Software on WestGrid Systems

Introduction - General comments on the scope of this documentation and where to look for software not explicitly listed.
Software on computational resources - Software listings for the main WestGrid computational sites under the categories:
- UNIX Environment - operating systems and command shells
- Files and Data - editors, specialized file format libraries
- Programming - compilers, utilities and libraries
- Mathematical Libraries and Applications - numerical libraries for linear algebra, Fourier transforms and statistical analysis.
- Graphics - Charting, mapping, image processing and graphics libraries
- Chemistry and Biochemistry Applications - electronic structure and molecular dynamics application
- Bioinformatics/Genomics Applications - Bioinformatics pipelines, genome assembly, sequence analysis
- Other Applications - general purpose applications such as MATLAB and more discipline-specific applications including those from electromagnetics, finite element analysis and geophysics.
Software on specialized resources - General descriptions of software available through some of the specialized WestGrid computing resources, such as the storage and visualization facilities.

Direct links to documentation on how to run specific software packages are available under the Software menu in the left side bar. However, it is recommended that you search for the package of interest on this page first, as the tables below will indicate all the systems on which the software is installed and whether there are version differences among the installations.

Note: Due to wide tables, this page is best viewed with a reduced text size or wide browser window. Font sizes may be more easily controlled in Firefox compared to Internet Explorer.

Introduction

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. When completed, the tables below will summarize the software available. In some cases, there are links to usage instructions or other notes.

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:

Facility	Head Node	Directories
Breezy (Appro AMD cluster)	breezy.westgrid.ca	/global/software
Bugaboo (Dell Xeon cluster)	bugaboo.westgrid.ca	(mostly on default path,/usr/local)
Checkers (SGI Xeon cluster)	checkers.westgrid.ca	/global/software
Glacier (IBM Xeon cluster)	glacier.westgrid.ca	/usr and /global/software
Grex	grex.westgrid.ca	/global/software
Hermes/Nestor (IBM Xeon clusters)	hermes.westgrid.ca nestor.westgrid.ca	/global/software
Lattice (HP Xeon L5520 cluster)	lattice.westgrid.ca	/global/software
Orcinus (HP Xeon cluster)	orcinus.westgrid.ca	/ global/software
Snowpatch (HP Intel Xeon blades)	snowpatch.westgrid.ca	(mostly on default path,/usr/local)

If software you require is not included in the lists here, please contact us to see if it can be installed.

Software on Computational Resources

UNIX Environment

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Operating system	All WestGrid systems run a variant of UNIX.	64-bit Linux CentOS 5.7 2.6.18...el5 #1 SMP	64-bit Scientific Linux 5.6 2.6.18...el5 #1 SMP	64-bit Scientific Linux 5.5 2.6.18...el5 #1 SMP	Red Hat Enterprise Linux AS Release 4 2.6.9...ELsmp #1 SMP	64-bit Linux CentOS 5.5 2.6.18...el5 #1 SMP	64-bit Scientific Linux 5.3 2.6.18...el5 #1 SMP		64-bit Linux CentOS 5.5 2.6.18...el5 #1 SMP	64-bit Red Hat Enterprise Linux Server 5.3 2.6.18...el5 #1 SMP
UNIX Command Shell	bash (default)	Y	Y	Y	Y	Y	Y		Y	Y
	tcsh	Y	Y	Y	Y	Y	Y		Y	Y
	sh	Link to bash	Link to bash	Link to bash	Link to bash	Link to bash	Link to bash		Link to bash	Link to bash
	csh	Link to tcsh	Link to tcsh	Link to tcsh	Link to tcsh	Link to tcsh	Link to tcsh		Link to tcsh	Link to tcsh
	ksh	Y (ksh93)	Y	Y (ksh93)	Y	Y (ksh93)	Y		Y (ksh93)	Y
	zsh	N	Y	Y	Y	Y	Y		N	N

Files and Data

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Editors	emacs - GNU version of this common text editor.	21.4.1	21.4	21.4.1	21.2.1	21.4	21.4.1		21.4.1	21.4.1
	nedit - a graphical editor recommended for PC users, but requires X Windows.		5.5	5.4	5.4	5.5	5.5		5.5	5.5
	nano - A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico)	1.3.12	1.3.12 (pico is just a link to nano)	1.3.12 (Also pico 5.04)	1.2.4 (Also pico 4.1)	1.3.12 (pico is just a link to nano)	1.3.12		1.3.12	1.3.12
	vim - an enhanced version of vi	7.0	7.0.109	6.3	6.1.265	7.0	7.0			7.0
Specialized file format libraries	HDF 4 - Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.		4.2.6		4.2r0 - no szip support (use with Portland Group compiler) /global /software /HDF4.2r0/pgi-5.2				4.2.5 /global /software /hdf/hdf425
	HDF 5 - Hierarchical Data Format - file format for storing a variety of data types.		1.8.7	1.8.3 /global /software/lib64	? /global /software /HDF5/intel	1.8.6 $HDF5HOME (module load hdf5)	1.8.4 /global /software /hdf5-1.8.4-patch1/		1.8.5-patch1 /global /software/lib	N
	NetCDF - Network Common Data Format is a file format for array-oriented scientific data. Also see NetCDF Operators and ncview entries on this page.		4.1.3 Fortan: -lnetcdff C: -lnetcdf C++: -lnetcdf_c++		3.6.1 /global /software /netcdf-3.6.1 (look in subdirectories for PGI and GNU GCC compiled versions)	4.1.1 $NETCDFHOME (module load netcdf)	4.1.1 /global /software /netcdf-4.1.1		4.1.1 /global /software /netcdf /netcdf4.1.1 (Also /global /software/lib)	4.0.1 /global /software /lib64/gcc /netcdf-4.0.1 (plus earlier versions for other compilers under /global /software /lib64)
	NCO - NetCDF Operators - a set of programs for manipulating data in NetCDF files.				N	4.0.8 (module load netcdf)	4.0.7 /global /software/ nco-4.0.7/
	Szip - A library for lossless compression of scientific data (incorporated into HDF 4 release 2)		2.1		N	2.1 /global /software	2.1 /global /software/ szip-2.1/		2.1 /global /software /lib

Programming

See the WestGrid Programming page for a general discussion of programming, including parallel programming, debugging and optimization. For those systems (Checkers and Glacier) for which separate pages are available giving examples of compiler usage and machine-specific details, the column headings provide links. Those examples are generally relevant for other WestGrid systems as well.

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Compilers	Fortran	GNU 4.1.2 (gfortran) f95 is link to gfortran GNU 4.4.4 (gfortran44)	f77 is wrapper script for $FC, $F77,defaulting to ifort f90 is wrapper script for $FC, $F90,defaulting to ifort f77 is wrapper script for $FC, $F95,defaulting to ifort Intel 12.1 (ifort, f77,f90,f95) GNU 4.4.4 (gfortran)	f77 links to g77 Intel 11.1 (ifort - Initialize with module load intel) GNU 4.3.2 (gfortran) GNU 3.4.6 (g77)	Portland Group 7.0-2 (pgf77, pgf90) Intel 9.1 (ifort) Absoft 8.2 (f90) GNU 3.2.3 (g77)	Intel 12.0.3.174 (ifort) GNU 4.4.0 (gfortran)	Intel 12.0.2 (/global/software/ intel12) Intel 11.1 Update 7 (ifort - Default) GNU 4.1.2 (gfortran) GNU 3.4.6 (g77)		Intel 12.0.2.137 (ifort - Initialize with module load intel/12) Intel 11.1 (ifort - Default) GNU 4.1.2 (gfortran)	Intel 11.0 (module load intel) (ifort) GNU 3.4.6 (g77) Portland Group 8.0-6 (module load pgi) (pgf77, pgf90, pgf95)
	C	cc is link to gcc GNU 4.1.2 (gcc) GNU 4.4.4 (gcc44)	cc is wrapper script for $CC, defaulting to icc Intel 12.1 (icc,cc) GNU 4.4.4 (gcc)	cc is link to gcc 3.4.6 Intel 11.1 (icc - Initialize with module load intel) GNU 4.3.2 (gcc)	Portland Group 7.0-2 (pgcc) Intel 9.1 (icc) GNU 3.2.3 (cc, gcc)	Intel 12.0.3.174 (icc) GNU 4.4.0 (gcc)	Intel 12.0.2 (/global/software/ intel12) Intel 11.1 Update 7 (icc - Default) GNU 4.1.2 (gcc)		Intel 12.0.2.137 (icc - Initialize with module load intel/12) Intel 11.1 (icc - Default) GNU 4.1.2 (gcc)	cc is link to gcc GNU 4.1.2 (gcc) Intel 11.0 (module load intel) (icc) Portland Group 8.0-6 (module load pgi) (pgcc)
	C++	c++ is same as g++ GNU 4.1.2 (g++) GNU 4.4.4 (g++44)	c++ is wrapper script for $CXX, defaulting to icpc Intel 12.1 (c++, icpc) GNU 4.4.4 (g++)	GNU 4.3.2 (g++,c++) GNU 3.4.6 (/usr/bin/g++) Intel 11.1 (icpc - Initialize with module load intel)	Portland Group 7.0-2 (pgCC) Intel 9.1 (icpc) GNU 3.2.3 (g++)	Intel 12.0.3.174 (icpc) GNU 4.4.0 (g++)	Intel 12.0.2 (/global/software/ intel12) Intel 11.1 Update 7 (icpc - Default) GNU 4.1.2 (g++)		Intel 12.0.2.137 (icpc- Initialize with module load intel/12) Intel 11.1 (icpc - Default) GNU 4.1.2 (g++)	GNU 4.1.2 (c++, g++) Intel 11.0 (module load intel) (icpc) Portland Group 8.0-6 (module load pgi) (pgCC)
Other Languages	Java	Sun Java 1.6.0_16-b01	OpenJDK 1.6.0	Sun Java 1.6.0_13	/global /software /j2sdk1.4.2_02 /bin /global /software/ jdk1.6.0_01 /bin	Sun Java 1.6.0_16	Sun Java SE JRE Oracle HotSpot 1.6.0_20		Default: Sun Java SE JRE Oracle HotSpot 1.6.0_23 /global /software /java /jre1.6.0_23 module unload intel will revert default to GCC gij 4.1.2	GNU 1.4.2 /usr/bin Sun Java 1.6.0_14 /global /software /java/ jdk1.6.0_14/ bin
	Perl	5.8.8	5.8.8		5.8.0	5.8.8 (default) ActivePerl 5.14.2.1402 (module load perl)	5.8.8		5.8.8
	Python	2.4.3 2.7.2 (add /global /software/ python/ python272/ bin to PATH. Includes NumPy 1.6.1, SciPy, mpi4py and matplotlib)	2.4.3 2.7.2 (module load python)	2.4.3 2.6.5 with NumPy 1.6.1 (module load python)	2.3.4 /usr/bin/python 2.4.3 /global /software/ ActivePython-2.4 (with NumPy 1.4.1)	2.4.3 (default) ActivePython 2.6.7 and 2.7.2 with NumPy, scipy, matplotlib 3.2.2 with numpy, scipy (run as python3) (module load python/ <version>)	2.4.3		2.4.3 2.7.2 NumPy 1.6.1 is available but contact WestGrid support for instructions.	2.4.3 (Use module load python2.4/ extra for NumPy 1.4.1 and SciPy 0.7.2)
	Ruby		1.8.7	1.8.5	1.8.1	1.8.5	1.8.5		1.9.3p0 /global /software /ruby/ruby193p0	1.8.5

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Utilities	CMake - Cross platform software build system	N	2.8.6	?	2.4.7 /global /software/ cmake-2.4.7	2.8.3				N
Utilities	Jam - Make replacement for C/C++ projects.	N			N	N
Debuggers	dbx - Common UNIX debugger				N	N
	ddd - Graphical front end to other debuggers		3.3.11		3.3.1	3.3.11
	gdb - GNU debugger		7.0.1		6.3.0.0-1.62rh	7.0
	idb - Intel debugger		12.1		7.3.2, 9.0-20 Look in /global /software/ intel	12.0	11.1 Update 7		11.1
	pgdbg - Portland Group graphical debugger				6.1-4
Libraries	Boost - An eclectic collection of C++ libraries. See www.boost.org for more information.	1.48.0 (gcc) /global /software /boost/gcc	1.33.1 (in default library search location)		1.33.1 (gcc) /global /software/ boost-1.33_1 1.32 /usr/lib, /usr/include /boost 1.31.0 (gcc) /global /software/ boost-1.31.0	1.33.1	1.33.1-10
	GNU libgomp - GNU implementation of the OpenMP Application Programming Interface (API).		4.4.4		N	4.4.0	4.4.0-6
	STLport - An implementation of the Standard Template Library.				N
Version Control	Subversion - An open source alternative to CVS for managing files for large development projects. The Subversion client, svn, is provided to give access to repositories outside of WestGrid.		1.6.11	1.6.5 /global/scratch/ software /subversion /bin/svn	N	1.4.2			1.4.2 /usr/bin/svn 1.6.15 /opt/ CollabNet_ Subversion /bin/svn
Version Control	Git - version control system			1.7.5 (module load git)		1.7.7.5 (module load git) 1.7.5.1 (module load git/1.7.5.1)			1.7.8.3 (module load git)

Mathematical Libraries and Applications

For descriptions of the various numerical libraries installed on WestGrid systems go to the Mathematical Libraries and Applications page , or click on the links in the table below.

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Comprehensive Libraries See also MATLAB below.	GSL - GNU Scientific Library. Notes on using GSL on WestGrid are here.	1.15 /global /software /gsl/gsl115	1.15 -lgsl	1.14 /global /scratch /software	1.10 (gcc version - /global /software/ gsl-1.10/gcc/)	1.13			1.14 /global /software/ gsl-1.14	1.9 /global /software/ lib64/gcc/gsl (module load gcc/gsl)
Comprehensive Libraries See also MATLAB below.	MKL - Intel Math Kernel Library.	10.3.x (in default Intel 12 environment)	10.3.6 -lmkl	10.2 (module load intel/mkl-64/10.2)	6.1	10.3 (module load intel)	10.2.6		10.2.6 (default with Intel 11.1 compiler) 10.3.x with module load intel/12	10.1.3.027 (module load intel)
Differential Equation Solvers	PETSc - Toolkit for parallel solution of differential equations. See WestGrid-related comments here .		3.2-p5 (module load petsc) Older versions are also available			3.2-p5 (module load petsc for 32-bit integer MKL interface) 3.1-p7 (module load petsc/3.1-p7)
Fourier Transforms	FFTW - A widely-used FFT implementation. See FFTW home page .	2.15 /global /software /fftw215_gcc 3.2.2 /global /software /fftw322	2.1.5, 3.3	3.2.1 /global /software /fftw	2.1.5, 3.0.1	3.1.1 /global /software /fftw	2.1.5,3.2.2			3.2.2 /global /software /lib64 /gcc/fftw-3.2.2 (module load gcc/fftw)

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Linear Algebra MKL refers to the Intel Math Kernel Library - see above. See also MATLAB below.	BLAS - Basic Linear Algebra Subprograms.	In MKL	-lblas (same as -lgoto2) GotoBlas2-1.13	In MKL	In MKL	In MKL or GotoBLAS2 (-lgoto2)	In MKL		In MKL	In MKL
	LAPACK - Linear algebra subroutine package.	In MKL	3.3.1 -llapack -lblas or Intel MKL 10.3.4.191 -lmkl	In MKL	In MKL	In MKL or GotoBLAS2 (-lgoto2)	In MKL		In MKL	In MKL
	ScaLAPACK - Scalable LAPACK.	In MKL	1.8.0 -lscalapack -lblacs -llapack -lblas	In MKL	1.7? in MKL	1.8.0 -lscalapack -lmkl	In MKL		In MKL	In MKL
	SLEPc - PETSc add-on eigenvalue solver for large sparse systems.		3.1p4 -lslepc
Mesh Partitioning	METIS - Mesh and graph partitioning.		METIS 5.0.2 ParMETIS 4.0.2		ParMETIS is in /global /software/ Complex-Fluids /petsc-2.3.3-p13 /external packages	N			METIS 4.0.1 /global /software (bin,lib,include)
Statistics	R - Software environment and language for statistical data analysis. A few notes related to using the software on WestGrid systems are given here.		2.13.1 (on default path)	2.13.1 (module load R)	2.7.1 /global /software /R-2.7.1 /gcc/bin/R 2.12.0 /global /software /R-2.12.0/ (see notes)	N	2.11.1

Graphics

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Animation	mencoder (MPEG encoding) mplayer (video player)				3.2.3 /global /software/ MPlayer/bin		/global /software/ mencoder-20100622/			4.1.2 /global /software/ mplayer/bin
General purpose scientific data visualization	VTK - Visualization Toolkit - Comprehensive libraries for visualization of many types of multi-dimensional data.		5.2 /usr/local/vtk	5.4.2 (initialize with module load vtk)
General purpose scientific data visualization	Paraview - GUI-based application for visualization of many types of multi-dimensional data. Based on VTK.		3.12.0 (On default path)
Charting	Grace/Xmgrace - GUI-based x-y plotting for thesis and publication-quality graphs. Also includes data transformations and curve fitting.		5.1.22 - no PDF support	5.1.22 - no NetCDF or PDF support /global /scratch /software /grace/ grace-5.1.22/ bin/xmgrace	5.1.19 - no netCDF or PDF support /ibm_global/ xmgrace/ bin/xmgrace	5.1.18 - no netCDF or PDF support /global /software/ grace-5.1.18/ grace/bin /xmgrace			5.1.22 - no netCDF or PDF support /global /sofwtare/ bin/xmgrace
	Gnuplot - Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.	4.4p0 /global /software/ bin/gnuplot	4.0.0		4.0p0	4.0	4.0
	Matplotlib - Python-based 2D (mostly) plotting library	1.1.0 rc1 (See Python 2.7.2 above)
Geographic data handling	GMT - Generic Mapping Tools - Script-driven package of utilities for gridding and contouring geographic and Cartesian data sets, with support for many map projections. Vector plots, surface plots and other types of graphics are supported. A few notes related to using the software on WestGrid systems are given here .		4.5.6 /usr/local /GMT (with GSHHS-2.1.1)		4.1.3 /global /software/ GMT4.1.3				4.5.6 /global /software/ gmt/gmt456
	NCAR Graphics - Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases and other visualization tools developed for the support of meteorological applications but with a broad range of applications in other disciplines.								6.0.0 (Set NCARG_ROOT to /global /software/ ncl/ ncl_ncarg_600)
	Ncview - Visual browser for NetCDF files.		2.1.1
	VISAT - An image processing and data analysis program for remotely sensed data. VISAT is part of the BEAM toolkit mentioned below .		4.7

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Image viewing, editing and conversion	Eye of GNOME - Image viewer (eog)			2.16.0.1	2.8.1	2.16.0.1				2.16.0.1
	ImageMagick - Software suite for image format conversion and editing. Note, not all versions support all features.	6.2.8	6.2.8	6.2.8	6.0.7	6.2.8	6.2.8		6.7.0.0 /global /software /imagemagick /ImageMagick-6.7.0-0	6.2.8
	libpng - Library for handling PNG raster images		1.2.10		1.2.2-16 /usr/lib	1.2.10	1.2.10-7.1
	libjpeg - Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg .		6b		6b-26 /usr/lib	6b	6b-37
	libtiff - TIFF (Tagged Image File Format) image library.		3.8.2		3.5	3.8.2	3.8.2-7
	Netpbm - Image conversion utilities and library.		10.35			10.35	10.35-6.1		10.35.80 /global /software/ netpbm/ netpbm-10.35.80
	pdflib - PDF file handling library ("PDFlib-Lite" for non-commercial use)
	zlib - Data compression library.		1.2.3		1.1.4	1.2.3	1.2.3-3
Molecular visualization	Rasmol -Molecular graphics visualization		2.7.5
Molecular visualization	VMD - Visual Molecular Dynamics See local VMD notes for access.		1.9			1.9 (module load vmd Also may need: module load mesa)			1.8.7 /global /software/ vmd/vmd-1.8.7/bin
OpenGL-related	Vendor's OpenGL
	Mesa		Y		?	Y	6.5.1-7.7
	GLUT		freeglut 2.4.0		?	Y
User interface development	Qt - Application and user interface development framework.		4.6.4	4.7.2 (module load qt/4.7.2)

Chemistry and Biochemistry Applications

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Lattice	Orcinus
Electronic structure calculations and molecular dynamics	ABINIT - a DFT-based package for electronic structure and other properties of molecules and periodic solids. It also includes options for molecular dynamics. Basic usage instructions are given here .		6.8.1 (older versions see "module avail")	N	N	N		6.8.1 (/global /software /abinit See notes)	N
	Amber - Suite of programs for molecular dynamics and other molecular simulations. Licensing restrictions and basic usage instructions are given here.		10 (use "module load amber/10") 11 (use "module load amber")	10 /global /software/ amber10 11 /global /software/ amber11	N	N		11 /global /software /amber /amber11	N
	CPMD - Software for ab initio molecular dynamics. Users should be aware of the license requirements .		3.15.1	N	N	N		3.13.2 (largely untested) /global /software/ cpmd MKL and GotoBLAS versions	N
	CP2K - Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets		2.1	N	N	N		N	N
	DL_POLY - A suite of programs for molecular dynamics. Licensing restrictions and basic usage instructions are given here .		N	DL_POLY 4.02 /global /software/ dlpoly/ dl_poly_4.02/ execute	N	N		DL_POLY CLASSIC 1.7 DL_POLY 4.02 See /global /software/ dl_poly	N
	EXCITING - a full-potential all-electron DFT package based on the linearized augmented plane-wave (LAPW) method.		Helium	N	N	N	N		N
	GAMESS - A general ab initio quantum chemistry package. Basic WestGrid usage instructions and licensing restrictions are given here .			/global /scratch /software /gamess /gamess. v25Mar2010		Aug2011 /global/software/gamess		/global /software /gamess/ gamess2010oct01
	Gaussian - A suite of programs for semi-empirical and ab initio molecular orbital calculations. Licensing restrictions and basic usage instructions are given here .	N	N	N	N	G09 C.01 (Initialize with module load gaussian See module avail for older versions and variants)	N	N	N
	GROMACS - A suite of programs for molecular dynamics calculations. Instructions for using GROMACS on WestGrid systems are given here .		4.0.7 (module load gromacs/4.0.7) 4.5.1 (module load gromacs/4.5.1) 4.5.4 (in default PATH)	4.5.4 (Initialize with module load gromacs/4.5.4 or module load gromacs) 4.5.3, 4.5.1 and 4.0.5, 4.0.7 are also available using module commands	3.3.1	N	4.0.7 /global /software/ gromacs-4.0.7-double /global /software/ gromacs-4.0.7-single	4.5.4 and 4.07 See /global /software/ gromacs	4.0.5, 4.0.7 and 4.5.4 See /global /software/ gromacs (Initialize with module load gromacs/version module load gromacs selects version 4.0.5)
Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Lattice	Orcinus
Electronic structure calculations and molecular dynamics (continued)	LAMMPS - Classic molecular dynamics simulator		110831 (lmp on default path) (older versions see "module avail")	14Aug11 lmp_checkers (module load lammps)	N	N			N
	Molden - A pre- and post-processing program for molecular and electronic structure. See the Molden and Molden OpenGL developer's site for more information.		4.7	4.9 (/global /scratch/ software/ molden/4.9)	N	5.0 (module load molden)			N
	NAMD - A molecular dynamics simulator for large biomolecular systems. License restrictions and basic job submission instructions are given here . Also see VMD entry in graphics section above.		2.8					2.7 (ibverbs) 2.7b3 (OpenMPI)	2.7b2 (module load namd)
	OpenBabel - Data conversion toolkit.		2.3.0			2.3.1 (module load openbabel) 2.2.3 (module load openbabel/2.2.3)
	ORCA - An ab initio, DFT and semiempirical SCF-MO package. See license restrictions and job submission instructions here.					2.8.0.2 (/global /software/ orca)		2.8.0.2 (/global /software/ orca)
	Quantum ESPRESSO - A suite of programs for electronic structure and materials modelling. Basic usage instructions are given here .		4.3.2 pseudo potentials in /usr/local /espresso /pseudo_library Examples are in /usr/local /espresso /examples	4.3 including examples and pseudo potentials, etc. in /global /software/ espresso-4.3 4.1.2 in /global /software/ espresso-4.1.2	N	N			4.1.2 /global /software/ espresso-4.1.2/bin (requires module load intel)
	SIESTA - An electronic structure and ab-initio quantum-mechanical molecular dynamics package. Note SIESTA is available only for approved license holders. Register here then write to support@westgrid.ca to request access.		3.1	3.0-b /global /scratch/ software/ siesta-3.0-b Note: No XML output due to compiler bug. In input use: WriteXML F		3.1 /global/software/siesta-3.1
	VASP - An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. Note VASP is available only for approved license holders. For more information about access, see here .		4.6.36 (vasp, vasp-gamma) 5.2 (vasp5, vasp5-gamma)	N	4.6	N		5.2.12 (Look in /global /software /vasp /vasp52)	4.6 /global /software /VASP /vasp.4.6/ vasp, vasp-gamma, 5.2 /global /software /VASP5 /vasp.5.2/ vasp, vasp-gamma,
	YAeHMOP - Yet Another extended Huckel Molecular Orbital Package		3.0.3 (module load yeahmop)	N	N	3.0.3 (module load yaehmop)			N

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Other Chemistry/Biochemistry Applications	AutoDock - A suite of programs for predicting how small molecules will bind to a target of known 3D structure.				4.2 /global /software /AutoDock /bin
	NEURON - An environment for simulating neurons and networks of neurons. See the NEURON site for more information.								7.1 /global /software /neuron /nrn-7.1
	Rosetta Software Suite - Protein design and analysis. Write to WestGrid support for access information.		3.3 (Older versions available through modules)

Bioinformatics/Genomics Applications

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Lattice	Orcinus
Bioinformatics, Sequence Analysis	ALLPATHS-LG - Sequence assembly program.	Revision 39750 /global /software /allpathslg /39750/bin				Revision 39099 (module load allpathslg)
	ARB - Sequence database handling and phylogenic analysis.		5.1 (module load arb)
	BEAGLE - Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations (such as with BEAST, below)		1.1
	BEAST - Bayesian Evolutionary Analysis by Sampling Trees.		1.6.2
	BioPerl - Collection of Perl-based tools for bioinformatics.		1.6.1			1.6.901 (module load perl)
	Biopython - Collection of Python-based tools for bioinformatics.		1.58
	BLAST - Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. See the BLAST site for more information.	NCBI BLAST 2.2.18 (Legacy BLAST) (linked from /global /software/ blast) NCBI BLAST+ 2.2.23+ (linked from /global /software/ ncbi-blast)	NCBI BLAST 2.2.25 (Legacy BLAST) mpiblast 1.6.0 NCBI BLAST+ 2.2.25+ Databases in /usr/local/ blast+/db
	BLAT - BLAST-Like Alignment Tool. See the BLAT site for more information.	34 /global /software/ blat/blat34 (linked from /global /software/ bin)	34
	Mothur - Bioinformatics software for microbial ecology	1.21.1 /global /software/ bin/ mothur	1.23.0
	MultiMap - Program for automated construction of genetic maps. Includes Cri-Map	2.95 /global /software/ multimap/bin (includes Cri-Map 2.41m)	2.96

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Lattice	Orcinus
Bioinformatics, Sequence Analysis (continued)	Picard tools - Java-based tools for manipulation of BAM (Binary sequence alignment map) data files.	1.57 /global /software /picard /picard157 /picard-tools-1.57
	RITA - Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis.		1.0.0 (Rank-specific setup only)
	SOAPdenovo - Short Oligonucleotide Analysis Package for Illumina GA short-read assembly	1.05 /global /software /soapdenovo /bin
	TPP - Trans-Proteomic Pipeline		4.5.0 (on default path) Web interface here.
	Velvet - Package for genomic sequence assembly from short-read data.	1.1.06 /global /software /velvet /velvet1106 /bin				1.1.06 (module load velvet)
	wgsim - Simulate sequence reads from a reference genome.	0.3.0 /global/software /bin/wgsim
	wgs-assembler - Celera whole-genome shotgun sequence assembler and conversion utilities. See usage note here.	6.1 /global /software/ wgs/bin	6.1 /usr/local/ wgs/bin

Other Applications

Category	Software/ Description	Breezy	Bugaboo/ Snowpatch	Checkers	Glacier	Grex	Hermes/ Nestor	Hungabee	Lattice	Orcinus
Computational Fluid Dynamics	OpenFOAM - Toolkit for building CFD applications		1.7.1 (module load openfoam)
Cosmology	Gadget - Simulation of cosmological structure formation.						2.0.6
Electromagnetics	Lumerical FDTD Solutions - Package employing finite-difference time-domain techniques primarily for electromagnetic propagation problems. Basic usage instructions are available here .				6.0.3					7.5.2 (module load lumerical /7.5.2) 6.5.3
General Purpose Numerical	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. Basic instructions for usage are available here .	For U of C only: Release 2011a (7.12.0) /global /software/ bin/matlab	For SFU only: Release R2009b		For UBC only: Release 14 (7.0.1) Release 2007b (7.5.0) Release 2010a (7.10.0)	For UofM only: r2009a			For U of C only: Release 2011a (7.12.0) /global /software/ bin/matlab Release 2010b (7.11.0)	R2011a, R2009a and R2009b 64-worker license for Distributed Computing Server
General Purpose Numerical	Octave - A general purpose numerical package that is largely compatible with MATLAB		3.2.3 (on default path)							3.2.2 /global /software/ octave-3.2.2 /bin/octave
Geophysics	Seplib - A seismic data processing package from the Stanford Exploration Project (SEP) .				6.3.12 /global /software/ seplib-6.3.12/intel - use with Intel compiler
Geophysics	*Seismic Unx** - An open source collection of software for seismic processing and research. Some brief usage notes on the WestGrid installation are here .		Release 42 (see usage notes )	Release 42 (see usage notes )
Meteorology	WRF - Weather Research & Forecasting Model (including WPS - WRF Pre-processing system)		3.3.0
Satellite Data Analysis	BEAM - a toolbox for viewing and analyzing remotely-sensed data, such as from earth-orbiting satellites. Included is VISAT, an image processing and data analysis program, command-line data processing tools and a JAVA API for extending the toolbox.		4.8

Software on Specialized Resources

Storage Facilities

See the Storage Facilities page for documentation for more information.

Visualization Server

The WestGrid Visualization Server supports remote visualization through a custom implementation of the widely used VNC desktop sharing software. This software environment is installed an running on a subset of the nodes on the Checkers cluster. For more information on using remote visualization software on WestGrid please refer to the WestGrid Visualization Server page.

Updated 2012-02-02.

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