Software on WestGrid Systems

Table of Contents

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. An abbreviated version of this table (without software descriptions, module commands, etc.) that may be a little easier to read is here.

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
Hungabee (SGI UV1000 Xeon E7-8837 SMP) hungabee.westgrid.ca /global/software
Jasper (SGI Xeon X5675 cluster) jasper.westgrid.ca /lustre/jasper/software
Lattice (HP Xeon L5520 cluster) lattice.westgrid.ca /global/software
Orcinus (HP Xeon cluster) orcinus.westgrid.ca /global/software
Parallel (HP Xeon E5649 cluster) parallel.westgrid.ca /global/software

 

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 for interactive and batch use

Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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 SLES 11 SP1 2.6.32.54-0.3-default  64-bit CentOS 5.7 2.6.18-274el5 

64-bit Linux
CentOS 5.5 (Lattice)
CentOS 5.7 (Parallel)

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 Y
tcsh Y 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  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  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
Distributed-memory parallel computing environment
All WestGrid systems support MPI (Message Passing Interface)




Open MPI
1.6.1
1.4.5
1.4.3

Intel MPI 4.1.0.030
4.0.3.008
4.0.1.007

(Run "module avail" and look for gcc/impi/<version> or intel/impi/<version> for module to load)

Intel MPI and Open MPI

(use module load)





Files and Data

Category Software/
Description
Breezy
Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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
 22.3.1 21.4.1  21.4.1
21.4.1
jEdit - a graphical editor for programmers (requires X Windows).           4.5.1        
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 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
2.2.6  1.3.12  1.3.12
1.3.12
Vim - an enhanced version of vi 7.0
7.3.144
6.3
6.1.265 7.0

7.0

7.3

(use module load)

 7.2 7.0  7.0.237
7.0
Specialized file format libraries and utilities
CDO - Climate Data Operators

 1.5.8

(module load cdo)

1.5.9
 

1.5.4

(module load cdo)

     
 
HDF 4 - Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.

4.2.8

/global/software/lib

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.

1.8.10

/global/software/lib

1.8.9

1.8.3

/global
/software/lib64

?
/global
/software
/HDF5/intel

1.8.9

$HDF5HOME

(module load hdf5/
1.8.9-intel)

1.8.4
/global
/software
/hdf5-1.8.4-patch1/

1.8.8

(module load library/hdf5/1.8.8)  

1.8.8

(module load library/hdf5/1.8.8, module load library/hdf5/1.8.8-parallel) 

1.8.5-patch1

/global
/software/lib

1.8.8

(module load intel-2011/hdf5)

NetCDF - Network Common Data Format is a file format for array-oriented scientific data.

Also see NetCDF Operators and ncview entries on this page.

C
4.2.1.1

Fortran
4.2

/global/software/lib

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)

4.1.3

$NETCDFHOME

(module load netcdf/
4.1.3-intel)

4.1.1
/global
/software
/netcdf-4.1.1

4.1.3

(module load library/netcdf/4.1.3) 

4.1.3

(module load library/netcdf/4.1.3) 

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.      
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
/global
/software
/lib
2.1
 

2.1

/global
/software

2.1
/global
/software/
szip-2.1/
   2.1
module load library
/szip/2.1
2.1
/global
/software
/lib
 
TecIO - A library for writing data for import into Tecplot   2009                

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 Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Compilers Fortran

f95 is link to gfortran

Intel 12.0.4 (ifort)

GNU 4.4.4 (gfortran44)

GNU 4.1.2
(gfortran)

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 13.0.1 (ifort, f77,f90,f95)

GNU 4.4.4 (gfortran, gfortran44)

GNU 4.7.1 (gfortran - module load gcc/4.7.1)

f77 links to g77

Intel 12.1, 11.1 (ifort - load appropriate module)

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 4.1.2
(gfortran)

GNU 3.4.6 (g77)

Intel 12.1.5.339
(ifort - see module avail for other versions)

GNU 4.4.6
(gfortran, gfortran44)

(See module avail for more recent, experimental GNU compilers)

Intel 13.0.1
12.0.2
Default:
11.1 Update 7
(ifort - see module avail)

 

GNU 4.4.6
(gfortran44)

GNU 4.4.4
(gfortran - module load gcc/4.4.4)

GNU 4.1.2
(gfortran)

GNU 3.4.6
(g77)

Intel 12.1.5

(ifort, module load compiler/
intel/12.1, loaded by default)

Portland Group 12.10

(pgf77, pgf90, pgf95 - module load compiler/pgi/12.10)

GNU 4.5.0
(gfortran - module load compiler/gcc/4.5.0)

GNU 4.3.4
(gfortran)

Intel 12.1

(ifort, module load compiler/
intel/12.1)

Portland Group 12.10

(pgf77, pgf90, pgf95 - module load compiler/pgi/12.10)

GNU 4.4.6
(gfortran, gfortran44 - module load compiler/gcc/4.4.6)

GNU 4.1.2
(gfortran)

Intel 12.1.10.319
(ifort - module load intel/2011-sp1.10.319)

Intel 11.1
(ifort - Default)

Portland Group 12.1-0
(pgf77, pgf90, pgf95 - module load pgi)

Parallel: GNU 4.4.4 Lattice:
GNU 4.4.0
(gfortran44)

GNU 4.1.2
(gfortran)

Intel 12.1.2
(ifort - module load intel-2011)

Intel 11.0
(ifort - module load intel)

Portland Group 8.0-6 (pgf77, pgf90, pgf95 - module load pgi)

GNU 4.4.0
(gfortran44)

GNU 4.1.2
(gfortran)

GNU 3.4.6
(g77)

C

cc is link to gcc

Intel 12.0.4
(icc)

GNU 4.4.4 (gcc44)

GNU 4.1.2
(gcc)

cc is wrapper script for $CC,
defaulting to icc

Intel 13.0.1 (icc,cc)

GNU 4.4.4 (gcc, gcc44)

GNU 4.7.1
(gcc - module load gcc/4.7.1)

cc is link to Intel icc 11.1

Intel 12.1, 11.1 (icc - load appropriate module)

GNU 4.3.2
(gcc)

GNU 3.4.6
(gcc34)

Portland Group 7.0-2
(pgcc)

Intel 9.1
(icc)

GNU 4.1.2
(gcc4)

GNU 3.4.6
(cc, gcc)

GNU 3.2.3
(gcc32)

Intel 12.1.5.339
(icc - see module avail for other versions)

GNU 4.4.6
(gcc, gcc44)

(See module avail for more recent, experimental GNU compilers)

Intel 13.0.1
12.0.2
Default: 11.1 Update 7
(icc- see module avail)

GNU 4.4.6
(gcc44)

GNU 4.4.4
(gcc - module load gcc/4.4.4)

GNU 4.1.2
(gcc)

Intel 12.1.5

(icc, module load compiler/
intel/12.1, loaded by default)

Portland Group 12.10

(pgcc - module load compiler/pgi/12.10)

GNU 4.5.0
(gcc - module load compiler/gcc/4.5.0)

GNU 4.3.4
(gcc)

Intel 12.1

(icc, module load compiler/
intel/12.1)

Portland Group 12.10

(pgcc - module load compiler/pgi/12.10)

GNU 4.4.6
(gcc, gcc44 - module load compiler/gcc/4.4.6)

GNU 4.1.2
(gcc)

Intel 12.1.10.319
(icc - module load intel/2011-sp1.10.319)

Intel 11.1
(icc - Default)

Portland Group 12.1-0
(pgcc - module load pgi)

Parallel: GNU 4.4.4 Lattice:
GNU 4.4.0
(gcc44)

GNU 4.1.2
(gcc)

cc is link to gcc

Intel 12.1.2
(icc - module load intel-2011)

Intel 11.0
(icc - module load intel)

Portland Group 8.0-6 (pgcc - module load pgi)

GNU 4.4.0
(gcc44)

GNU 4.1.2
(gcc)

C++

c++ is same as g++

Intel 12.0.4
(icpc)

GNU 4.4.4 (g++44)

GNU 4.1.2
(g++)

c++ is wrapper script for $CXX,
defaulting to icpc

Intel 13.0.1
(c++, icpc)

GNU 4.4.4 (g++, g++44)

GNU 4.7.1 (g++ - module load gcc/4.7.1)

Intel 12.1, 11.1 (icpc - load appropriate module)

GNU 4.3.2
(g++,c++)

GNU 4.1.2
(/usr/bin/g++)

GNU 3.4.6
(g++34)

Portland Group 7.0-2 (pgCC)

Intel 9.1 (icpc)

GNU 4.1.2
(g++4)

GNU 3.4.6 (g++)

GNU 3.2.3
(g++32)

Intel 12.1.5.339
(icpc - see module avail for other versions)

GNU 4.4.6
(g++, g++44)

(See module avail for more recent, experimental GNU compilers)

Intel 13.0.1
12.0.2
Default: 11.1 Update 7
(icpc - see module avail)

GNU 4.4.6
(g++44)

GNU 4.4.4
(g++ - module load gcc/4.4.4)

GNU 4.1.2
(g++)

Intel 12.1.5

(icpc, module load compiler/
intel/12.1, loaded by default)

Portland Group 12.10

(pgCC - module load compiler/pgi/12.10)

GNU 4.5.0
(g++ - module load compiler/gcc/4.5.0)

GNU 4.3.4
(g++)

Intel 12.1

(icpc, module load compiler/
intel/12.1)

Portland Group 12.10

(pgCC - module load compiler/pgi/12.10)

GNU 4.4.6
(g++, g++44 - module load compiler/gcc/4.4.6)

GNU 4.1.2
(g++)

Intel 12.1-10.319
(icpc- module load intel/2011-sp1.10.319)

Intel 11.1
(icpc - Default)

Portland Group 12.1-0 (pgCC- module load pgi)

Parallel: GNU 4.4.4 Lattice:
GNU 4.4.0
(g++44)

GNU 4.1.2
(g++)

Intel 12.1.2
(icpc - module load intel-2011)

Intel 11.0
(icpc - module load intel)

Portland Group 8.0-6 (pgCC - module load pgi)

GNU 4.4.0
(g++44)

GNU 4.1.2
(c++, g++)

Other Languages

C#

Mono .NET development environment

 


 

(Contact support for installation status)
 

/global
/software
/mono-2.10.2

GNU Data Language (GDL)
 


  0.9.2
/global
/software
/gdl-0.9.2


 

 

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
Java 1.6.0_25  OpenJDK 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

5.14.2

(use module load)

 5.10.0 5.8.8  5.8.8  
Python

2.4.3

2.7.2
(module load python,
Includes NumPy 1.6.1, SciPy, mpi4py and matplotlib)

2.4.3

2.7.2
with NumPy 1.6.1
(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
with NumPy 1.4.1
/global
/software/
ActivePython-2.4

2.4.3
(default)

ActivePython 2.6.7 and 2.7.2 with NumPy 1.6.1, scipy 0.9.0, matplotlib 1.0.1

3.2.2 with NumPy 1.6.1, SciPy 0.9.0 (run as python3)

(module load python/
<version>

2.4.3

2.7.2
with NumPy 1.6.2, SciPy 0.10.1,
matplotlib 1.1.1
(module load python)

2.6

(default)

2.7.3
(module load application/
python
/2.7.3)

2.4.3
(default)

 

2.7.3
(module load application/
python/
2.7.3)

2.4.3

2.7.2
with
NumPy 1.6.1
Matplotlib 1.1.0
(module unload intel
module load intel/12
module load python)

2.7.3
with NumPy 1.6.2, SciPy 0.11.0 and matplotlib 1.2.0
(module load python)

2.4.3
(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
 1.8.7 1.8.5  1.9.3p0
/global
/software
/ruby/
ruby193p0

1.8.5


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Utilities CMake - Cross platform software build system

2.8.6 ? 2.4.7
/global
/software/
cmake-2.4.7
2.8.3

 2.8.3
(module load cmake)

 2.8.10.2

(module load utility/cmake/2.8.10.2)

 2.8.9
(module load utility
/cmake-2.8.9)

2.8.4
/global/
software/
bin/cmake

2.8.7
(module load cmake)
Jam - Make replacement for C/C++ projects. N     N N
   3.1.16      
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   7.5
  6.3.0.0-1.62rh 7.0
7.0.1
7.3-0.6.1   7.0.1-37.el5_7.1    
idb - Intel debugger   13.0.1
  7.3.2, 9.0-20
Look in
/global
/software/
intel
12.0
11.1 Update 7
 12.1

12.1

(module load compiler/intel/12.1) 

11.1
 
pgdbg - Portland Group graphical debugger       6.1-4
         
Libraries Blitz++ - C++ template library for dense vectors and multi-dimensional arrays. 0.9
/global
/software
/blitz/
blitz09
0.9
 

 


         
Boost - An eclectic collection of C++ libraries. 1.48.0 (gcc)
/global
/software
/boost/gcc

1.51.0

(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

1.48.0

1.49.0

(module load library/boost/1_49_0) 

     
Eigen - C++ template library for linear algebra.   3.1.1                
GNU libgomp - GNU implementation of the OpenMP Application Programming Interface (API).   4.4.4  
4.4.0 4.4.0-6
       
STLport - An implementation of the Standard Template Library.      
           
tvmet - Tiny Vector Matrix library using Expression Templates
1.7.2
/global
/software
/tvmet
/tvmet172
                 
Xerces-C++ - XML parser and writer    2.8.0            3.1.1
(module load application
/xerces-c
/3.1.1 )
3.1.1
/global
/software
/xercesc
/xercesc311
 
Version Control Git - version control system
  1.7.4.1

1.7.5
(module load git)

 

1.7.7.5
(module load git)

1.7.5.1
(module load git/1.7.5.1)

  1.6.0.2 

 1.7.10.1

(module load application/
git/
1.7.10.1)

1.7.8.3
(module load git)
1.7.9.4
(module load git)
Mercurial - source code management tool
  2.3
       1.8.3



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
1.6.11 1.6.5
/global/scratch/
software
/subversion
/bin/svn

1.4.2
1.6.17
1.5.7  1.6.11 

1.4.2
/usr/bin/svn

1.6.15
/opt/
CollabNet_
Subversion
/bin/svn

 

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 Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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)

   

1.14
/global
/software/
gsl-1.14

1.9
/global
/software/
lib64/gcc/gsl

(module load gcc/gsl)

MKL - Intel Math Kernel Library.

10.3.x
(in default Intel 12 environment)

10.3.9

-lmkl

10.2

(module load intel/mkl-64/10.2)

6.1 In Intel 12 environment

10.2.6

In Intel 12 environment

In Intel 12 environment  In Intel 12 environment 

10.2.6
(default with Intel 11.1 compiler)

10.3.x
with module load intel/12

10.1.3.027

(module load intel)

Trilinos - Object-oriented framework for linear algebra, meshing, preconditioners, solvers.

 

10.12.2

(module load mpi
/openmpi
/1.4.5)






 

Differential Equation Solvers and Frameworks
deal.II - Library for partial differential equation solution with adaptive finite elements.  

7.2.0

(module load mpi
/openmpi
/1.4.5)

               
FEniCS - A framework for solution of differential equations by finite element methods.  DOLFIN is a key component of the FEniCS environment.
 
   

DOLFIN 1.1.0

(module load application
/dolfin
/1.1.0)

     
FreeFem++ - Partial differential equation solver, typically applied for multiphysics non-linear systems.  

3.20

(module load mpi
/openmpi/1.4.5)

   

       
Nektar++ - Framework for partial differential equation solvers based on finite-element methods.
 
   

3.2.0

(module load application
/nektar++
/3.2.0)

     
PETSc - Toolkit for parallel solution of differential equations. See WestGrid-related comments here .  

3.2-p7

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)

3.2-p5 and 3.2-p7 with and without 64 indexing

(use module load)

 

3.0.0-p7

(module load application/petsc/3.0.0-p7) 

3.3-p6

(module load application/petsc/3.3-p6)

   
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
3.2.1
/global
/software
/fftw
2.1.5, 3.0.1

3.1.1

/global
/software
/fftw

2.1.5,3.2.2

3.3.1

(module load library/
fftw/
3.3.1) 

2.1.5

(module load library/fftw2/2.1.5)

3.3.1

(module load library/
fftw/
3.3.1) 

2.1.5, 3.2.2

/global/software/
fftw

(module load intel/12
for the Intel 12 versions)

3.2.2

/global
/software
/lib64
/gcc/
fftw-3.2.2

(module load gcc/fftw)

Graphs Networkx - A Python-based package for creating and analyzing graphs (networks of nodes and edges)

1.6

for use with Python 2.7.2

(module load python)

1.6

for use with Python 2.7.2

(module load python)

   

1.6

for use with Python 2.6

(module load python)

 

1.7

(module load application
/python
/2.7.3) 

1.7

(module load application
/python
/2.7.3) 

   


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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 In MKL In MKL
LAPACK - Linear algebra subroutine package. In MKL

3.4.1

-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  In MKL In MKL
MUMPS - Parallel direct solver for sparse systems.

4.10.0

(module load mpi
/openmpi
/1.4.5)









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  In MKL In MKL
SLEPc - PETSc add-on eigenvalue solver for large sparse systems.  

3.2-p5

-lslepc

     

 3.2-p3

(/global/software/slepc-3.2-p3)

       
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
       

METIS 4.0.1

/global
/software

(bin, lib, include)

 
MMG3D - Anisotropic tetrahedral remesher/moving mesh generation.   4.0.0
               
p4est - Parallel adaptive mesh refinement.   0.3.4
(module load mpi
/openmpi
/1.4.5)
               
SCOTCH - Graph and mesh partitioning, sparse matrix ordering.   5.1.12
(module load mpi
/openmpi
/1.4.5)
          6.0.0
(module load application
/scotch
6.0.0)
   
TetGen - Tetrahedral mesh generation and 3D Delaunay triangulator.
  1.4.3
               
Optimization Ipopt - Interior Point OPTimizer for large-scale nonlinear optimization.   3.10.3
 
 


   
  NLopt - Nonlinear optimization library.

2.2.4
     


 

   
Statistics JAGS - Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. 3.3.0
/global
/software
/jags
/jags330
3.1.0
3.3.0
(module load jags)

2.2.0
/global
/software
/JAGS-2.2.0


3.2.0
(module load jags)


 

   
R - Software environment and language for statistical data analysis.

A few notes related to using the software on WestGrid systems are given here.
2.15.1
/global
/software
/r/R-2.15.1
/bin/R

2.15.1

(older versions available via module load)

2.15.2
(module load R/2.15.2)

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)

 

2.11.1

2.14.2

(use module load)

2.15.0

(module load application/R/2.15.0) 

2.15.1

(module load application/R/2.15.1) 

   
OpenBUGS - Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
3.2.2
/global
/software
/openbugs
/openbugs322
3.2.2
3.2.2
(module load openbugs)





 

   
SAS - Statistical analysis software

9.3
(sas - on default path)

Licensed for SFU researchers only







 

   

Graphics

Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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
Bioinformatics Circos (Oriented towards genomic data display but can be applied to other data).
 0.60
(module load circos)
0.62-1
             
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)


5.8.0

/global/software/vtk-5.8.0/()

5.10.1

module load application/vtk/5.10.1 

5.10.1

module load application/vtk/5.10.1 



Paraview - GUI-based application for visualization of many types of multi-dimensional data. Based on VTK.   3.12.0
(in default path)>
            3.14.1
/global
/software
/ParaView
/ParaView-3.14.1
 
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

5.1.18 - no netCDF or PDF support
/global
/software/
grace-5.1.18/
grace
/bin
/xmgrace
   
 

5.1.22 - no netCDF or PDF support

/global
/software
/bin
/xmgrace

5.1.22 - no netCDF or PDF support

/global
/software
/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
4.6p0
  4.0p0 4.0

4.0

4.4.4

(use module load)

4.2  4.0 

 4.6p0
/global
/software
/bin/gnuplot

 
Matplotlib - Python-based 2D (mostly) plotting library
1.1.0 rc1
(See Python 2.7.2 above)

 

under python 2.7.2

(use module load)

       
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, etc.      

6.0.0

(Set NCARG_ROOT to
/global
/software
/ncl
/ncl_ncarg
_600)

     

6.0.0

(Set NCARG_ROOT to
/global
/software
/ncl
/ncl_ncarg
_600)

 
Ncview - Visual browser for NetCDF files.  

2.1.1

         

2.1.1

module load application
/ncview
/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 Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Image viewing, editing and conversion
Eye of GNOME - Image viewer (eog)
 
2.16.0.1 2.8.1
2.16.0.1

2.28.2
  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 6.4.3 6.2.8

6.7.0.0

/global
/software
/image
magick
/Image
Magick-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)

7.0.5
/global
/software
/pdf
/pdflib_lite_705

   

 

7.0.5
/global
/software
/pdf
/pdflib_lite
_705
 
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  

   

 

VMD - Visual Molecular Dynamics

See local VMD notes for access.

  1.9.1  

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. 4.8.2
/global
/software
/qt/qt482

4.8.2

/usr/local
/qt-4.8.2

4.7.2
(module load qt/4.7.2)
     
 

4.8.2
/global
/software
/qt4
/qt4.8.2

4.2.1-1

Chemistry and Biochemistry Applications

Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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 .  

6.12.3

(older versions see "module avail")

   

6.12.3

(module load abinit
/6.12.3)

 

6.12.3

(module load application
/abinit
/6.12.3) 

6.12.3

(module load application
/abinit
/6.12.3) 

6.8.1

(/global
/software
/abinit
See notes)

 
Amber - Suite of programs for molecular dynamics and other molecular simulations. Licensing restrictions and basic usage instructions are given here.  

10
(module load amber/10)

11
(module load amber/11)

12
(module load amber)

10
/global
/software/
amber10

11
/global
/software/
amber11


12
(module load amber)
   

12

(module load application/
amber/12) 

12
/global
/software
/amber
/amber12_mkl

11
/global
/software
/amber
/amber11
+at15

 
Adaptive Poisson-Boltzmann Solver (APBS) - Software for modelling biomolecular solvation  


1.4
(module load apbs/1.4)
     

BigDFT - A massively-parallel wavelet-based DFT code for solid
state/nanoclusters modeling for material science. (BigDFT code is also incorporated into ABINIT - see above).

 
 
1.6.0
(module load bigdft/1.6.0)
     

 


CPMD - Software for ab initio molecular dynamics. Users should be aware of the license requirements .  

3.15.1
(includes PLUMED 1.3 plugin)

       

 3_15_3

(module load application
/cpmd
/v3_15_3)

3_15_3

(module load application
/cpmd
/v3_15_3) 

3.15.3p1

3.13.2

Under /global
/software/
cpmd


CP2K - Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets  

2.2
/usr/local
/cp2k-2.2
(in default path)

2.1
/usr/local
/cp2k-2_1-branch




       
DIRAC - Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations  

11.0.1
module load dirac

12.5
module load dirac/12

use "pam" script to run program

   
         
DL_POLY - A suite of programs for molecular dynamics. Licensing restrictions and basic usage instructions are given here .  

DL_POLY 4.02

/global
/software/
dlpoly/
dl_poly_4.02/
execute



   

4.03

(module load application
/dl_poly
/4.03) 

 

4.04

(module load application
/dl_poly/4.04 )

DL_POLY CLASSIC 1.7

DL_POLY 4.02

See
/global
/software/
dl_poly


EXCITING - a full-potential all-electron DFT package based on the linearized augmented plane-wave (LAPW) method.

  Helium



     
GAMESS - A general ab initio quantum chemistry package. Basic WestGrid usage instructions and licensing restrictions are given here .  

18Aug2011
v01Oct2010
v25Mar2010
v12Jan2009

(module load gamess/
<version>)


Aug2011

/global/
software/
gamess

 

18Aug2011

(module load application/
gamess/
20110818) 

1May2012

(module load application
/gamess
/20120501)

 

18Aug2011

(module load application
/gamess
/20110818) 

/global
/software
/gamess/
gamess
2010oct01

Gaussian - A suite of programs for semi-empirical and ab initio molecular orbital calculations. Licensing restrictions and basic usage instructions are given here .



G09 C.01

(Initialize with module load gaussian

See module avail for older versions and variants)

 

G09b1

(for UofA only, module load application/
gaussian/
g09-b1)

G09b1

(for UofA only, module load application/
gaussian/
g09-b1) 



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)

4.6.1
(module load gromacs/4.6.1)

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

4.0.7

4.0.5

4.5.5

(use module load)

4.5.5

(module load application/
gromacs/
4.5.5) 

4.5.5

(module load application/
gromacs/
4.5.5) 

4.6.1

(module load application/gromacs/4.6.1)

4.6, 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 Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Electronic structure calculations and molecular dynamics (continued) LAMMPS - Classic molecular dynamics simulator  

121206
(lmp in default path)

(older versions see "module avail")

14Aug11
lmp_checkers
(module load lammps)

4Dec12

lmp_checkers

(module load lammps/4Dec12)

 



   4Dec12

lmp_hungabee

(module load application
/lammps/4Dec12)

 4Dec12

lmp_jasper

(module load application/
lammps/
4Dec12)

4Dec12

lmp_parallel

in /global
/scratch
/lammps
/bin


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)

5.0
(module load molden)

         
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.
  2.9


       

2.9.1, 2.7
(ibverbs)

2.7b3
(OpenMPI)

2.7b2
(module load namd)
NWChem - Scalable open-source solution for large scale molecular simulations    

6.0

(module load nwchem/6.0)

 

6.1.1

(module load nwchem/
6.1.1)

6.1.1

(module load nwchem/6.1.1)

6.1.1

(module load application/
nwchem/
6.1.1)

6.1.1

(module load application/
nwchem/
6.1.1)

   
OpenBabel - Data conversion toolkit.   2.3.0    

2.3.1
(module load openbabel)

2.2.3
(module load openbabel/
2.2.3)

     
 
OpenMX (Open Materials Explorer) - DFT code for nano-scale material science. Includes ADPACK for generation of pseudopotentials and numerical orbitals.  


OpenMX 3.6p1

ADPACK 2.2

(module load openmx/
3.6p1)

     

 


ORCA - An ab initio, DFT and semiempirical SCF-MO package. See license restrictions and job submission instructions here.
       

2.9.0
/global
/software
/orca
orca_2_9_0_
linux_x86-64

(2.8 is also available)

   

2_9_1

(module load application
/orca
/2_9_1) 

2.9.0
/global
/software
/orca
orca_2_9_0_
linux_
x86-64

(2.8.0.2 is also available)

 
Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Electronic structure calculations and molecular dynamics (continued) PDB2PQR  - Preparing structures for continuum electrostatics calculations - See APBS above.  

 


1.8
       
PSI3 General quantum chemistry/electronic structure suite.         3.4.0
(module load psi3/3.4.0)
         
Qbox DFT-based electronic structure and molecular dynamics program.                 1.56.2
 
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

   

4.3.2

(module load espresso
/4.3.2-opt)

5.0.1

(module load application
/espresso/5.0.1-openmp)

5.0.1

(module load application
/espresso
/5.0.1)

 

4.3.2
See /global
/software
espresso-4.3.2

(module load intel-2011
and
module load activeTCL)

4.1.2
also available.

SIESTA - An electronic structure and ab-initio quantum-mechanical molecular dynamics package. Write to support@westgrid.ca for access, after acknowledging license here.   3.1

trunk-348
(module load siesta/
trunk-348)

3.0-b
(module load siesta/3.0-b)

Note: No XML output due to compiler bug. In input use:

WriteXML F


3.1

/global
/software
/siesta-3.1

       

3.1

(module load siesta)

Includes tranSIESTA

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)


4.6

5.3.2
(module load vasp/5.3.2)

5.2
(module load vasp/5.2)

     

5.3.3

/global
/software
/vasp
/vasp533

5.2.12

(several variations 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)



3.0.3

(module load yaehmop)

         
Yambo - ab initio code for quasi-particle excited state energies and optical properties for solid state and molecular physics applications.           3.2.5

module load yambo
/3.2.5-dp

module load yambo
/3.2.5-sp

module load yambo
/3.2.5-sp-dbg
       


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
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


     
Chaste - Cancer, Heart and Soft Tissue Environment - tissue and cell level electro-physiology, discrete and soft tissue modelling.   3.0
        3.1
(module load application
/chaste
/release_3.1
 
 
NEURON - An environment for simulating neurons and networks of neurons.                 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 Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus

Bioinformatics,

Sequence Analysis

ABySS - Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.

1.3.4

   

 

 1.3.2

(module load abyss/1.3.2)

 1.3.2

(module load
application
/ABySS
/1.3.2)

1.3.2

(module load
application
/ABySS
/1.3.2) 

   
ALLPATHS-LG - Sequence assembly program.

Revision 41301

/global
/software
/allpathslg
/41301/bin

     


Revision 39099

(module load
allpathslg)

 

Revision 43500

(module load application
/allpathslg
/43500)

Also available:
42069
40691

     
ARB - Sequence database handling and phylogenic analysis.  

5.1
(module load arb)

     

5.1

(module load arb/5.1)

       
BEAGLE (beagle-lib) - Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations (such as with BEAST, below)

1.1


         1.1.0
/global
/software
/beaglelib
/beaglelib
_1086

BEAST - Bayesian Evolutionary Analysis by Sampling Trees.
1.7.5


         
BEDTools - Utility suite for comparing genomic features.   2.16.2
               
BioPerl - Collection of Perl-based tools for bioinformatics.
1.6.1


1.6.901
(module load perl)

 1.6.1

(module load perl
/5.14.2)

     
Biopython - Collection of Python-based tools for bioinformatics. 1.59
(module load python)
1.58



1.58

(module load python
/2.7.2)

     
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




 ncbi-2.2.25+

ncbi-2.2.26+

(use module load)

     
BLAT - BLAST-Like Alignment Tool. See the BLAT site for more information.

34

/global
/software/
blat/blat34

(linked from
/global
/software/
bin)

34



3.4

(module load blat/3.4)

   


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus

Bioinformatics,

Sequence Analysis

(continued)

Bowtie  - Short read DNA sequence aligner.

2.0.0-beta 7

     

2.0.0

0.12.7

(use module load)

0.12.8

(module load application
/bowtie
/0.12.8)

     
BWA  - Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.          

0.6.1

(module load bwa)

0.6.2

 (module load application/bwa/0.6.2)

     
Coral  - Error correction software for DNA sequence analysis.
1.4

 

               
Cufflinks  - Transcript assembly from RNA-Seq data.

2.0.2

     

 1.2.1

2.0.2

(use module load)

       

ExaML/RAxML - Phylogenetic tree analysis

RAxML 7.28a ExaML 1.0.0
               
FastQC  - Quality control tool for high throughput sequence data.          

0.10.1

(module load fastqc)

       
HMMER  - Homolog search and protein sequence alignments.          

 3.0

(module load hmmer)

       
IMa2  - Isolation and migration effects in population genetics
 

8.27.12

               
JELLYFISH  - DNA substring (k-mer) counting.
1.1.6                  
MEME Suite - identify motifs (patterns) in sequences

4.8.1




       
Mothur - Bioinformatics software for microbial ecology

1.21.1

/global
/software/
bin/
mothur

1.23.0




1.23.0

1.22.2

(use module load)

     
MrBayes - Bayesian inference for phylogenetic and evolutionary models.

3.2.1

(parallel)


3.2 (serial)

/global
/software
/BioSciences
/mrbayes-3.2

(Parallel version of 3.1.2 is available, but better to upgrade 3.2)


       
MultiMap - Program for automated construction of genetic maps. Includes Cri-Map

2.95

/global
/software/
multimap/bin

(includes Cri-Map 2.41m)

2.96




       
MUMmer - Alignment of large DNA and protein sequences

 




3.23

(module load MUMmer)

     


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus

Bioinformatics,

Sequence Analysis

(continued)

Nemo - Stochastic simulation to study evolution of life
history/phenotypic traits and population genetics.





2.2.0 - serial version

(module load nemo)

     
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




       

PLINK - Analysis of genotype/phenotype data.

          1.07        

QIIME - Quantitative Insights into Microbial Ecology.

 

1.5.0

(module load qiime)




       

Ray - de novo genome assembly.

          1.7        
RESM -

RNA-Seq by Expectation-Maximization.

Package for estimating gene and isoform expression levels from RNA-Seq data

 

1.1.8




       
RITA - Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis.

 

1.0.0
(Rank-specific setup only)




       
SAMTools- Utilities for manipulating SAM (Sequence Alignment/Map) format files.    0.1.18      

0.1.18

(module load samtools)

0.1.18

(module load application
/samtools
/0.1.18) 

     


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus

Bioinformatics,

Sequence Analysis

(continued)

SOAPdenovo - Short Oligonucleotide Analysis Package for Illumina GA short-read assembly

SOAPdenovo
2.04, pregraph_sparse 1.0.3
See /global
/software
/soapdenovo
/r223/bin

 




       

TopHat - Exon splice junction mapper based on BowTie RNA-Seq alignments.

  2.0.6
     

2.0.4

(module load tophat/2.0.4)

       
TPP - Trans-Proteomic Pipeline

4.5.0
(in default path)

Web interface here.





   

Trans-ABySS - a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

1.3.2

(use module load Trans-ABySS and copy /usr/local
/trans-ABySS-1.3.2/configs)

1.2.0 also available.

   

 

1.3.2

(module load trans-ABySS/1.3.2)

       
Trinity  - de novo reconstruction of transcriptomes from RNA-seq data

   

 

 

 2012-06-08

(module load
application
/trinity/r2012
-06-08)

 

2012-10-05

(module load application/trinity/r2012-10-05)

     
Velvet - Package for genomic sequence assembly from short-read data. 1.1.06
/global
/software
/velvet
/velvet1106
/bin



1.2.01
(module load velvet/1.2.01)

1.1.06
(module load velvet)


1.2.03

(module load application
/velvet
/1.2.03) 

 

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.

7.0
/global
/software
/wgs
/wgs-7.0
/Linux-amd64
/bin

6.1
/global
/software/
wgs/bin

6.1
(in default PATH)
   
         

Other Applications

Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Computational Fluid Dynamics OpenFOAM - Toolkit for building CFD applications  

2.1.1
(module load openfoam)

   

2.0.1

2.1.1
(use module load)

 

 2.1.1
(module load application/
OpenFOAM/
2.1.1 ;
source $OPENFOAM_
SETUP)

   
Cosmology
Gadget - Simulation of cosmological structure formation.           2.0.6
     
Electromagnetics Lumerical FDTD Solutions - Finite-difference time-domain techniques primarily for electromagnetic propagation problems. Basic instructions are available here .       6.0.3          

8.0.2
(module load lumerical
/8.0.2)

Also available:
7.5.2
6.5.3

MEEP - Finite difference time-domain (FDTD) electromagnetic simulation package      

1.2

(module load meep/1.2)

 1.2

(module load meep)

     
Finite Element Modelling
ABAQUS - Comprehensive finite element modelling package    

(U of A only)

6.12-1
/global
/software
/ABAQUS
/Abaqus6.12
/SIM_Abaqus
.media

       

(U of A only)

6.12-2
module load application
/abaqus
/6.12

6.12-1 and 6.10-EF2 also available

(U of C only)

6.12-2
6.11-1
6.10-1

See /global
/software
/abaqus

(U of A only)
6.12-2
6.10-EF2

See /global
/software
/abaqusua

 
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 2011b
(7.13.0)
/global
/software/
bin/matlab

For SFU only:

Release R2011b

(7.13.0.564)

module load matlab_2011b

 

R2012a
(in default path)

 

For UBC only:

Release 14 (7.0.1)

Release R2007b (7.5.0)

Release R2010a (7.10.0)

 

For UofM only:

R2009a

For UVic only:

R2012a
(module load matlab/R2012a)

R2010b
(module load matlab)

For U of A only:

R2013a
module load
uofa
/matlab
/R2013a

R2012b, R2011b also available

For U of A only:

R2013a
module load
uofa
/matlab
/R2013a

R2012b, R2012a also available

For U of C only:

Release 2011b
(7.13.0)
/global
/software/
bin/matlab

Release 2011a and 2010b also available

R2012b, R2012a, R2011a,
R2009a and R2009b
160-worker license for Distributed Computing Server

For UBC only:
R2011b
(/global
/software
/matlab
/bin/matlab)

Octave - A general purpose numerical package that is largely compatible with MATLAB  

3.6.2
(in default path)

   

3.6.2
(module load octave)

3.4.3

(module load octave/3.4.3)

      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
           
Seismic Un*x - 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 )

             
Geospatial Analysis/
Geomatics
GDAL - Geospatial Data Abstraction Library

1.9.2
/global
/software
/gdal
/gdal192

        1.9.0
module load gdal
       
libLAS - ASPRS LiDAR data translation tools           1.7.0
/global
/software
/libLAS-1.7.0
       

Meteorology

(also see NCO and CDO above)

WRF - Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System)
 

WRF 3.4

WPS 3.4

WRF-Chem 3.4

For WRF EMS:
module load wrfems/
3.2.1.5.34.beta.new

      3.4
       
Satellite Data Analysis BEAM - a toolbox for viewing and analyzing remotely-sensed data. Included is VISAT, an image processing and data analysis program.   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 2013-04-08.