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Brief Software Summary

 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.

 Introduction

Note:  This page gives only a terse summary.  Please see an expanded version of this page for additional information about the packages, module commands to use for setting up the environment for a given package, links to usage notes, etc.

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 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

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. CentOS 5.7 Scientific Linux 5.6 Scientific Linux 5.5 Red Hat Enterprise Linux AS Release 4 CentOS 5.5 Scientific Linux 5.3 SLES 11   CentOS 5.7

CentOS 5.5 (Lattice)
CentOS 5.7 (Parallel)

Red Hat Enterprise Linux Server 5.3
UNIX Command Shell bash (default) Y 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  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 N
Distributed computing environment
All WestGrid systems support MPI.         Open MPI
1.6.1
1.4.5
1.4.3

Intel MPI
4.0.3.008
4.0.1.007
     

 

 

 Files and Data

Category Software/
Description
Breezy  Bugaboo Checkers Glacier Grex Hermes/
Nestor 
Hungabee Jasper Lattice/
Parallel
Orcinus
Editors Emacs 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
NEdit  5.5 5.5 5.4 5.4 5.5 5.5    5.5  5.5 5.5
jEdit           4.5.1         
nano 1.3.12 1.3.12 1.3.12 1.2.4 1.3.12 1.3.12  2.2.6 1.3.12  1.3.12 1.3.12
Vim 7.0 7.0.109 6.3 6.1.265 7.0 7.0  7.2  7.0 7.0.237  7.0
Specialized file format libraries and utilities
CDO 1.5.8  1.5.9      1.5.4          
HDF 4 4.2.8  4.2.6   4.2r0         4.2.5  
HDF 5 1.8.10  1.8.7  1.8.3 ? 1.8.9 1.8.4  1.8.8 1.8.8  1.8.5p1 1.8.8

NetCDF

C: 4.2.11
Fortran: 4.2
4.1.3   3.6.1 4.1.3 4.1.1 4.1.3 4.1.3 4.1.1 4.0.1
NCO         4.0.8 >4.0.7        
Szip  2.1 2.1     2.1 2.1   2.1  2.1  
TecIO    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

GNU 4.1.2

GNU 4.4.4


Intel 12.1.3

GNU 4.4.4


GNU 4.3.2

GNU 3.4.6

Portland Group 7.0-2

Intel 9.1 

Absoft 8.2 

GNU 3.2.3

Intel 12.1.5.339

GNU 4.4.0

Intel 12.0.2

Intel 11.1

GNU 4.1.2

GNU 3.4.6

Intel 12.1

Portland Group 12.10

GNU 4.3.4 

Intel 12.1

Portland Group 12.10

GNU 4.1.2 

Intel 12.1.10.319

Intel 11.1

Portland Group 12.1-0

GNU 4.1.2

Intel 11.0

GNU 3.4.6

Portland Group 8.0-6

C

GNU 4.1.2

GNU 4.4.4


Intel 12.1.3

GNU 4.4.4


Intel 11.1

GNU 4.3.2

Portland Group 7.0-2

Intel 9.1

GNU 3.2.3 

Intel 12.1.5.339

GNU 4.4.0

Intel 12.0.2

Intel 11.1

GNU 4.1.2

Intel 12.1

Portland Group 12.10

GNU 4.3.4 

Intel 12.1

Portland Group 12.10

GNU 4.1.2 

Intel 12.1.10.319

Intel 11.1

Portland Group 12.1-0

GNU 4.1.2


GNU 4.1.2

Intel 11.0

Portland Group 8.0-6

C++

GNU 4.1.2

GNU 4.4.4


Intel 12.1.3

GNU 4.4.4

GNU 4.3.2

GNU 3.4.6

Intel 11.

Portland Group 7.0-2

Intel 9.1

GNU 3.2.3

Intel 
12.1.5.339
GNU 4.4.0

Intel 12.0.2

Intel 11.1

GNU 4.1.2

Intel 12.1

Portland Group 12.10

GNU 4.3.4 

Intel 12.1

Portland Group 12.10

GNU 4.1.2 

Intel 12.1-10.319

Intel 11.1

Portland Group 12.1-0

GNU 4.1.2

GNU 4.1.2

Intel 11.0

Portland Group 8.0-6

Other Languages C#
Mono .NET environment
            2.10.9     2.10.2 
GDL         0.9.2          
Java Sun Java
1.6.0_16-b01
OpenJDK 1.6.0  Sun Java
1.6.0_13 
? sdk1.4.2_02

? jdk1.6.0_01
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

Sun Java SE JRE
Oracle HotSpot
1.6.0_23

GCC gij 4.1.2

GNU 1.4.2

Sun Java 1.6.0_14

Perl 5.8.8 5.8.8    5.8.0

5.8.8

ActivePerl
5.14.2.1402

5.8.8 5.10.0  5.8.8  5.8.8  
Python

2.4.3

2.7.2
NumPy 1.6.1, SciPy, mpi4py and matplotlib

2.4.3

2.7.2 with NumPy 1.6.1

2.4.3

2.6.5 with NumPy 1.6.1

2.3.4

2.4.3
ActivePython-2.4
with
NumPy 1.4.1

2.4.3

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

2.4.3

2.7.2 with NumPy 1.6.2, SciPy 0.10.1, matplotlib 1.1.1

2.6

2.7.3

2.4.3

2.7.3

2.4.3

2.7.2
NumPy 1.6.1
matplotlib 1.1.0

2.4.3

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 1.8.5


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Utilities CMake   2.8.6 ? 2.4.7 2.8.3   2.8.10.2 2.8.9

2.8.4

2.8.7
Jam              3.1.16      
Debuggers dbx                    
ddd   3.3.11   3.3.1 3.3.11          
gdb   7.0.1    6.3.0.0-1.62rh 7.0    7.3-0.6.1  7.0.1-37.el5_7.1     
idb   12.1.3    7.3.2, 9.0-20 12.0  11.1 Update 7 12.1  12.1  11.1   
pgdbg       6.1-4            
Libraries Blitz++ 0.9    

 

           
Boost 1.48.0

1.51.0

 

1.33.1

1.32

1.31.0

1.33.1  1.33.1-10   1.49.0      
Eigen   3.1.1                
GNU libgomp   4.4.4     4.4.0 4.4.0-6         
STLport                    
tvmet 1.7.2                  
Xerces-C++   2.8.0            3.1.1 3.1.1   
Version Control Git   1.7.4.1

1.7.5

 

1.7.7.5

1.7.5.1

   1.6.0.2 1.7.10.1  1.7.8.3 1.7.9.4
Mercurial   2.3                
Subversion  1.6.11 1.6.11 1.6.5 N 1.4.2    1.5.7   1.6.11

1.4.2

1.6.15

 

 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 alsoMATLAB below.

GSL

1.15 1.15 1.14 1.10 1.13      

1.14

1.9
MKL 10.3.x 10.3.9 10.2 6.1 Intel 12 10.2.6 Intel 12 Intel 12 10.2.6
10.3.x
10.1.3.027
Trilinos   10.12.2                
Differential Equation Solvers and Frameworks
deal.II  

7.2.0

               
FEniCS            

DOLFIN 1.1.0

     
FreeFem++  

3.20

               
Nektar++            

3.2.0

     
PETSc  

3.2-p7

(and older)

   

3.2-p5

3.1-p7

3.2-p5

3.2-p7

       
Fourier Transforms FFTW

2.15

3.2.2

2.1.5, 3.3 3.2.1 2.1.5, 3.0.1

3.1.1

2.1.5,3.2.2 3.3.1  2.1.5, 3.3.1 

2.1.5, 3.2.2

3.2.2

Graphs Networkx 1.6 1.6     1.6   1.7 1.7    


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 alsoMATLABbelow.

 

BLAS In MKL

GotoBlas2-1.13

In MKL In MKL In MKL or GotoBLAS2 In MKL In MKL  In MKL  In MKL In MKL
LAPACK In MKL

3.4.1

Intel MKL 10.3.4.191

In MKL In MKL In MKL or GotoBLAS2 In MKL In MKL  In MKL  In MKL In MKL
MUMPS   4.10.0                 
ScaLAPACK In MKL 1.8.0 In MKL 1.7? in MKL 1.8.0 In MKL In MKL  In MKL  In MKL In MKL
SLEPc  

3.1p4

               
Mesh Partitioning METIS  

METIS 5.0.2

ParMETIS 4.0.2

  In PETSc 2.3.3-p13        

METIS 4.0.1

 
MMG3D   4.0.0                
p4est   0.3.4                
SCOTCH   5.1.12                
TetGen   1.4.3                
Optimization Ipopt    3.10.3                
NLopt   2.2.4                
Statistics JAGS 3.3.0 3.1.0 3.3.0 2.2.0   3.2.0        
R 2.15.1

2.15.1

2.15.2

2.13.1

2.7.1

2.12.0

 

2.11.1

2.14.2

2.15.0

2.15.1

   
OpenBUGS 3.2.2 3.2.2 3.2.2              
SAS  

9.3
SFU only

         

 

   

 Graphics

Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Animation mencode       3.2.3   20100622       4.1.2
General purpose scientific data visualization VTK   5.2 5.4.2       5.10.1   5.10.1    
Paraview   3.12.0             3.14.1  
Charting Grace/Xmgrace   5.1.22

5.1.22

5.1.18        

5.1.22

5.1.22

Gnuplot 4.4p0 4.6p0    4.0p0 4.0  4.0  4.2  4.0   4.6p0  
Matplotlib 1.1.0                  
Geographic data handling GMT - Generic Mapping Tools  

4.5.6

  4.1.3         4.5.6  
NCAR Graphics         6.0.0      

6.0.0

 
Ncview   2.1.1           2.1.1    
VISAT   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     2.16.0.1 2.8.1 2.16.0.1   2.28.2     2.16.0.1 
ImageMagick 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

6.2.8
libpng   1.2.10    1.2.2-16  1.2.10 1.2.10-7.1         
libjpeg   6b    6b-26  6b  6b-37        
libtiff   3.8.2    3.5 3.8.2  3.8.2-7         
Netpbm   10.35      10.35 10.35-6.1     

10.35.80

 
pdflib

7.0.5

              7.0.5  
zlib   1.2.3   1.1.4 1.2.3  1.2.3-3        
Molecular visualization

Rasmol

  2.7.5                

VMD

  1.9.1    

1.9

     

1.8.7

 
OpenGL-related Vendor's OpenGL                    
Mesa     ? Y 6.5.1-7.7         
GLUT   freeglut 2.4.0   ?          
User interface development Qt  4.8.2 4.8.2 4.7.2            4.8.2 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  

6.12.3

        6.12.3  6.12.3 

6.8.1

 
Amber  

10

11

10

11

  12      12

11

12

 
APBS          1.4          

BigDFT

        1.6.0      

 

 
CPMD   3.15.1         3_15_3  3_15_3 

3.13.2

 
CP2K  

2.2

2.1

               
DIRAC  

11.0.1

               
DL_POLY    

DL_POLY 4.02

       

4.03 

4.04

DL_POLY CLASSIC 1.7

DL_POLY 4.02

 

EXCITING

  Helium                
GAMESS    

18Aug2011
v01Oct2010
v25Mar2010
v12Jan2009

 

Aug2011

  18Aug2011 

1May2012

18Aug2011

2010oct01   
Gaussian        

G09 C.01

  G09b1 (UofA)  G09b1 (UofA)     
GROMACS   4.0.7
4.5.1
4.5.4
4.5.4
4.5.3
4.5.1
4.0.7
4.0.5
3.3.1  

4.0.7

4.5.5  4.5.5 

4.5.4
4.07

4.0.5
4.0.7
4.5.4
Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Electronic structurecalculations and molecular dynamics(continued) LAMMPS  

120321

14Aug11

4Dec12

      4Dec12   4Dec12     
Molden   4.7 4.9  

5.0

         
NAMD   2.9            

2.7

2.7b3

2.7b2
NWChem    

6.0

 

6.1.1

  6.1.1  6.1.1     
OpenBabel - Data conversion toolkit.   2.3.0    

2.3.1

2.2.3

         
OpenMX        

OpenMX 3.6p1

ADPACK 2.2

     

 

 
ORCA        

2.9.0

2.8

    2_9_1 

2.9.0

2.8.0.2

 
Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor
Hungabee Jasper Lattice/
Parallel
Orcinus
Electronic structurecalculations and molecular dynamics(continued) PDB2PQR  

 

 

  1.8           
PSI3          3.4.0          
Qbox  

 

            1.56.2   
Quantum ESPRESSO  

4.3.2

4.3

4.1.2

 

5.0

4.3.2 with GIPAW

    5.0.1   

4.3.2

4.1.2

SIESTA   3.1

3.0-b

 

3.1

       

3.1 with tranSIESTA

VASP  

5.2

4.6.36

  4.6

5.3.2

5.2

     

5.2.12

5.2

4.6

YAeHMOP  

3.0.3

   

3.0.3

         


Category Software/
Description
Breezy Bugaboo Checkers Glacier Grex Hermes/
Nestor 
Hungabee Jasper Lattice/
Parallel
Orcinus
Other Chemistry/
Biochemistry Applications
AutoDock       4.2            
Chaste   3.0          3.1      
NEURON                 7.1  
Rosetta Software Suite  

3.3

               

Bioinformatics/Genomics Applications

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

Bioinformatics,

Sequence Analysis

ABySS  

1.3.4

   

 

  1.3.2  1.3.2     
ALLPATHS-LG

41301

     

39099

 

43500
42069
40691

     
ARB  

5.1

               
BEAGLE (beagle-lib)   1.1             1.1.0   
BEAST   1.6.2                
BEDTools   2.16.2                
BioPerl   1.6.1    

1.6.901

         
Biopython 1.59 1.58                
BLAST

NCBI BLAST 2.2.18

NCBI BLAST+ 2.2.23+

NCBI BLAST
2.2.25

mpiblast 1.6.0

NCBI BLAST+ 2.2.25+

               
BLAT

34

34                


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

Bioinformatics,

Sequence Analysis

(continued)

Bowtie   2.0.0-b7       2.0.0
0.12.7
0.12.8      
BWA           0.6.1         
Coral 1.4                  
Cufflinks   2.0.2       1.2.1
2.0.2
       
ExaML/RAxML RAxML 7.28a ExaML 1.0.0                 
FastQC           0.10.1         
HMMER           3.0         
 IMa2    8.27.12                 
Jellyfish 1.1.6                  
MEME Suite  

4.8.1

               
Mothur

1.21.1

1.23.0

      1.23.0
1.22.2
       
MrBayes    3.2.1  

3.2 (serial)

3.1.2

           
MultiMap

2.95 plus Cri-Map 2.41m

2.96

               
MUMmer           3.23         


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

Bioinformatics,

Sequence Analysis

(continued)

Nemo           2.2.0         
Picard tools 1.57                  
PLINK

 

 

      1.07         
QIIME

 

1.5.0

               
Ray

 

 

      1.7         
RESM   1.1.8                
RITA

 

1.0.0                
SAMtools   0.1.18        0.1.18         
SOAPdenovo

1.05

 

               
TopHat

 

2.0.6       2.0.4         
TPP  

4.5.0

               
Trans-ABySS  

1.3.2

1.2.0

   

 

         
Trinity            

2012-06-08

2012-10-05

     
Velvet 1.1.06       1.2.01
1.1.06
  1.2.03      
wgsim 0.3.0                  
wgs-assembler 7.0
6.1
6.1                

 Other Applications

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

1.7.1

           2.1.1    
Cosmology Gadget           2.0.6         
Electromagnetics Lumerical FDTD Solutions       6.0.3          

8.0.2
7.5.2
6.5.3

Finite Element Modelling ABAQUS     6.12-1          U of A only: 6.12-2
6.12-1
6.10-EF2

U of C only:
6.12-2
6.11-1
6.10-1

U of A only:
6.12-2
6.10-EF2

 
General Purpose Numerical MATLAB

U of C only:
R2011a

SFU only:
R2011b
R2012a

 

UBC only:
R2010a

UofM only: R2009a     

U of A only:

R2012a

U of C only:
R2011a
R2010b

R2011a,
R2009a and R2009b
64-worker DCS license

UBC only:
R2011b

Octave   3.6.2     3.6.2         3.2.2
Geophysics Seplib       6.3.12            
Seismic Un*x  

Release 42

Release 42

             
Geospatial Analysis/
Geomatics
GDAL           1.9.0         
libLAS             1.7.0         

Meteorology

(also see NCO and CDO above)

WRF  

3.4

               
Satellite Data Analysis  BEAM   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.