Software

Environment Modules

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.

Example Usage

$ module load R
$ which R
$ module unload R
$ module load openbugs

Module Subcommands

Command Description example
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

Private Modules

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.

Available Modules

The following list of software is available on the cluster.

If there is software missing that you need please email sph-biostat-help@umich.edu to have it added to the repository. As always you are free to install software in your home directory.

Module Versions Description Licenses Available Notes
biostat 1.0 Biostatistics local repository N/A Vendor
gurobi 5.6.2 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
matlab R2013a Matlab is an interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design. 16 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 3.1.1 R is a language and environment for statistical computing and graphics. N/A Vendor
sas 9.3 SAS Statistical Analysis package unlimited Vendor
slurm 14.03.6 SLURM Resource Manager and Job Scheduler N/A Vendor