ARSC Academic Systems Software Index
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Software by System: All | Fish | Pacman | Bigdipper | Linux WorkstationsSoftware Matrix: All | Fish | Pacman | Bigdipper | Linux Workstations
All Installed Packages
Software Packages on Fish
- Abaqus - General purpose finite element and interactive postprocessing program (Access Restrictions)
- ACML (AMD Core Math Library) - Optimized math library for AMD processors; Contains BLAS, LAPACK and FFT routines.
- ANTLR - ANTLR is a widely-used open-source parser and translator generator tool
- CCE - Cray Compiling Environment
- CMake - Cross Platform Make
- Comsol - Multiphysics is a finite element analysis and solver software package for various physics and engineering applications. (Access Restrictions)
- CUBIT - Geometry and Mesh Generation Toolkit (Access Restrictions)
- CUDA - CUDA is NVIDIA's parallel computing architecture that utilizes system GPUs.
- Ferret - Ferret is an interactive computer visualization and analysis environment designed for large gridded data sets.
- FFTW - FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions
- GIT - Fast version control system.
- GNU Compilers - The GNU compiler suite
- GrADS - An interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.
- GSL (GNU Scientific Library) - The GNU Scientific Library.
- HDF - Heirarchical Data Format library and utilities
- IDL/Envi - Graphics & Data Representation Libraries & Toolkits
- ImageMagick - A software suite to create, edit, and compose bitmap images
- Jasper - The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part
- Java Development Kit - The Java compiler and runtime environment
- Matlab - Interactive matrix laboratory for tasks involving matrices, graphics and general numerical computation (Access Restrictions)
- Nano - GNU editor similar to pico
- NCL - NCAR Command Language
- NCO - Set of tools for the manipulation of netcdf datasets.
- NCView - Netcdf file viewer
- Nedit - X windows text editor
- NetCDF - Unidata Network Common Data Form library
- PetSC - Portable, Extensible Toolkit for Scientific Computation
- PGI - The Portland Group, Inc. Compiler Suite includes compilers for C, C++, Fortran 77, Fortran 90, and Fortran 95.
- pNetCDF - parallel netcdf
- qt - Using Qt, you can write web-enabled applications once and deploy them across desktop, mobile and embedded operating systems. Needed for paraview.
- TotalView Debugger - X-window source-level debugger for parallel programs
- udunits - Unit conversion and manipulation package
Software Packages on Pacman
- Abaqus - General purpose finite element and interactive postprocessing program (Access Restrictions)
- ACML (AMD Core Math Library) - Optimized math library for AMD processors; Contains BLAS, LAPACK and FFT routines.
- ANTLR - ANTLR is a widely-used open-source parser and translator generator tool
- Autoconf - M4 macros used to produce shell scripts for automagically configuring software source code pkgs.
- Automake - Works in conjuntion with autoconf and processes makefile.am files.
- Beagle-lib - A general purpose library for evaluating the likelihood of sequence evolution on trees
- Beast - BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
- BLACS - Basic Linear Algebra Communication Subprograms
- boost - The boost libraries are an extension of C++ standard routines and are slated for future additions to the C++ standard.
- bowtie - Bowtie is an ultrafast, memory-efficient short read aligner.
- CDO - CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
- charm - parallel c++ library, Required to build NAMD and ChaNGa. Note that NAMD includes a Charm++ tarball which is the version built here.
- CMake - Cross Platform Make
- Comsol - Multiphysics is a finite element analysis and solver software package for various physics and engineering applications. (Access Restrictions)
- CUBIT - Geometry and Mesh Generation Toolkit (Access Restrictions)
- CUDA - CUDA is NVIDIA's parallel computing architecture that utilizes system GPUs.
- CULA - CULA is a GPU-accelerated linear algebra library that utilizes the NVIDIA CUDA parallel computing architecture
- DMol3 - DMol3 is a unique, accurate, and reliable density functional theory (DFT) quantum mechanical code. (Access Restrictions)
- Ferret - Ferret is an interactive computer visualization and analysis environment designed for large gridded data sets.
- ffmpeg - Tools to record, convert, stream and play multimedia content
- FFTW - FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions
- Garli - GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion.
- Gaussian - provides state-of-the-art capabilities for electronic structure modeling. (Access Restrictions)
- GaussView - GUI setup and viewing utility for Gaussian
- GEOS - GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS).
- GIT - Fast version control system.
- GMT - Generic Mapping Tools.
- GNU Compilers - The GNU compiler suite
- GNUPlot - GNUPlot is a portable command-line driven graphing utility
- Grace - Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif.
- GrADS - An interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.
- GSL (GNU Scientific Library) - The GNU Scientific Library.
- GV - GNU gv allows to view and navigate through PostScript and PDF documents
- HDF - Heirarchical Data Format library and utilities
- IDL/Envi - Graphics & Data Representation Libraries & Toolkits
- IM/IMA - IM/IMa are progams for population genetic analysis
- IMA2 - IMa2 is a progam for population genetic analysis
- ImageMagick - A software suite to create, edit, and compose bitmap images
- Intel Compilers - The intel compilers. (access restrictions)
- Jasper - The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part
- Java Development Kit - The Java compiler and runtime environment
- Matlab - Interactive matrix laboratory for tasks involving matrices, graphics and general numerical computation (Access Restrictions)
- Mexnc - Matlab netcdf interface
- Migrate - estimation of population sizes and gene flow using the coalescent
- NAMD - Scalable Molecular Dynamics
- NCL - NCAR Command Language
- NCO - Set of tools for the manipulation of netcdf datasets.
- NCView - Netcdf file viewer
- NetCDF - Unidata Network Common Data Form library
- netcdf_toolbox - used with mexnc and matlab to process netcdf files
- NWChem (open source) - A computational chemistry simulation package
- Octave - GNU Octave is a high-level language, primarily intended for numerical computations.
- OpenFOAM - OpenFOAM is a free, open source CFD software package
- OpenMPI - The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
- osg - OpenSceneGraph, scene-graph based C++ graphics library
- PAPI - PAPI provides a consistent interface to hardware performance counters
- Paraview - An open-source, multi-platform data analysis and visualization application.
- PetSC - Portable, Extensible Toolkit for Scientific Computation
- PGI - The Portland Group, Inc. Compiler Suite includes compilers for C, C++, Fortran 77, Fortran 90, and Fortran 95.
- pNetCDF - parallel netcdf
- PyNGL - A python package providing an inferface to NCL routines
- PyNIO - PyNIO is a Python package that supports a variety of data formats
- Python - An interpreted, interactive, object-oriented programming language
- qt - Using Qt, you can write web-enabled applications once and deploy them across desktop, mobile and embedded operating systems. Needed for paraview.
- R - Open source statistical package based on S.
- ScaLAPACK - Scalable Linear Algebra Package
- Silo - A mesh and field I/O library and scientific database. Maintained and written by LLNL.
- Structure - a free software package for using multi-locus genotype data to investigate population structure
- Subversion - An open-source revision control system.
- szip - Szip compression software, providing lossless compression of scientific data
- TAU - TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs
- TotalView Debugger - X-window source-level debugger for parallel programs
- Trinity - Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
- udunits - Unit conversion and manipulation package
- Vis5D+ - A free OpenGL-based volumetric visualization program for scientific datasets in 3+ dimensions
- VisIt - Scientific Visualization Software
- vtk - Visualization ToolKit library for graphics development and data analysis
- wgrib2 - Utility for the manipulation of grib2 files
- xemacs - x11 version of emacs
- yasm - Yasm is a complete rewrite of the NASM assembler
Software Packages on Bigdipper
Software Packages on Linux Workstations
- Abaqus - General purpose finite element and interactive postprocessing program (Access Restrictions)
- Autoconf - M4 macros used to produce shell scripts for automagically configuring software source code pkgs.
- Automake - Works in conjuntion with autoconf and processes makefile.am files.
- Avizo - Tool for visualizing, manipulating, and understanding 3D scientific and industrial data.
- Blender - Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License.
- boost - The boost libraries are an extension of C++ standard routines and are slated for future additions to the C++ standard.
- CMake - Cross Platform Make
- Comsol - Multiphysics is a finite element analysis and solver software package for various physics and engineering applications. (Access Restrictions)
- CUBIT - Geometry and Mesh Generation Toolkit (Access Restrictions)
- eclipse - sdk which provides templates used to begin developing code
- GIT - Fast version control system.
- GMT - Generic Mapping Tools.
- GNU Compilers - The GNU compiler suite
- Google Earth - 3D viewing software for satellite imagery, maps, terrain, 3D buildings, etc.
- GSL (GNU Scientific Library) - The GNU Scientific Library.
- HDF - Heirarchical Data Format library and utilities
- IDL/Envi - Graphics & Data Representation Libraries & Toolkits
- IDV - Integrated Data Viewer
- ImageMagick - A software suite to create, edit, and compose bitmap images
- Matlab - Interactive matrix laboratory for tasks involving matrices, graphics and general numerical computation (Access Restrictions)
- Mexnc - Matlab netcdf interface
- NCL - NCAR Command Language
- NCView - Netcdf file viewer
- OpenFOAM - OpenFOAM is a free, open source CFD software package
- Paraview - An open-source, multi-platform data analysis and visualization application.
- PGI - The Portland Group, Inc. Compiler Suite includes compilers for C, C++, Fortran 77, Fortran 90, and Fortran 95.
- Python - An interpreted, interactive, object-oriented programming language
- qt - Using Qt, you can write web-enabled applications once and deploy them across desktop, mobile and embedded operating systems. Needed for paraview.
- R - Open source statistical package based on S.
- Subversion - An open-source revision control system.
- TotalView Debugger - X-window source-level debugger for parallel programs
- Vapor - Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers
- VisIt - Scientific Visualization Software