Overview

Many popular math and statistics software packages are available on the HPC system.

General considerations

Available Math & Statistics Software

To get an up-to-date list of the installed math applications, log on to UVA HPC and run the following command in a terminal window:

module keyword math

To get more information about a specific module version, run the module spider command, for example:

module spider mathematica

List of Math & Statistics Software Modules

Module	Category	Description
clapack	math	C version of LAPACK
eigen	math	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
elpa	math	Eigenvalue SoLvers for Petaflop-Applications .
geos	math	GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
gmp	math	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gurobi	math	The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.
jags	math	JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
libxsmm	math	LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
lpsolve	math	Mixed Integer Linear Programming (MILP) solver
mcr	math	The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
metis	math	METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
mpfr	math	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
netlogo	math	NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL.
ntl	math	NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.
openbugs	math	OpenBUGS is a software application for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods.
sas	math	Statistical analysis package
scotch	math	Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
stata	math	Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
sundials	math	SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
voro++	math	Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.

Using a Specific Software Module

To use a specific software package, run the module load command. The module load command in itself does not execute any of the programs but only prepares the environment, i.e. it sets up variables needed to run specific applications and find libraries provided by the module.

After loading a module, you are ready to run the application(s) provided by the module. For example:

module load mathematica