The Environment Modules package provides for the dynamic modification of a user’s environment via modulefiles.
Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the environment can be modified on a per-module basis using the module command which interprets modulefiles. Typically modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. modulefiles may be shared by many users on a system and users may have their own collection to supplement or replace the shared modulefiles.
$ module load R $ which R $ module unload R $ module load openbugs
|list||List current loaded modules||module list|
|avail||List all modules available in the system||module avail|
|show||Display details of a module||module show R|
|load||Load a module into your environment||module load R|
|unload||Remove a currently loaded module from your environment||module unload R|
|whatis||Display the module description information||module whatis R|
To load a list of modules different then the default you have the ~/privatemodules/ directory at your disposal. To load specific modules at login that are not in the site defaults put the module commands into the file default file in ~/privatemodules/default. You can put any module command in this default file. So if you would like to run a different version of an existing package you can unload that modules and then load it via the default file.
The following list of software is available on the cluster.
If there is software missing that you need please email firstname.lastname@example.org to have it added to the repository. As always you are free to install software in your home directory.
|Module||Versions (D)efault||Description||Licenses Available||Notes|
|Biostatistics local repository||N/A||Vendor|
|GCC is the GNU C/C++/Fortran compiler suite.||N/A||Vendor|
|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.||N/A||Vendor|
|The Gurobi Optimizer is a state-of-the-art solver for linear programming (LP), quadratic programming (QP) and mixed-integer programming (MILP and MIQP). It was designed from the ground up to exploit modern multi-core processors.||N/A||Vendor|
|hwloc||1.9||The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, …) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.||http||Vendor|
|JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.||N/A||Vendor|
|LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.||N/A||Vendor|
|matlab||R2013a||Matlab is an interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design.||16||Vendor|
|mpc||1.1.0||GNU MPC is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result||N/A||Vendor|
|mpfr||4.0.1||The MPFR library is a C library for multiple-precision floating-point computations with correct rounding||N/A||Vendor|
|openbugs||3.2.3||BUGS is a software package for performing Bayesian inference Using Gibbs Sampling.||N/A||Vendor|
|openmpi||1.8.1||The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.||N/A||Vendor|
|perl||5.18.2||Local perl cpan installation.||N/A||Vendor|
|R is a language and environment for statistical computing and graphics.||N/A||Vendor|
|SAS Statistical Analysis package||unlimited||Vendor|
|slurm||17.02.9||Slurm Resource Manager and Job Scheduler||N/A||Vendor|