From Documentation

Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham. |

SHARCNET provides official support, including installing and maintaining the software, for a limited number of supported software packages. In addition, we also provide documentation that we and our user community have written while installing other, less frequently requested packages. Packages in each group can be found listed below. If you would like for SHARCNET to support a particular package please email help@sharcnet.ca.

For SHARCNET supported software packages all version info, installation listings, announcements and mailing list information can be found in the SHARCNET web portal. Usage documentation for each of the packages can be found in the following list.

Package Name | Brief Description |
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ABAQUS | Abaqus Unified FEA Suite from Simulia (commercial, groups: abaqus, uw_abaqus) |

ABINIT | Calculate Ground State & Response Functions using Density-Functional Theory |

ADF/BAND | Amsterdam Density Functional Software (commercial, group adf) |

AMBER | Molecular Dynamics Simulation On Biomolecules (commercial) |

ANSYS | Fluent, CFX and Icemcfd CFD Software Collection (commercial, group: fluent) |

BIOPERL | Toolkit of Perl Modules For Bioinformatics |

BLAST | Basic Local Alignment Search Tool |

BLCR | checkpoint resume software |

CDF | The Common Data Format |

COMSOL | Finite Element Analysis |

CPMD | Parallelized Plane Wave Implementation of DFT |

DeMON | Package for Density Functional Theory (DFT) Calculations |

DLPOLY | General Purpose Molecular Dynamics Simulation Package |

ESPRESSO | Plane-Wave Self-Consistent Field (PWSCF) |

FIREFLY | Ab Initio and DFT Computational Chemistry Program (PC GAMESS) |

GAUSSIAN | Computational Chemistry Software (commercial, group: gaussian) |

GEANT4 | The Geant4 Toolkit |

GROMACS | Molecular Dynamics for Biomolecular Systems |

HARMINV | Program and Library to Solve Harmonic Inversion |

ILOG/CPLEX | Optimizer to Solve Very Large Optimization Problems (group: wlu_users) |

JDK | Java Standard Edition Development Kit |

LAMMPS | Large-scale Atomic/Molecular Massively Parallel Simulator |

LS-DYNA | General Purpose Transient Dynamic FE Program (commercial, groups: lsdyna, uw_lsdyna) |

LUMERICAL | High Performance Microscale Optics Simulation Software (commerical, group lumerical) |

MAPLE | MAPLE (commercial, groups: uwo_users, brocku_users |

MATLAB | MATLAB and Parallel Computing Toolbox (commercial, groups: matlab, uwmatlab) |

MPIBLAST | Parallel Implementation of NCBI BLAST |

MrBAYES | Bayesian estimation of phylogeny. |

NAMD | Parallel Molecular Dynamics Program |

NWCHEM | Computational Chemistry Package |

OCTAVE | High level language mostly compatible with Matlab. |

PHYLIP | Phylogeny Inference Package |

R | Language/environment for statistical computing |

SIESTA | Linear-scaling DFT based on Numerical Atomic Orbitals |

TORQUE | Resource Manager and Cluster Scheduler (development use) |

ActivePerl | A More Recent Release of Perl from the ActivePerl Community Edition |

CUDA | NVIDIA Cuda Toolkit for General Purpose Computation on GPU Equipped Systems |

FPC | Free Pascal Compiler |

GCC | GNU Compiler Collection |

GPC | Gnu Pascal Compiler |

IBM XL | IBM XL compilers for multicore acceleration (Cell) |

INTEL | Intel Compilers and Performance Tools |

Open64 | The AMD x86 Open64 Compiler Suite (for evaluation) |

OpenCL | Open Computing Language - framework for heterogeneous computing (GPGPU) |

Pathscale | Default Compiler on Opteron Based Clusters |

Portland | PGI Fortran, C and C++ Compiler |

Python | Powerful Dynamic Programming Language (includes mpi4py and numpy) |

Yorick | Interpreted Programming Language for Scientific Simulations (NEW!) |

DDT | Powerful Parallel Debugger with Graphical Interface |

VALGRIND | Memory debugging |

ACML | AMD Core Math Library |

ATLAS | Automatically Tuned Linear Algebra Software (removal pending jan 2011) |

BLACS | Basic Linear Algebra Communication Subprograms |

BLAS | Basic Linear Algebra Subprograms |

CHARM++ | Parallel language and library based on C++ |

FFTW | Library for Computing the DFT |

GMP | GNU Multiple Precision Arithmetic Library |

GSL | GNU Scientific Library |

HDF | Library and File Format to Store Scientific Data |

HP-MPI | HP's MPI implementation |

IMSL | IMSL Fortran Numerical Library (commercial, group: imsl) |

IPM | Parallel Code Profiling Library |

JASPER | Toolkit for Image Processing |

LAPACK | Linear Algebra PACKage |

MKL | Intel Math Kernel Library (threaded lapack, blas, fft, etc) |

MPFR | Multiple-Precision Floating-Point Computations with Correct Rounding |

MPFUN | Fortran-90 Arbitrary Precision Package |

NAG | Fortran Library and Parallel Library (commercial) |

NetCDF | Network Common Data Form |

OpenMPI | Open source MPI implementation |

PARI/GP | Computer Algebra System |

PERLMODULES | User requested cluster installed perl modules |

PETSc_SLEPc | Parallel solver for systems of PDEs and Scalable Library for Eigenvalue Problem Computations |

PNETCDF | A High Performance API for NetCDF File Access |

QD | Double-Double and Quad-Double Arithmetic |

ScaLAPACK | Parallel Linear Algebra Calculations |

SPRNG | Scalable Parallel Pseudo Random Number Generators Library |

OPT | Optimization and MPI Profiling Tool |

CLN | Class Library for Numbers |

CP2K | Atomistic and Molecular Simulations of Solid State, Liquid, Molecular and Biological Systems |

FREEFEM++ | A Language Dedicated to the Finite Element Method |

MPICH2 | An implementation of the Message-Passing Interface |

OpenFOAM | An open-source based CFD software |

PARPACK | Parallel ARPACK to Solve Large Scale Eigenvalue Problems |

WRF | The Weather Research and Forecasting Model |

BINUTILS | A Collection of Recently Updated Binary Tools |

CMAKE | Cross Platform Make |

COMPILE | Generic compilation script |

GIT | The Fast Distributed Version Control System |

MERCURIAL | A distributed source control management tool |

NXCLIENT | Remotely Connect to a Virtual Desktop on an X11 Computer |

RLWRAP | Readline Feature Command Line Wrapper (NEW!) |

SQ | SHARCNET queueing scripts |

SUBVERSION | A Full-Featured Version Control System |

UTIL | Command Line Tools to Check User, Queue, Job and System Status |

VIM | Highly Configurable and Efficient Text Editor |

GNUPLOT | A command-driven interactive 2d and 3d function plotting program |

GRAPHVIZ | Represent structural information as diagrams of abstract graphs and networks |

HYPERMESH | Altair Hyperworks Suite (commercial, hyperworks group, limited access) |

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ImageMagick | Software for the creation, modification and display of bitmap images |

NXCLIENT_NEW | A tool for enabling remote desktop access. (NEW!) |

PARAVIEW | Parallel Visualization Application |

Scilab | Open Source Platform for Numerical Computation |

VisIt | VisIT Visualization Tool |

VMD | Visual Molecular Dynamics |

XCrySDen | Crystalline and Molecular Structure Visualisation |

RMPI | R wrapper for MPI support |

FEniCS | Free software package for automated, efficient solution of differential equations. |