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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 | Brief Description | |
|---|---|---|
| GROMACS | A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins. | |
| ABINIT | Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids. | |
| Amber | A suite of programs for molecular calculations, including molecular dynamics. | |
| CP2K | Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets. | |
| CPMD | Software for ab initio molecular dynamics. Users should be aware of the license requirements. | |
| 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". | |
| Elk | An electronic structure code for determining the properties of crystalline solids. | |
| LAMMPS | LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator | |
| NAMD | A molecular dynamics simulator for large biomolecular systems. | |
| NEURON | An environment for simulating neurons and networks of neurons. | |
| ORCA | An ab initio, DFT and semiempirical SCF-MO package. | |
| Qbox DFT | Based electronic structure and molecular dynamics program. | |
| Quantum ESPRESSO | A suite of programs for electronic structure and materials modelling. |
| Software | Brief Description | |
|---|---|---|
| BEAGLE (beagle-lib) | Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations. | |
| 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. | |
| Ray | De novo genome assembly. |
| Software | Brief Description | |
|---|---|---|
| CMake | Cross platform software build system | |
| Compilers - C, C++ and Fortran | Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95) | |
| Git | Version control system. | |
| idb | Intel debugger. | |
| Java | Java is a programming language and computing platform. | |
| Julia | Julia is a high-level, dynamic language for technical computing | |
| LIKWID - Performance analysis tools | LIKWID - Performance analysis tools for OpenMP and hybrid OpenMP/MPI programs. | |
| Mono (C# environment) | Mono .NET environment to provide a platform for running C# programs. | |
| Perl | Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. | |
| Python | Python is an interactive, object-oriented, extensible programming language. | |
| ROOT (data analysis framework) | ROOT is an object-oriented framework aimed at solving the data analysis challenges of high-energy physics. | |
| Ruby | A dynamic, interpreted, open source programming language with a focus on simplicity and productivity. | |
| SCons | SCons is an Open Source software construction tool | |
| Subversion | An open source alternative to CVS for managing files for large development projects. | |
| Xerces-C++ | XML parser and writer. |
| Software | Brief Description | |
|---|---|---|
| Emacs | GNU version of this common text editor. | |
| HDF 4 | Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types. | |
| HDF 5 | Hierarchical Data Format - file format for storing a variety of data types. | |
| nano | A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico). | |
| NEdit | A graphical editor recommended for PC users, but requires X Windows. | |
| 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. | |
| Szip | A library for lossless compression of scientific data. | |
| Vim | An enhanced version of the vi text editor. |
| Software | Brief Description | |
|---|---|---|
| FFmpeg (video encoding) | FFmpeg - create a movie file from a series of images | |
| Gnuplot | Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features. | |
| Grace/Xmgrace | GUI-based x-y plotting for thesis and publication-quality graphs. | |
| ImageMagick | Software suite for image format conversion and editing. | |
| NCAR Graphics and NCL | Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc. | |
| Netpbm | Image conversion utilities and library. | |
| ParaView | GUI-based application for visualization of many types of multi-dimensional data. | |
| pdflib | PDF file handling library ("PDFlib-Lite" for non-commercial use). | |
| Qt | Application and user interface development framework. | |
| VMD | VMD is a program for displaying and animating large biomolecular systems. |
| Software | Brief Description | |
|---|---|---|
| BLAS | Basic Linear Algebra Subprograms. | |
| FFTW | A widely-used FFT implementation. | |
| Gerris Flow Solver | Gerris Flow Solver - solve partial differential equations for incompressible flow | |
| GSL | A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines. | |
| LAPACK | Linear algebra subroutine package. | |
| 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. | |
| METIS | Mesh and graph partitioning. | |
| 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. | |
| ScaLAPACK | ScaLAPACK is a parallelized subset of the LAPACK linear algebra package. | |
| SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) | SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) |
| Software | Brief Description | |
|---|---|---|
| 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. | |
| bash (default) | Bash is a Unix shell. | |
| csh | The improved version of tcsh. | |
| 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. | |
| sh | ||
| tcsh | It is a command language interpreter usable both as an interactive login shell and a shell script command processor. |
| Software | Brief Description | |
|---|---|---|
| ABAQUS | Comprehensive finite element modelling package | |
| ANSYS simulation software, including Fluent and CFX | ANSYS simulation software, including computational fluid dynamics packages Fluent and CFX | |
| 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. | |
| OpenFOAM, OpenFOAM+ and OpenFOAM Extend | Toolkit for building CFD applications. |