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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: UNIX Environment
Software
Brief Description
zsh Zsh is a shell designed for interactive use, although it is also a powerful scripting language.
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
sh
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.
MVAPICH2 MVAPICH2 is an MPI implementation
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.
Intel MPI A multi-fabric message passing library that implements the Message Passing Interface.
csh The improved version of tcsh.
bash (default) Bash is a Unix shell.
64-bit Scientific Linux An operating system distributed by CERN that is similar to and compatible with CentOS.
Software Category: Graphics
Software
Brief Description
zlib Data compression library.
xv Image display and manipulation utility
wkhtmltox Convert HTML to PDF and various image formats
VTK - Visualization Toolkit Comprehensive libraries for visualization of many types of multi-dimensional data.
VMD VMD is a program for displaying and animating large biomolecular systems.
VISAT An image processing and data analysis program for remotely sensed data.
Rasmol Molecular graphics visualization.
Qt Application and user interface development framework.
ParaView GUI-based application for visualization of many types of multi-dimensional data.
Netpbm Image conversion utilities and library.
Ncview Visual browser for NetCDF files.
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
Matplotlib Python-based 2D (mostly) plotting library.
links View HTML files or URL
libtiff TIFF (Tagged Image File Format) image library.
libpng Library for handling PNG raster images.
libjpeg Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg.
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.
GLUT A toolkit that implements a simple windowing application programming interface (API) for OpenGL.
Gbrowse GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
Circos Oriented towards genomic data display but can be applied to other data.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
YAeHMOP Yet Another extended Huckel Molecular Orbital Package.
VASP An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set.
SIESTA An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package.
ShengBTE - solving Boltzmann Transport Equation for phonons ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
Rosetta Software Suite Protein design and analysis. Write to WestGrid support for access information.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
Open Babel Data conversion toolkit.
NAMD A molecular dynamics simulator for large biomolecular systems.
Molden A visualization, pre- and post-processing program for molecular and electronic structure.
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
Gulp GULP is a program for performing a variety of types of simulation on materials
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
GAMESS A general molecular ab initio quantum chemistry package
EXCITING A full-potential all-electron DFT package based on the linearized augmented plane-wave (LAPW) method.
dl_meso The DL_MESO Mesoscale Simulation Package
DIRAC Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations.
DFTB+ - Density Functional based Tight Binding (DFTB) method with extensions DFTB+ - Package implementing the Density Functional based Tight Binding (DFTB) method with extensions
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
CP2K Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets.
Chaste Cancer, Heart and Soft Tissue Environment - tissue and cell level electro-physiology, discrete and soft tissue modelling.
Cantera Cantera is an object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes
ASE ASE is an Atomistic Simulation Environment written in the Python
Amber A suite of programs for molecular calculations, including molecular dynamics.
ABINIT Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids.
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.
Mercurial Distributed version control system
Java Java is a programming language and computing platform.
idb Intel debugger.
GNU libgomp GNU implementation of the OpenMP Application Programming Interface (API).
Git Version control system.
gdb GNU debugger.
Expat Expat is an XML parser library written in C.
Eigen C++ template library for linear algebra.
ddd Graphical front end to other debuggers.
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.
Blitz++ C++ template library for dense vectors and multi-dimensional arrays.
Software Category: Other Applications
Software
Brief Description
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).
Seismic Un*x An open source collection of software for seismic processing and research.
PROJ.4 Cartographic Projections library
OpenSees Open System for Earthquake Engineering Simulation
OpenFOAM, OpenFOAM+ and OpenFOAM Extend Toolkit for building CFD applications.
Octave A general purpose numerical package that is largely compatible with MATLAB.
MOM The Modular Ocean Model (MOM) is a numerical ocean model based on the hydrostatic primitive equations.
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.
GRIB-API GRIB-API is an API for working with GRIB meteorological data format.
GDAL Geospatial Data Abstraction Library.
BEAM A toolbox for viewing and analyzing remotely-sensed data.
Software Category: Files and Data
Software
Brief Description
Vim An enhanced version of the vi text editor.
TecIO A library for writing data for import into Tecplot.
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.
NCO A set of programs for manipulating data in NetCDF files.
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.
Hadoop Tool for map/reduce-style calculations
gedit - graphical text editor gedit - graphical text editor with syntax highlighting
Emacs GNU version of this common text editor.
Climate Data Operators (CDO) A command line suite for manipulating and analysing climate data.
Software Category: Bioinformatics / Genomics Applications
Software
Brief Description
Velvet Package for genomic sequence assembly from short-read data.
VCFtools a program package designed for working with VCF files
Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
Trans-ABySS A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
TPP The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
TMHMM Prediction of transmembrane helices in proteins
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
SOAPdenovo Short Oligonucleotide Analysis Package for Illumina GA short-read assembly.
smalt SMALT aligns DNA sequencing reads with a reference genome.
SignalP SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
SHRiMP SHRiMP - SHort Read Mapping Package
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
RSEM Package for estimating gene and isoform expression levels from RNA-Seq data.
RNAmmer RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
RITA Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis.
QIIME Quantitative Insights into Microbial Ecology.
Pandaseq To align Illumina reads and reconstruct an overlapping sequence
orthomcl
Nemo Stochastic simulation to study evolution of life history/phenotypic traits and population genetics.
Muscle multiple alignment program
MrBayes Bayesian inference for phylogenetic and evolutionary models.
Mothur Bioinformatics software for microbial ecology.
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.
MetaVelvet An extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
MEME Suite Identify motifs (patterns) in sequences.
LepMAP
Image Iterative Mapping and Assembly for Gap Elimination
Ima2p
IMa2 Isolation and migration effects in population genetics.
HMMER Homolog search and protein sequence alignments.
hisat2 graph-based alignment of next generation sequencing reads to a population of genomes
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
GapCloser The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenevo
freebayes
FastTree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
ExaML/RAxML - Phylogenetic tree analysis Phylogenetic tree analysis.
Cufflinks Transcript assembly from RNA-Seq data.
Censor Censor compares and masks protein or nucleotide sequences.
Celera Whole-Genome Shotgun Assembler Celera whole-genome shotgun sequence assembler and conversion utilities.
Cd-hit CD-HIT is a program for clustering DNA/protein sequence database at high identity with tolerance.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Bowtie2 Short read DNA sequence aligner.
Bowtie Short read DNA sequence aligner.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
Biopython Collection of Python-based tools for bioinformatics.
BioPerl Collection of Perl-based tools for bioinformatics.
BEDTools Utility suite for comparing genomic features.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
ARB Sequence database handling and phylogenic analysis.
ALLPATHS-LG Sequence assembly program.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
Software Category: Mathematical Libraries and Applications
Software
Brief Description
Trilinos Object-oriented framework for linear algebra, meshing, preconditioners, solvers.
TetGen Tetrahedral mesh generation and 3D Delaunay triangulator.
SuiteSparse a Suite of sparse matrix packages
SLEPc PETSc add-on eigenvalue solver for large sparse systems.
SCOTCH Graph and mesh partitioning, sparse matrix ordering.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
SAS Statistical analysis software.
R Software environment and language for statistical data analysis.
PETSc Toolkit for parallel solution of differential equations.
p4est Parallel adaptive mesh refinement.
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
NLopt Nonlinear optimization library.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
MUMPS Parallel direct solver for sparse systems.
MMG3D Anisotropic tetrahedral remesher/moving mesh generation.
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.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
Ipopt Interior Point OPTimizer for large-scale nonlinear optimization.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
FreeFem++ - Partial Differential Equation Solver FreeFem++ is typically applied to solve multiphysics non-linear systems.
FFTW A widely-used FFT implementation.
deal.II Library for partial differential equation solution with adaptive finite elements.
CGAL A C++ library for geometric algorithms.
BLAS Basic Linear Algebra Subprograms.
AlmaBTE A Solver of the Space- and Time-Dependent Boltzmann Transport Equation for phonons.
Software Category: Database management and tools
Software
Brief Description
PostgreSQL PostgreSQL is a powerful, open source object-relational database system.
MySQL MySQL is a popular open source database