Software

Installed Application Software.

It is policy to retain only the two most recent versions.

Ansys

Ansys is a suite of finite element based applications that provide real-world simulations of structural, thermal, electromagnetic and fluid-flow behavior of 3-D product. All Ansys products integrate with CAD environments. This is normally access via the WorkBench interface.

Abaqus

Abaqus is a suite of applications used by many in the engineering community for the analysis of multi-body dynamics problems that aid the medical, automotive, aerospace, defense, and manufacturing community.

Comsol

Comsol is specifically designed to easily couple transport phenomena, including computational fluid dynamics (CFD) as well as mass and energy transport to chemical-reaction kinetics and process-related modelling. Licensed Modules include: MultiPhysics, Chemical Engineering, Acoustics, Structural Mechanics, Script.

Chimera

Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

Cubit

CUBIT is a Geometry and Mesh Generation Toolkit

Desmond

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.

FFmpeg

FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library.

FE-Safe

The Abaqus add-on product FE-Safe is a highly effective tool for fatigue analysis of Finite Element models.

gnuplot

Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types.

ggobi

GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.

GAMS See GAMS info at bottom of page on Network Concurrent Licenses

Gromacs

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

GAMESS

GAMESS is a program for ab initio molecular quantum chemistry.

GMT

GMT is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets.

Imagemagick

ImageMagick® is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.

Jupyter

The Jupyter Notebook is an open source web application for interactive data science and scientific computing across over 40 programming languages. It allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more.

slurm

Slurm software is a distributed load sharing and queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages and monitors resources and load on the cluster.

Matlab

MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. MATLAB Compiler Runtime (MCR)

The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components without using MATLAB licensing. This is useful for running a large number of jobs that might exceed the license counts.

Maple

Maple is a well known environment for mathematical problem-solving, exploration, data visualization, and technical authoring. In may ways it is similar to Mathematica and Matlab.

MCEE

MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics.

Mathematica

Mathematica, advertised as a one stop for technical work that integrates a numeric and symbolic computational engine, graphics system, programming language, documentation and advanced connectivity to other applications. Not only does this application have parallel functionality built into it from the ground up. The Wolfram Mathematica web site has extensive documentation, including numerous detailed tutorials.

NGSPICE
Spice is a general-purpose electric circuit simulation program for nonlinear dc, nonlinear transient and linear ac analysis.

NCAR
(The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization.

Namd
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here

Paraview

ParaView is a multi-platform visualization application designed to visualize large data sets.

Parallel

GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel.

PySpark

PySpark is the Python interface to Apache Spark, a powerful open source cluster computing framework. Spark is a fast and general-purpose cluster computing system and provides programmers with an interface centered on the Resilient Distributed Dataset (RDD). The RDD is a data structure that is distributed over a cluster of computers and is maintained in a fault-tolerant way.

Python

Python is a widely used high-level, general-purpose, interpreted programming language. It is often used as the "glue" within the High Performance Computing community.

R

R is a widely available object oriented statistical package. The current list of installed packages, to numerous to list, can be found in directory
/opt/shared/R/2.15.0-rhel6/lib64/R/library/.

This represents an augmented base installation suitable for most routine tasks, however not all available packages as found on the R web site are installed. If some other R package is needed, please make a software installation request as outlined above. However, for many people use of RStudio will allow for local installations in your home directory. Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example

Note BioConductor and many genetics related R packages are installed as well.

RStudio
RStudio is a free and open source integrated development environment(IDE) for R.

Stata

Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.

SAS
Sas is general purpose statistics package. Education Analytical Suite of programs is licensed. These include:

• Base SAS • SAS Bridge for ESRI • SAS Enterprise Guide • SAS Integration Technologies • SAS/ACCESS • SAS/AF • SAS/ASSIST • SAS/CONNECT • SAS/EIS • SAS/ETS • SAS/FSP • SAS/GRAPH • SAS/IML • SAS/INSIGHT • SAS/LAB • SAS/OR • SAS/QC • SAS/SECURE 168-bit • SAS/SHARE • SAS/STAT SAS Enterprise Guide SAS/Genetics

TensorFlow

TensorFlow is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API.