Software on WestGrid Systems
Table of Contents
- 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 applications
- 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.
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 |
| Bugaboo (Dell Xeon cluster) | bugaboo.westgrid.ca | (on default path) |
| Breezy | breezy.westgrid.ca | /global/software |
| Bugaboo (Dell Xeon cluster) | bugaboo.westgrid.ca | (on default path) |
| Checkers (SGI Xeon cluster) | checkers.westgrid.ca | /global/software |
| Cortex (IBM P5s) | cortex.westgrid.ca | /opt/freeware , /usr/local and /ibm_global |
| Glacier (IBM Xeon cluster) | glacier.westgrid.ca | /usr and /global/software |
| Hermes/Nestor (IBM Xeon clusters) | hermes.westgrid.ca nestor.westgrid.ca | /global/software |
| Nexus (SGIs) | nexus.westgrid.ca | /usr/freeware , /usr/local and /usr/global |
| Orcinus (HP Xeon cluster) | orcinus.westgrid.ca | / global/software |
| Robson (IBM JS20 blades) | robson.westgrid.ca | /usr/local |
| Snowpatch (HP Intel Xeon blades) | snowpatch.westgrid.ca | (on default path) |
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 | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Operating system | All WestGrid systems run a variant of UNIX. | 64-bit Linux 2.6.18-164.6.1.el5 #1 SMP | 64-bit Scientific Linux 5.3 2.6.18-128.1.1.el5 | 64-bit Scientific Linux 4.7 2.6.28.2 | AIX 5.3.0.30 | Linux 2.4.20-24.9gpfs | 64-bit Linux Linux m129 2.6.18-53.1.21.el5.6hp | IRIX 6.5.28f | 64-bit Red Hat Enterprise Linux Server 5.3 2.6.18-128.1.10.el5 | 64-bit Linux 2.6.5-7.97 | 64-bit Linux 2.6.18-164.11.1.el5 | |
| UNIX Command Shell | bash (default) | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | |
| tcsh | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | ||
| sh | Link to bash | Link to bash | Link to bash | Y | Link to bash | Link to bash | Y | Link to bash | Link to bash | Link to bash | ||
| csh | Link to tcsh | Link to tcsh | Link to tcsh | Y | Link to tcsh | Link to tcsh | Y | Link to tcsh | Link to tcsh | Link to tcsh | ||
| ksh | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | ||
| zsh | N | Y | Y | Y | Y | Y | Y | N | N | Y |
Files and Data
| Category | Software/Description | Breezy | Bugaboo | Checkers | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Editors | emacs - GNU version of this common text editor. | 21.4.1 | 21.4 | 21.3.1 | 21.1.1 | 21.2.1 | 21.3.1 | 20.7.1 | 21.4.1 | 21.3.1 | 21.4 | |
| nedit - a graphical editor recommended for PC users, but requires X Windows. | N | 5.5 | 5.4 | 5.4 | 5.2 | 5.5 | 5.3 | 5.5 | 5.5 | 5.5 | ||
| pico - A simple non-graphical text editor with on-screen reminders for commonly-used commands. | N | link to nano 1.3.12 | N | 4.2 | 4.2 | N | 4.4 | N | N | link to nano 1.3.12 | ||
| vim - an enhanced version of vi | 7.0 | 7.0.109 | 6.3 | 6.3 | 6.1.265 | 7.0 | 6.1 | 7.0 | 6.2 | 7.0.109 | ||
| 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. | N | 4.r1 | 4.2r0 - no szip support (use with Portland Group compiler) /global/software/ HDF4.2r0/pgi-5.2 | 4.2r1p4 /usr/apps/hdf42r1p4 | 4.1 /usr/freeware/lib | 4.2r1 | N | ||||
| HDF 5 - Hierarchical Data Format - file format for storing a variety of data types. | 1.8.3 | 1.8.3 /global/software/lib64 | N | /global/software/HDF5/intel/ | 5-1.6.6 /usr/apps/lib | /usr/global/HDF/5-1.6.5-irix64pp | N | 1.8.1 (1.6.7 in /usr/local/hdf5-1.6.7/lib64) | 1.8.4p1 | |||
| NetCDF - Network Common Data Format is a file format for array-oriented scientific data. | 4.0.1 Fortan: -lnetcdff C: -lnetcdf C++: -lnetcdf_c++ | 3.6.0-p1 /ibm_global/netcdf 3.6.1 /ibm_global/netcdf64 (64-bit version) | 3.6.1 | 3.6.1 /usr/apps/lib | 3.5.1 /usr/global/netcdf-3.5.1 | 3.6.1 /usr/local/lib64 | 4.0.1 Fortran: -lnetcdff C: -lnetcdf C++: -lnetcdf_c++ | |||||
| NCO - NetCDF Operators - a set of programs for manipulating data in NetCDF files. | N | N | N | 3.9.2 /usr/global/bin | 3.9.5 | N | ||||||
| Szip - A library for lossless compression of scientific data (incorporated into HDF 4 release 2) | 2.1 | ? | N | 2.0 /usr/apps/lib | N | 2.0 | 2.1 |
Programming
See the WestGrid Programming page for a general discussion of programming, including parallel programming, debugging and optimization. For those systems for which separate pages are available giving examples of compiler usage and machine-specific details, the column headings provide links.
| Category | Software/Description | Breezy | Bugaboo | Checkers | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Compilers | Fortran | GNU 4.1.2 f95 is link to 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 11.1 (ifort, f77,f90,f95) GNU 4.3.2 (gfortran) Open64 4.2.2.1 (openf90, openf95) | f77 links to g77 Intel 11.1 (ifort - Initialize with GNU 4.3.2 GNU 3.4.6 | IBM XL 10.1 (xlf_r, xlf90_r, xlf95_r, f77) | Portland Group 7.0-2 (pgf77, pgf90) Intel 9.1 (ifort) Absoft 8.2 (f90) GNU 3.2.3 (g77) | f95 links to gfortran Portland Group 8.0-1 (pgf77, pgf90) GNU 4.1.2 | MIPSpro Compilers Version 7.4 (f77 and f90) GNU 3.2.2 (g77) | Intel 11.0 GNU 3.4.6 Portland Group 8.0-6 (module load pgi) | IBM XL 10.1 (xlf, xlf90, xlf95, f77, f90, f95) GNU 3.3.3 (g77) GNU 4.2.2 (gfortran) | Intel 11.0 f90 (same as f77, ifort) GNU 4.4.0 gfortran | |
| C | cc is link to gcc GNU 4.1.2 | cc is wrapper script for $CC, Intel 11.1 (icc,cc) GNU 4.3.2 (gcc) Open64 4.2.2.1 (opencc) | cc is link to gcc 3.4.6 Intel 11.1 GNU 4.3.2 | IBM XL C 8.0 (xlc, cc, c89, c99) GNU 4.2.0 (gcc) | Portland Group 7.0-2 (pgcc) Intel 9.1 (icc) GNU 3.2.3 (cc, gcc) | Portland Group 8.0-1 (pgc, pgcc) GNU 3.4.6 (cc, gcc) | MIPSpro Compilers Version 7.4 (cc, c89, c99) GNU 3.2.2 (gcc) | cc is link to gcc GNU 4.1.2 Intel 11.0 Portland Group 8.0-6 (module load pgi) | IBM XL 8.0 (xlc) GNU 4.2.2 (gcc4) | Intel 11.0 cc (same as icc) GNU 4.4.0 gcc | ||
| C++ | c++ is same as g++ GNU 4.1.2 | c++ is wrapper script for $CXX, Intel 11.1 GNU 4.3.2 (g++) Open64 4.2.2.1 (openCC) | GNU 4.3.2 GNU 3.4.6 Intel 11.1 | IBM XL C/C++ 8.0 (xlC) GNU 4.2.0 (g++) | Portland Group 7.0-2 (pgCC) Intel 9.1 (icc) GNU 3.2.3 (g++) | Portland Group 8.0-1 (pgCC) GNU 3.4.6 (g++) | MIPSpro Compilers Version 7.4 (CC) GNU 3.2.2 (g++) | GNU 4.1.2 Intel 11.0 Portland Group 8.0-6 (module load pgi) | IBM XL 8.0 (xlC) GNU 4.2.2 (g++4) | Intel 11.0 c++ (same as icpc) GNU 4.4.0 g++ | ||
| Other Languages | Java See java.sun.com | Sun Java 1.6.0_16-b01 | OpenJDK 1.6.0 | Sun Java 1.6.0_13 | IBM AIX classic VM with JIT 1.4.2 /usr/java14/bin IBM AIX J9 VM ppc-32 with JIT 1.5.0 /usr/java5/bin IBM AIX J9 VM ppc64-64 with JIT 1.5.0 /usr/java5_64/bin | /global/software/j2sdk1.4.2_02/ bin /global/software/jdk1.6.0_01/ bin | /usr/lib/jdk1.5.0_09/ bin | Sun 1.1.8 /usr/java Sun Java HotSpot Client 1.4.1_06 /usr/java2 | GNU 1.4.2 | 1.4.2 | OpenJDK 1.6.0 | |
| Perl ( /usr/bin/perl unless otherwise noted ) See www.perl.org | 5.8.8 | 5.8.8 | 5.8.2 | 5.8.0 | 5.8.5 | 5.6.1 /usr/sbin/perl | 5.8.3 | 5.8.8 | ||||
| Python See: www.python.org | 2.4.3 | 2.4.3 | 2.3.4 /usr/bin/python | 2.2.3 /usr/bin/python | 2.5, with NumPy 1.0.2 (/usr/apps/python25/ bin/python) | 2.2.3 | 2.3.3 /usr/bin/python | 2.4.3 | ||||
| Utilities | CMake - Cross platform software build system | N | 2.6-patch 4 | ? | 2.0.5 | 2.4.7 /global/software/ cmake-2.4.7 | N | N | N | 2.4-patch 7 | 2.6-patch 4 | |
| filepp - Generic file preprocessor | N | N | N | N | N | N | ||||||
| ftnchek - FORTRAN 77 syntax checker | N | N | N | N | N | N | ||||||
| Jam - Make replacement for C/C++ projects. See: www.perforce.com/jam/jam.html | N | 2.5 /ibm_global/jam/jam | N | N | N | N | N | |||||
| Debuggers | cvd - CASEVision/ProDev Workshop (graphical) debugger | N | N | N | Y /usr/sbin/cvd | N | N | |||||
| dbx - Common UNIX debugger | Y | N | N | 7.3.4 | N | N | ||||||
| ddd - Graphical front end to other debuggers | 3.3.11 | 3.3.1 | 3.3.1 | N | N | N | 3.3.11 | |||||
| gdb - GNU debugger | 6.8 | 6.0 | 6.3.0.0-1.62rh | 6.3.0.0-1.143.el4rh | 6.0 | 6.3 | 6.8 | |||||
| idb - Intel debugger | 11.1 | N | 7.3.2, 9.0-20 Look in /global/software/intel | N | N | N | 11.0 | |||||
| ladebug - Debugger for HP systems Supports parallel debugging | N | N | N | N | N | N | ||||||
| pgdbg - Portland Group graphical debugger | N | 6.1-4 | 8-0.1 | N | N | N | ||||||
| totalview - Etnus Totalview commercial graphical debugger Note - the license has not been renewed so this is becoming outdated. | N | N | N | N | N | N | ||||||
| Libraries | Boost - An eclectic collection of C++ libraries. See www.boost.org for more information. | 1.33.1 (in default library search location) | 1.33.0 (xlC 5.0, 32-bit) /usr/local/lib /usr/local/include/boost-1_33 | 1.33.1 (gcc) 1.32 1.31.0 (gcc) | N | 1.37.0 (not all tests passed) | 1.33.1 (gcc, 64bit) /usr/local/boost/lib64 (see README.boost.robson in /usr/local/boost) | N | ||||
| GNU libgomp - GNU implementation of the OpenMP Application Programming Interface (API). See gcc.gnu.org/onlinedocs/libgomp/ for more information. | 4.3.2 | 4.2.0-2 /opt/freeware/lib/gcc/powerpc-ibm-aix5.3.0.0/4.2.0 | N | N | N | 4.2.2 | 4.4.0 | |||||
| STLport - An implementation of the Standard Template Library. See www.stlport.org for more information. | 4.6.2 /usr/local/lib /usr/local/include/stlport | N | N | N | N | 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. See http://subversion.tigris.org/ for more information. | 1.4.2 | 1.6.5 /global/scratch/software /subversion/bin/svn | 1.4.3 /ibm_global/subversion/subversion/ | N | 1.4.5 /usr/apps/bin/svn | 1.4.3 /usr/global/subversion/bin | N | 1.4.2 |
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 | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Comprehensive Libraries See also MATLAB below. | ESSL - IBM Engineering and Scientific Subroutine Library. | /usr/ilb/ | N | N | N | Y | N | |||||
| GSL - GNU Scientific Library. | 1.12 -lgsl | 1.8 /ibm_global/gsl/gsl-1.8-32 (32-bit) /ibm_global/gsl/gsl-1.8-64 (64-bit) | 1.10 (gcc version - /global/software/ gsl-1.10/gcc/) | N | 1.7 /usr/global/gsl | 1.9 (module load gcc/gsl) | 1.11 -lgsl | 1.13 -lgsl | ||||
| MKL - Intel Math Kernel Library. | 10.2.0.013 -lmkl | 10.2 (module load intel/mkl-64/10.2) | N | 6.1 | N | N | 10.1.3.027 (module load intel) | N | 10.0.1 | |||
| SCSL - Scientific Computing Software Library. | N | N | N | N | N | 1.4.1.3 | N | N | N | |||
| Differential Equation Solvers | PETSc - Toolkit for parallel solution of differential equations. See WestGrid-related comments here . | 3.1-p0 | Y | 3.0.0 | ||||||||
| Fourier Transforms | FFTW - A widely-used FFT implementation. See FFTW home page . | 2.15 3.2.2 | 2.1.5, 3.2.2 | 3.2.1 /global/software/fftw | 2.1.5, 3.1,2 /ibm_global/fftw | 2.1.5, 3.0.1 | 2.1.5, 3.0.1 /usr/apps | 2.1.3, 3.0.1 | 3.2.2 /global/software/lib64/gcc/fftw-3.2.2 (module load gcc/fftw) | 2.1.5, 3.1.2 | 2.1.5, 3.2.2 | |
| Linear Algebra See also MATLAB below. | BLAS - Basic Linear Algebra Subprograms. | -lblas (same as -lgoto) | In ESSL | In the Intel Math Kernel Library | In the AMD Core Math Library (link with -lacml) | In SGI SCSL | In ESSL | -lblas (same as -lgoto2) | ||||
| LAPACK - Linear algebra subroutine package. | 3.2.1 -llapack -lblas | LAPACK 3.0 (both 32-bit and 64-bit) /usr/local/lib/liblapack.a | In the Intel Math Kernel Library | In the AMD Core Math Library (link with -lacml) Examples | In SGI SCSL | LAPACK 3.0 is in /usr/local/lib64 | 3.2.1 -llapack | |||||
| PIM - Parallel Iterative Methods. | N | N | 2.3 /usr/apps/src/pim/pim23 | N | N | N | ||||||
| ScaLAPACK - Scalable LAPACK. | 1.8.0 -lscalapack -lblacs -llapack -lblas | See Parallel ESSL (ScaLAPACK 1.5 compatible) Also ScaLAPACK 1.7 is in /usr/local/lib | 1.7? in the Intel Math Kernel Library | 1.7.3 /usr/apps/src/scalapack | 1.7 | ScaLAPACK 1.7 is in /usr/local/lib64 Also see Parallel ESSL (ScaLAPACK 1.5 compatible) | 1.8.0 -lscalapack -lblacs -llapack -lblas | |||||
| WSMP - Watson Sparse Matrix Package. | 4.08.05 /usr/local/ihpct/wsmp-AIX | N | N | N | N | N | ||||||
| Mesh Partitioning | METIS - Mesh and graph partitioning. | METIS 4.0.1 ParMETIS 3.1.1 /usr/local (bin,lib64,include) | N | ParMETIS is in /global/software/Complex-Fluids/\ petsc-2.3.3-p13/\ externalpackages/ | METIS 4.0.1 /usr/apps (bin,lib,include) | N | N | 4.0.1 -lmetis | ||||
| Statistics | R - Software environment and language for statistical data analysis. A few notes related to using the software on WestGrid systems are given here. | 2.10.1 | 2.7.2 /ibm_global/R/R-2.7.2/bin/R | 2.7.1 /global/software/R-2.7.1/gcc/bin/R | N | 2.6.0 (2.0.1 and 2.4.1 also available) |
/usr/local/bin/R | 2.10.1 |
Graphics
| Category | Software/Description | Breezy | Bugaboo | Checkers | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Animation | mencoder (MPEG encoding) mplayer (video player) | N | N | N | 3.2.3 /global/software/MPlayer/bin | N | N | 4.1.2 /global/software/mplayer/bin | N | N | ||
| 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 | 5.1.19 - 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 support. /usr/apps/bin/xmgrace. Set LD_LIBRARY_PATH to include /usr/apps/lib | 5.1.19 - no netCDF or PDF support /usr/global/xmgrace/ bin/xmgrace | N | N | ||||
| 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 | 3.7p1 | 4.0p0 | 4.0p0 | 3.7p1 | 3.7p3 | 4.0.0 | ||||
| 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 . | N | N | 4.1.3 /ibm_global/gmt/gmt-4.1.3 | 4.1.3 /global/software/GMT4.1.3 | N | 4.1.3 /usr/global/gmt/gmt | N | 4.3.1 /usr/local/gmt | N | ||
| 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. | N | N | N | 4.4.0 /usr/global/ncarg/ncarg | 5.0.0 /usr/local/ncarg | N | ||||||
| VISAT - An image processing and data analysis program for remotely sensed data. VISAT is part of the BEAM toolkit mentioned below . | 4.7 | N | N | N | N | 4.5 /usr/local/bin/visat | N | |||||
| Image format handling | libpng - Library for handling PNG raster images | 1.2.10 | Y | 1.2.2-16 /usr/lib | 1.2.5 | 1.2.6 | 1.2.5 | 1.2.10 | ||||
| libjpeg - Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg . | 6b | Y | 6b-26 /usr/lib | 6b /usr/apps/lib | 6a | Y | 6b | |||||
| libtiff - TIFF (Tagged Image File Format) image library. | 3.8.2 | Y | 3.5 | 3.6 3.9.0b | 3.5.7 | Y | 3.8.2 | |||||
| Netpbm - Image conversion utilities and library. | 10.35 | N | N | 10.41.02 | N | N | 10.35 | |||||
| pdflib - PDF file handling library ("PDFlib-Lite" for non-commercial use) | N | N | 5.0.3 | N | N | N | ||||||
| zlib - Data compression library. | 1.2.3 | 1.2.2-4 | 1.1.4 | 1.2.3 /usr/apps/lib | 1.2.1 | 1.2.1 | 1.2.3 | |||||
| OpenGL-related | Vendor's OpenGL | 5.3 | ? | N | 3.1 | N | N | |||||
| Mesa | Y | ? | ? | ? | ? | Y | Y | |||||
| GLUT | ? | ? | ? | ? | Y | Y |
Chemistry and Biochemistry Applications
| Category | Software/Description | Breezy | Bugaboo | Checkers | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| 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 . | 5.8.3 | N | N | N | 4.6. /usr/apps/src/abinit/abinit-4.6.5 | N | N | N | 5.8.4 | ||
| AMBER - Suite of programs for molecular dynamics and other molecular simulations. Licensing restrictions and basic usage instructions are given here. | 10 | 10 | N | N | N | N | N | N | N | |||
| CPMD - Software for ab initio molecular dynamics. Users should be aware of the license requirements . | 3.13.2 | N | N | N | 3.11.1 (Unexplained performance problems) | N | N | 3.13.2 /usr/local/cpmd-3.13.2 | 3.13.2 | |||
| DL_POLY - A suite of programs for molecular dynamics. Licensing restrictions and basic usage instructions are given here . | N | N | 2.17, 3.07 /ibm_global/dl_poly | N | 2.18, 3.08 /usr/apps/dl_poly | N | N | N | N | |||
| GAMESS - A general ab initio quantum chemistry package. Basic WestGrid usage instructions and licensing restrictions are given here . | N | /global/scratch/software/gamess/gamess.v25Mar2010 | N | N | N | N | N | 20070324-R6 /usr/local/bin | N | |||
| Gaussian - A suite of programs for semi-empirical and ab initio molecular orbital calculations. Licensing restrictions and basic usage instructions are given here . | N | G09 A.02 G03 | N | N | N | N | 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 | 4.0.7 (Intialize with module load gromacs) 4.0.5 | N | 3.3.1 | 4.0.7 /usr/apps/gromacs407/bin (Also 3.2.1,3.3.2, | 3.1.4, 3.2 | 4.0.5 /global/software/gromacs/4.0.5/intel/bin (Initialize with module load gromacs) | 3.3.2, 4.0.2 | 4.0.7 | |||
| LAMMPS - Classic molecular dynamics simulator | 20090821 | N | N | N | 20100115 /usr/apps/src/lammps/lammps-15Jan10/src/lammps (untested) | N | N | 20071005 (lammps on default path) | 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) | 4.4 | N | N | 4.3 (/usr/local/bin/molden /usr/local/bin/moldenogl) | N | N | N | |||
| NAMD - A molecular dynamics simulator for large biomolecular systems. License restrictions and basic job submission instructions are given here . Note: NAMD is also available on Tantalus . | 2.7b2 | N | N | N | 2.6 | N | 2.7b2 (module load namd) | N | N | |||
| Quantum ESPRESSO - A suite of programs for electronic structure and materials modelling. Basic usage instructions are given here . | 4.1.2 examples, pseudo potentials, documentation in /usr/local/espresso | 4.1.2 | 3.2 /ibm_global/espresso-3.2/ bin | N | 3.2.3 | N | 4.1.2 (requires module load intel) | 3.1.1 /usr/local/espresso/bin | N | |||
| 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. | 2.0.2 | 3.0-b /global/scratch/software/siesta-3.0-b Note: No XML output due to compiler bug. In input use: WriteXML F | N | N | 2.0 was tried but had some problems | N | N | N | 3.0-b | |||
| 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 | N | 4.6 | 4.6 (untested) | N | 4.6 5.2 | N | N | |||
| YAeHMOP - Yet Another extended Huckel Molecular Orbital Package | N | N | N | N | N | N | N | 3.0.3 /usr/local/yaehmop | 3.0.3 /usr/local/yaehmop | |||
| Sequence Analysis | 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) NCBI BLAST+ 2.2.23+ | NCBI BLAST mpiblast 1.5.0 NCBI BLAST+ 2.2.23+ Databases in /usr/local/blast+/db | N | N | N | N | N | N | N | N | |
| ARB - Sequence database handling and phylogenic analysis. | 5.1 | N | N | N | N | N | N | N | N | |||
| Specialized Applications | NEURON - An environment for simulating neurons and networks of neurons. See the NEURON site for more information. | N | N | 5.8 | N | N | 5.8 | N | N | N |
Other Applications
| Category | Software/Description | Breezy | Bugaboo | Checkers | Cortex | Glacier | Hermes/Nestor | Matrix | Nexus | Orcinus | Robson | Snowpatch |
| Electromagnetics | Lumerical FDTD Solutions - Package employing finite-difference time-domain techniques primarily for electromagnetic propagation problems. Basic usage instructions are available here . | N | N | N | 6.0.3 | N | N | 6.5.3 | N | N | ||
| 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 . | N | N | N | For UBC only: Release 14 (7.0.1)
| N | For U of A only: Release 13 (6.5.1) (May no longer be available) | R2009a and R2009b Ask at support@westgrid.ca to participate in testing. | N | For SFU only: Release 2007b (7.5.0) R2009b | ||
| Octave - A general purpose numerical package that is largely compatible with MATLAB | 3.2.3 | 2.1.57 (on default path) | N | N | N | N | N | N | 3.2.4 | |||
| Geophysics | Seplib - A seismic data processing package from the Stanford Exploration Project (SEP) . | N | N | N | 6.3.12 /global/software/seplib-6.3.12/intel - use with Intel compiler | N | 6.3.12 64-bit OpenMP in /usr/global/seplib-6.3.12omp 32-bit serial in /usr/global/seplib-6.3.12 | N | N | N | ||
| 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 ) | N | N | N | N | N | N | N | |||
| 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. | 4.7 | N | N | N | N | 4.5 /use/local/beam/ | N |
Software on Specialized Resources
Storage Facilities
See the Silo QuickStart Guide for documentation for the storage facility at the University of Saskatchewan.
At the SFU WestGrid storage facility there is a login server called blackhole.westgrid.ca and a file server called gridstore.westgrid.ca used for network file storage within WestGrid.
The operating system on blackhole is Linux 2.6.13-15.7-smp and the GCC 4.0.2 compilers (gcc, g++, gfortran) are available. Look in /usr/bin and /usr/local/bin for other software.
Gridstore runs the IBM AIX 5L 5.3 operating system. A restricted form of login access to the file server is provided in order to give the best performance for large file transfers. For a list of file server commands, type:
ls -1 /usr/local/rbin
Visualization Server
Hydra (hydra.westgrid.ca), the WestGrid Visualization Server supports remote visualization through standard X Windows as well using specialized software called VizServer. To read about how this can be used to deliver advanced scientific graphics to an end user's desktop, visit the VizServer software page .
Among the visualization software packages that are installed for use with VizServer are AVS, VTK and OpenDX.
Updated 2010-08-31.
