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Software Overview

National Systems

For information on software available on Compute Canada's national systems please refer to the Available Software page on the Compute Canada User Documentation wiki. 

WestGrid Systems

On the WestGrid systems there is a core of common software, but due to user requirements or limitations of licensing or architecture, there are some differences in the programs offered at the various WestGrid sites. The tables below and the associated database summarize the majority of the software that has been added to the basic Linux environment.  Not every package has an entry in this database. For example, software that is licensed only to a specialized group of researchers may not be listed. Also, add-on modules for R, Perl and Python are less likely to be listed.

New software requests on WestGrid systems are no longer being accepted.  You are responsible for installing new software in your own directory.

Once you have located software of interest, either by scrolling through the full listing or by using the Search button and associated pull-down menus to filter the software by category or system, click on the software title.  That will lead to a page showing the software versions available on WestGrid systems as well as usage instructions for some packages.

The executables for commonly used software can usually be found on the PATH supplied by the default login environment at each WestGrid site. Some of the software is configured with the module command. Additional software, libraries, including files, documentation and other supporting files sometimes do not fit readily into a rigid installation scheme, but are usually installed under one or two standard directories for each site, such as /global/software.

All WestGrid Software

Software Category: Programming
Software
Brief Description
Xerces-C++ XML parser and writer.
Subversion An open source alternative to CVS for managing files for large development projects.
SCons SCons is an Open Source software construction tool
Ruby A dynamic, interpreted, open source programming language with a focus on simplicity and productivity.
ROOT (data analysis framework) ROOT is an object-oriented framework aimed at solving the data analysis challenges of high-energy physics.
Python Python is an interactive, object-oriented, extensible programming language.
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
Mono (C# environment) Mono .NET environment to provide a platform for running C# programs.
LIKWID - Performance analysis tools LIKWID - Performance analysis tools for OpenMP and hybrid OpenMP/MPI programs.
Julia Julia is a high-level, dynamic language for technical computing
Java Java is a programming language and computing platform.
idb Intel debugger.
Git Version control system.
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
CMake Cross platform software build system
Boost An eclectic collection of C++ libraries.
Allinea DDT Powerful commercial debugger/profiler/Analyzer with useful GUI.
Software Category: Graphics
Software
Brief Description
VMD VMD is a program for displaying and animating large biomolecular systems.
VisIT - general purpose visualization tool VisIT - general purpose scientific visualization tool
Qt Application and user interface development framework.
pdflib PDF file handling library ("PDFlib-Lite" for non-commercial use).
ParaView GUI-based application for visualization of many types of multi-dimensional data.
Netpbm Image conversion utilities and library.
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
ImageMagick Software suite for image format conversion and editing.
Grace/Xmgrace GUI-based x-y plotting for thesis and publication-quality graphs.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Gephi - interactive network graph visualization Gephi - an interactive program for network graph visualization
FFmpeg (video encoding) FFmpeg - create a movie file from a series of images
Ezys - GPU-accelerated non-rigid 3D medical image registration Ezys - GPU-accelerated non-rigid 3D medical image registration
Software Category: Files and Data
Software
Brief Description
Vim An enhanced version of the vi text editor.
Szip A library for lossless compression of scientific data.
NetCDF A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
NEdit A graphical editor recommended for PC users, but requires X Windows.
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
HDF 4 Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.
Emacs GNU version of this common text editor.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
VASP An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
Qbox DFT Based electronic structure and molecular dynamics program.
ORCA An ab initio, DFT and semiempirical SCF-MO package.
NEURON An environment for simulating neurons and networks of neurons.
NAMD A molecular dynamics simulator for large biomolecular systems.
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
HOOMD-blue particle simulation toolbox HOOMD-blue - General purpose particle simulation toolkit.
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
Elk An electronic structure code for determining the properties of crystalline solids.
DL_POLY DL_POLY is a suite of programs developed at Daresbury Laboratory for molecular dynamics simulations of a variety of systems, including "macromolecules, polymers, ionic systems and solutions".
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
Amber A suite of programs for molecular calculations, including molecular dynamics.
Software Category: UNIX Environment
Software
Brief Description
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
sh
ksh It is an interactive command language that provides access to the UNIX system and to many other systems, on the many different computers and workstations on which it is implemented.
csh The improved version of tcsh.
bash (default) Bash is a Unix shell.
64-bit Linux CentOS CentOS is an Enterprise-class Linux Distribution derived from sources freely provided to the public by a prominent North American Enterprise Linux vendor.
Software Category: Mathematical Libraries and Applications
Software
Brief Description
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers)
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
MKL MKL is a vendor optimized numerical library with C and Fortran bindings for BLAS, LAPACK, ScaLAPACK, FFT, a sparse system solver, random number generators and vector versions of common mathematical functions.
METIS Mesh and graph partitioning.
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 on computers that do not have MATLAB installed.
LAPACK Linear algebra subroutine package.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
Gerris Flow Solver Gerris Flow Solver - solve partial differential equations for incompressible flow
FFTW A widely-used FFT implementation.
BLAS Basic Linear Algebra Subprograms.
Software Category: Bioinformatics / Genomics Applications
Software
Brief Description
Ray De novo genome assembly.
Migrate (Migrate-n) - Population genetics program to estimate migration rates and population sizes Migrate-n is a population genetics program for estimating migration rates and population sizes.
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
Software Category: Other Applications
Software
Brief Description
OpenFOAM, OpenFOAM+ and OpenFOAM Extend Toolkit for building CFD applications.
MuMax3 - Micromagnetic Simulation MuMax3 - micromagnetic simulator
MATLAB A general purpose numerical package with a high-level programming language for linear algebra, signal processing, image processing, 2-D and 3-D graphics, etc.
ANSYS simulation software, including Fluent and CFX ANSYS simulation software, including computational fluid dynamics packages Fluent and CFX
ABAQUS Comprehensive finite element modelling package