sample applications useful for testing the codec.
ImageMagick ImageMagick is an open source software suite for displaying, converting, and editing raster image files. It can read and write over 200 image file formats.
Blender Blender is a free and open-source 3D computer graphics software product used for creating animated films, visual effects, art, 3D printed models, interactive 3D applications and video games. Blender's features include 3D modeling, UV unwrapping, texturing, rigging and skinning, fluid and smoke simulation, particle simulation, soft body simulation, animating, match moving, camera tracking, rendering, video editing and compositing.

Compilers and Language Tools

Intel C/C++ and Fortran Compilers Intel® Compiler suites include C compiler, C++ compiler, and Fortran compiler, including optimization features and multithreading capabilities; highly optimized performance libraries; and error-checking, security, and profiling tools, allowing developers to create multithreaded applications and maximize application performance, security, and reliability.
Portland Group C/C++ and Fortran Compilers PGI compilers incorporate global optimization, vectorization, software pipelining, and shared-memory parallelization capabilities.
NVIDIA CUDA Compiler Nvidia CUDA Compiler is Nvidia's CUDA compiler. NVCC separates these two parts and sends host code (the part of code which will be run on the CPU) to a C compiler, and sends the device code (the part which will run on the GPU) to the GPU. The device code is further compiled by NVCC.
ANTLR ANTLR (pronounced Antler), or ANother Tool for Language Recognition, is a parser generator that uses LL(*) parsing.
FLTK The Fast, Light Toolkit, FLTK, is a GUI library made to accommodate 3D graphics programming.
GADL Graphical Programming project.
Gengetopt Gengetopt is a tool to write command line option parsing code for C programs.

A tool that easily allows a developer to wrap C/C++ functions for use with scripting languages.