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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 | |
|---|---|---|
| 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. | |
| GLOST | ||
| Intel MPI | A multi-fabric message passing library that implements the Message Passing Interface. | |
| 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. | |
| Open MPI | 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. | |
| Parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. | |
| sh | ||
| Singularity | Singularity is a containers solution for HPC applications | |
| tcsh | It is a command language interpreter usable both as an interactive login shell and a shell script command processor. | |
| zsh | Zsh is a shell designed for interactive use, although it is also a powerful scripting language. |
| Software | Brief Description | |
|---|---|---|
| ABINIT | Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids. | |
| Adaptive Poisson-Boltzmann Solver (APBS) | Software for modelling biomolecular solvation. | |
| Amber | A suite of programs for molecular calculations, including molecular dynamics. | |
| ASE | ASE is an Atomistic Simulation Environment written in the Python | |
| AutoDock | A suite of programs for predicting how small molecules will bind to a target of known 3D structure. | |
| AutoDock_vina | AutoDock Vina is an open-source program for doing molecular docking. | |
| BigDFT | A massively-parallel wavelet-based DFT code for solid state/nanoclusters modeling for material science. | |
| CP2K | Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets. | |
| Dalton | Together, the two programs, Dalton and LSDalton, provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite. | |
| GAMESS | A general molecular ab initio quantum chemistry package | |
| Gaussian | A suite of programs for semi-empirical and ab initio molecular orbital calculations. | |
| GPAW | ||
| GROMACS | A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins. | |
| LAMMPS | LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator | |
| MGLTools including AutoDockTools | MGLTools, including AutoDockTools (ADT) is a suite of programs for molecular structure visualization and analysis. | |
| Molden | A visualization, pre- and post-processing program for molecular and electronic structure. | |
| MOPAC | MOPAC (Molecular Orbital PACkage) is a general-purpose semiempirical quantum chemistry package for the study of solid state and molecular structures and reactions. | |
| NAMD | A molecular dynamics simulator for large biomolecular systems. | |
| NBO | NBO: Natural Bond Orbital analysys program | |
| NWChem | Scalable open-source solution for large scale molecular simulations. | |
| Open Babel | Data conversion toolkit. | |
| OpenMX | Open Materials Explorer - O(N) massively parallel DFT code for nano-scale material science. | |
| ORCA | An ab initio, DFT and semiempirical SCF-MO package. | |
| PDB2PQR | Preparing structures for continuum electrostatics calculations. | |
| Phonopy | Phonopy is an open source package of phonon calculations based on the supercell approach. | |
| Priroda | Priroda is a fast parallel relativistic DFT/ab initio code for molecular modeling | |
| PSI | PSI is an open-source suite of ab initio quantum chemistry programs | |
| Quantum ESPRESSO | A suite of programs for electronic structure and materials modelling. | |
| QWalk | QWalk is an efficient Quantum Monte Carlo code by the group of Lucas Wagner | |
| ShengBTE - solving Boltzmann Transport Equation for phonons | ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. | |
| SIESTA | An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package. | |
| Sire | Sire is a free, open source, multiscale molecular simulation framework, written to allow computational modelers to quickly prototype and develop new algorithms for molecular simulation and molecular design. | |
| VASP | An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. | |
| WebMO | WebMO is a web portal for running and visualization of Computational Chemistry computations | |
| XCrySDen | XCrySDen is a crystalline and molecular structure visualisation program | |
| YAeHMOP | Yet Another extended Huckel Molecular Orbital Package. |
| Software | Brief Description | |
|---|---|---|
| ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below. | |
| ADMIXTURE | ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. | |
| ALLPATHS-LG | Sequence assembly program. | |
| BioPerl | Collection of Perl-based tools for bioinformatics. | |
| BLAST | A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences. | |
| BLAT | BLAST-Like Alignment Tool. See the BLAT site for more information. | |
| Bowtie2 | Short read DNA sequence aligner. | |
| Bridger | ||
| DIAMOND - sequence aligner | Program for local aligments of translated nucleotide or amino acid sequences to protein references | |
| HMMER | Homolog search and protein sequence alignments. | |
| JELLYFISH | DNA substring (k-mer) counting. | |
| Kraken | Kraken is a Taxonomic Sequence Classification System | |
| MetaVelvet | An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. | |
| Prodigal | Prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm | |
| SAMtools and HTSlib utilities | SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files. | |
| STAR | STAR: Spliced Transcripts Alignment to a Reference | |
| Velvet | Package for genomic sequence assembly from short-read data. |
| Software | Brief Description | |
|---|---|---|
| AlmaBTE | A Solver of the Space- and Time-Dependent Boltzmann Transport Equation for phonons. | |
| BLAS | Basic Linear Algebra Subprograms. | |
| FETK | FETK: The Finite Element ToolKit for solving differential equations. | |
| GSL | A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines. | |
| JAGS | Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. | |
| 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. | |
| 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. | |
| NetworkX | A Python-based package for creating and analyzing graphs (networks of nodes and edges). | |
| OpenBUGS | Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation. | |
| PETSc | Toolkit for parallel solution of differential equations. | |
| R | Software environment and language for statistical data analysis. | |
| ScaLAPACK | ScaLAPACK is a parallelized subset of the LAPACK linear algebra package. | |
| scikit-learn | Scikit-Learn a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. |
| Software | Brief Description | |
|---|---|---|
| Boost | An eclectic collection of C++ libraries. | |
| 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) | |
| ddd | Graphical front end to other debuggers. | |
| Eigen | C++ template library for linear algebra. | |
| Git | Version control system. | |
| GNU Data Language (GDL) | A tool for data analysis and visualization in such disciplines as astronomy, geosciences and medical imaging. | |
| Go | The Google Go programming language | |
| Java | Java is a programming language and computing platform. | |
| Julia | Julia is a high-level, dynamic language for technical computing | |
| Lua | Lua is a powerful, fast, lightweight, embeddable scripting language. | |
| Mercurial | Distributed version control system | |
| Mono (C# environment) | Mono .NET environment to provide a platform for running C# programs. | |
| Node.JS | Node.JS asynchronous, event driven, standalone JavaScript language implementation. | |
| OCaml | OCaml: industrial strength programming language supporting functional, imperative and object-oriented styles | |
| Perl | Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. | |
| Python | Python is an interactive, object-oriented, extensible programming language. | |
| Ruby | A dynamic, interpreted, open source programming language with a focus on simplicity and productivity. | |
| Subversion | An open source alternative to CVS for managing files for large development projects. |
| Software | Brief Description | |
|---|---|---|
| Climate Data Operators (CDO) | A command line suite for manipulating and analysing climate data. | |
| 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). | |
| NCO | A set of programs for manipulating data in NetCDF files. | |
| 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 | |
|---|---|---|
| Eye of GNOME | Image viewer (eog). | |
| GDIS | GDIS is a scientific visualization program for the display, manipulation, and analysis of molecular and periodic structures. | |
| GLUT | A toolkit that implements a simple windowing application programming interface (API) for OpenGL. | |
| 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. | |
| libjpeg | Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg. | |
| libpng | Library for handling PNG raster images. | |
| libtiff | TIFF (Tagged Image File Format) image library. | |
| Luscus | Luscus is a program for graphical display and editing of molecular systems. | |
| Mesa | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | |
| MINC - Toolkit | Medical Imaging NetCDF (MINC) Toolkit | |
| Molekel | Molekel is an open-source multi-platform molecular visualization program | |
| NCAR Graphics and NCL | Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc. | |
| Ncview | Visual browser for NetCDF files. | |
| Netpbm | Image conversion utilities and library. | |
| PLplot | PLplot is a cross-platform software package for creating scientific plots. | |
| VMD | VMD is a program for displaying and animating large biomolecular systems. | |
| zlib | Data compression library. |
| Software | Brief Description | |
|---|---|---|
| GATE | GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. | |
| GDAL | Geospatial Data Abstraction Library. | |
| Geant4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. | |
| GRIB-API | GRIB-API is an API for working with GRIB meteorological data format. | |
| 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. | |
| MEEP | Finite difference time-domain (FDTD) electromagnetic simulation package. | |
| Octave | A general purpose numerical package that is largely compatible with MATLAB. | |
| OpenFOAM, OpenFOAM+ and OpenFOAM Extend | Toolkit for building CFD applications. | |
| OpenSees | Open System for Earthquake Engineering Simulation | |
| PROJ.4 | Cartographic Projections library | |
| WRF | Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System). |