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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.
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.
VTK - Visualization Toolkit Comprehensive libraries 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.
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
mencoder (MPEG encoding) mplayer (video player).
Matplotlib Python-based 2D (mostly) plotting library.
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.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
Yambo Ab initio code for quasi-particle excited state energies and optical properties for solid state and molecular physics applications.
SIESTA An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
NWChem Scalable open-source solution for large scale molecular simulations.
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
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
CP2K Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets.
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).
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.
MEEP Finite difference time-domain (FDTD) electromagnetic simulation package.
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.
libLAS ASPRS LiDAR data translation tools.
GDAL Geospatial Data Abstraction Library.
Gadget Simulation of cosmological structure formation.
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.
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).
jEdit A graphical editor for programmers (requires X Windows).
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
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
Trans-ABySS A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
SNPTEST SNPTEST - Program for whole-genome SNP association studies
SHAPEIT (estimation of haplotypes) SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data
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.
Ray De novo genome assembly.
PLINK Analysis of genotype/phenotype data.
Nemo Stochastic simulation to study evolution of life history/phenotypic traits and population genetics.
MUMmer Alignment of large DNA and protein sequences.
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.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
HMMER Homolog search and protein sequence alignments.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
FastQC Quality control tool for high throughput sequence data.
DosageConverter DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
Cufflinks Transcript assembly from RNA-Seq data.
Clustal Omega Clustal Omega - Multiple protein sequence alignment
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.
BioPerl Collection of Perl-based tools for bioinformatics.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
ARB Sequence database handling and phylogenic analysis.
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
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers)
SLEPc PETSc add-on eigenvalue solver for large sparse systems.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
R Software environment and language for statistical data analysis.
PETSc Toolkit for parallel solution of differential equations.
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.
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.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
FFTW A widely-used FFT implementation.
BLAS Basic Linear Algebra Subprograms.
Software Category: Programming
Software
Brief Description
Subversion An open source alternative to CVS for managing files for large development projects.
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.
OpenCV
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).
gdb GNU debugger.
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.