Applications are standard SuSE applications as well as additional applications installed in /apps. See the Modules section on configuring the environment to enable access to some of these applications. Not all applications will be in your PATH initially.
Third-party applications are generally to be found under /apps, although you should find these in your path already. Currently installed applications and libraries include:
- the Intel C/C++ and Fortran compilers (various versions)
- CFX
- NetCDF
- FFTW
- editors such as vim, emacs, xemacs and nedit.
- ANSYS
- GAUSSIAN 03
- Octave
Please feel free to request the installation of additional applications. However we request that you also try and supply some information such as license used, source code availability and Itanium64 binaries. Please do not email us large binary attachments as we would prefer it on CD.
Modules
Environment modules allow you to easily manipulate your shell environment to allow the use of software you wish to use. Modules allow you to select different versions of the same software for each individual user. (eg, selecting between two different versions of a C compiler) The “module” syntax is the same in any shell.
- “module avail” - show what modules are available.
- “module load
” load a module into the environment
- “module help
“module show
” details of the commands in the module
More information on modules
Example of use:
To load one of these applications, use the environment modules. eg:
myshellprompt-~> module load xemacs
If you require a specific version, use 'module avail' to see the list of available modules. eg:
myshellprompt-~> module avail
--- /usr/share/modules/modulefiles -----
....
intel-mkl/7.2.1
intel-mkl/8.0.2.004
intel-mkl/8.1.1.004
intel-mkl/9.0.018(default)
....
myshellprompt-~> module load intel-mkl/8.1.1.004
Permanent Module Use:
Most applications are not in your environment by default.
What you want to do is run 'add.modules'. This will ensure that your .login/.profile files contain a default modules setup. Then you can edit your profile files to ensure the appropriate modules are loaded.
For example, if you wanted to ensure that xemacs along with Gaussian are in the environment, try:
myshellprompt-~> touch .profile .bashrc .login .cshrc
myshellprompt-~> add.modules
Then modify .profile and .login (depending on if you use bash or tcsh respectively) to include your module preferences.
eg: .profile :
if [ -f /etc/profile.d/modules.sh ]
then
. /etc/profile.d/modules.sh
# put your own module loads here
module load gaussian/g03d02
module load xemacs
fi
eg: .login :
if ( -e /etc/profile.d/modules.csh ) then
source /etc/profile.d/modules.csh
# put your own module loads here
module load gaussian/g03d02
module load xemacs
endif
Resource Limits
Accounts are initially limited in the amount of resources they can use. This is to prevent a single process to overload the system and prevent other users from doing work. This only applies to programs run from the command line. If you were to run through the batch job processor, there will be no limits applied. Therefore if you wish to run a program that reaches its memory limits, try running it as an interactive batch job (see later).
Current limits:
Maximum process size: 6 gigs
Maximum cpu time for a single process: 24 hours.
If you exceed your limit, you will receive an error such as “killed” and a reason. Some applications silently ignore these errors and you may get strange results (ie, loading a file finishes but nothing is displayed). You can use “ulimit -a” to see your current limits.
Application List
Statistics & Mathematics
- Matlab (emulated! not full speed)
- Octave (runs simple matlab scripts, is 64 bit version which allows large matrices (greater than 2 Gbytes))
- R
Chemistry:
Data Models
Development
- gcc c and fortran
- intel c and fortran
- intel debugger
- MPT/MPI
CFD & Engineering:
- CFX
- ANSYS Mechanical
- icemcd
Biology:
- Genehunter
- haploview
- loki
- mega2
- Mendel
- Merlin
- Pedcheck
- Simwalk
- SOLAR
Math Libraries
- BLAS
- FFTW
- LAPACK
- Intel Math Kernel Library
Editors
- emacs
- xemacs
- nedit
- gedit
- vim
Detailed Descriptions
ANSYS: ANSYS Mechanical and ANSYS Multiphysics are self contained analysis tools incorporating pre-processing (geometry creation, meshing), solver and post processing modules in a unified graphical user interface. ANSYS is a general purpose finite element modeling package for numerically solving a wide variety of mechanical problems. These problems include: static/dynamic structural analysis (both linear and non-linear), heat transfer and fluid problems, as well as acoustic and electro-magnetic problems.
More information.
BLAS: SCSL (SGI Scientific Computing Software Library) provides a variety of mathematical subroutines. There are procedures for dense linear algebra (LAPACK), signal processing routines, direct and iterative linear equation solvers, parallel random number generators and ScaLAPACK for distributed memory routines.
CFX: CFX is a Computational Fluid Dynamics (CFD) and Engineering package.
More information.
CSIRO Mk3L: Climate Modelling & Earth Systems
EMACS: GNU Emacs is the extensible, customizable, self-documenting real-time display editor. GNU Emacs is developed by the GNU Project.
More information.
FFTW: FFTW, the Fastest Fourier Transform in the West is a comprehensive collection of fast C routines for computing the discrete Fourier transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size.
More information.
Gaussian: Gaussian is an ab initio quantum chemistry program, purchased from Gaussian Inc
More information.
gedit: gedit is the official text editor of the GNOME desktop environment.
More information.
Genehunter: Genehunter is software package for locating human genetic diseases using linkage analysis.
Haploview: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
Intel Debugger: The Intel Debugger comes with the Intel compilers. It is a command line utility that helps find problems in code at run time.
LAPACK: LAPACK is a collection of routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers.
More information.
Loki: Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees. Loki was originally designed for linkage analysis of quantitative traits, though there is some limited support for qualitative trait linkage analysis.
MatLab: Matlab is a general purpose analysis and graphics plotter from Mathworks. With more than 600 mathematical, statistical, and engineering functions, MATLAB provides immediate access to high-performance numerical computing. This functionality is extended with interactive graphical capabilities for creating plots, images, surfaces, and volumetric representations.
More information.
CFX: is a Computational Fluid Dynamics (CFD) and Engineering package.
Mega2: During a linkage analysis project, it can often be quite difficult to get one's data in the proper format desired by each different computer program. Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created Mega2.
Mendel: The Mendel software program performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several novel, statistical genetic tests. Where appropriate, the analysis will use either the Elston-Stewart or Lander-Green-Kruglyak algorithms, whichever is more efficient for each individual pedigree.
Merlin: MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around
MPT/MPI: MPI (Message Passing Interface) is a parallel program interface for explicitly passing messages between parallel processes - you must have added message passing constructs to your program.
nedit: nedit is a popular X-windows editor available on most linux distributions.
More information.
NetCDF: NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data.
More information.
Octave: GNU Octave is a high-level language, primarily intended for numerical computations. It is mostly compatible with Matlab
More information.
Pedcheck: Program for detecting marker typing incompatibilities in pedigree data.
R: R is `GNU S' - A language and environment for statistical computing and graphics. R is similar to the award-winning S system, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).
More information.
Simwalk: Stochastic Statistical Analysis of Qualitative Traits. Available analyses include: Haplotyping, Parametric Linkage, Non-Parametric Linkage (NPL), Identity-by-Descent (IBD), and Mistyping. SimWalk2 analyzes large pedigrees using MCMC estimation techniques.
Solar: SOLAR is a flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening.
vim: VIM is an improved version of the editor 'vi', one of the standard text editors on UNIX systems. VIM adds many of the features that you would expect in an editor : Unlimited undo, syntax coloring, split windows, visual selection, graphical user interface (read: menus, mouse control, scrollbars, text selection), and much much more.
More information.
