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Applications
Application Name Description
ABAQUS is a FORTRAN program developed by Hibbitt, Karlsson & Sorenson, Inc. for engineering analysis and modeling based on the finite element method. Its areas of applicability range from stress analysis and heat transfer to fluid mechanics.
Online reference: /usr/local/apps/abaqus/abaqus/Documentation/docs/v6.4/.
AMBER is a molecular modeling package created by Peter Kollman's research group at the University of California at San Francisco, used for the creation and modification of macro-molecular structures in vacuo and in solutions having periodic boundary conditions. Computation modules include:
  • Energy minimization
  • Molecular dynamics
  • Free energy perturbation
  • Analysis of dynamic, energy and structure normal modes
Online reference: man amber.
BLAST BLAST (Basic Local Alignment Search Tool) provides a method for rapid searching of nucleotide and protein databases. The National Center for Biotechnology (NCBI) makes BLAST and several other tools available to the public. NCBI BLAST Online How To: /opt/BioBrew/NCBI/6.1.0/doc/blast.txt Online reference: man blast.
AVS 5 stands for Application Visualization System and is a set of visualization tools tailored for scientific researchers from Advanced Visual Systems, Inc.. AVS is built on a visual programming paradigm that makes it easy to visualize scientific data without requiring extensive programming knowledge or expertise in advanced visualization techniques. A large collection of vendor-supplied and public domain modules is available from the International AVS Center at the North Carolina Supercomputing Center. AVS has standard subsystems for handling image, geometry, volume, and chemistry data and a graph manipulation package for plotting.

Univerisity of Texas at Austin students, faculty, staff, and other authorized agents of the university can get a free copy of AVS 5.5 by completing the form located at http://www.tacc.utexas.edu/resources/software/avs/.

AVS 5 Manuals

The following is a complete set of online manuals for the Application Visualization System 5, a general-purpose, data-flow visualization tool. AVS 5 provides access to a rich array of techniques for science and engineering-related visualization via a graphical user interface. Beginning users should refer to the AVS Tutorial Guide and the AVS User's Guide.

AVS/Express a general-purpose, data-flow visualization tool. AVS/Express also provides an object-oriented environment for developing interactive visualization applications for use with data from science and engineering related sources. Beginning users should refer to the Getting Started and Using AVS/Express guides.

Univerisity of Texas at Austin students, faculty, staff, and other authorized agents of the university can get a free copy of AVS/Express by completing the form located at http://www.tacc.utexas.edu/resources/software/avs/.

FITPACK is a library of over 80 FORTRAN-callable routines, developed by Pleasant Valley Software, that perform curve- and surface-fitting using splines under tension. Features of the package include a variety of dimensions for base and target spaces, approximation of data with apparent poles, and the approximation of integrals, derivatives, and lengths of the approximating curves.

Online reference: man fitpack.
FFTW the Fastest Fourier Transform in the West, is a comprehensive library of C routines for computing discrete Fourier transforms (DFT). The library routines can transform single- and multi-dimensional real and complex data, of arbitrary input size. FFTW also includes parallel implementations for shared- and distributed-memory systems. (These may not be implemented on TACC systems.)
FFTW features include:
Cooley-Tukey algorithm
Prime Factor algorithm {most efficient with small prime factors (2,3,5, and 7)}
Rader's algorithm for prime sizes
split-radix algorithm (with a variation due to Dan Bernstein)
automatic performance adaptation

Performance adaptation is accomplished by calling a "planner" that learns the fastest machine-related (memory, cache) parameters to use for the transform. It then uses the "plan" for the transform. For codes that use the same FFT's multiple times, the planner is an ideal mechanism for optimizing turn-around time. For a once-called FFT transform in a code, the planner/transform time may be significantly higher than other (e.g. essl, scilib) package FFT libraries.

See http://www.fftw.org for benchmarks, FAQs, documentation, and details of features.

Online reference: module load fftw; man fftw {www.fftw.org --> documentation}.
GAMESS is the General Atomic and Molecular Electronic Structure System from the Gordon research group at Iowa State University, an ab initio quantum chemistry package that calculates the following atomic and molecular wavefunctions:
  • RHF (restricted Hartree-Fock)
  • URHF (unrestricted Hartree-Fock)
  • ROHF (restricted, open shell Hartree-Fock)
  • GVB (generalized valence bond)
  • MCSCF (multi-configuration self-consistent field)
  • CI (configuration interaction)
GAMESS provides an X interface.

Online references: man gamess and man rungamess.
Globus is an emerging standard for building grids and grid related applications. Globus addresses the fundamental needs for a functional computational grid such as security and authentication protocols, resource management, data management, and information services. Globus is built around the following four cornerstone technologies: GSI (Grid Security Infrastructure), GRAM (Globus Resource Allocation Management), MDS (Monitoring and Discovery Service), and GridFTP.

Globus User Guide coming soon.
GNUPLOT is a command-driven interactive/batch plotting package that supports many different interfaces. (Execute "set term" inside the gnuplot program-- on the "gnuplot>" command line, to see the supported drivers.) New users should read the FAQ first. An overview of the features is provided at the beginning of the man page.

Online reference: man gnuplot.

Manual,Tutorial, Info http://www.gnuplot.info/.
IRIS Explorer is a dataflow oriented visualization system developed by Numerical Algorithms Group, Inc. similar to AVS that allows you to build applications for visualizing data. Explorer modules are task-oriented, such as data filtering, transformations, object rendering and plotting (including line graphs, histograms, contours, surfaces, isosurfaces, volumes, and vector plots) and displaying objects with full 3D interaction.
METIS is a collection of C routines for partitioning unstructured graphs and producing fill reducing orderings for sparse matrices developed by George Karypis at the University of Minnesota. These routines are particularly useful for performing domain decomposition on unstructured finite-element and finite-volume meshes and provide high-quality partitions suitable for distributed computing.

More info including FAQs and tutorials can be found at: METIS
For online library linking information, see: module help metis
MKL The "Math Kernel Library" consists of functions in the following computational areas:
  • BLAS (vector-vector, matrix-vector, matrix-matrix operations) and extended BLAS for sparse computations
  • LAPACK for linear algebraic equations solutions and eigensystem analysis
  • Fast Fourier transforms
  • Interface for use by both C and Fortran compilers, for all of the above functionality in addition to availability for all precisions and/or types. Some of functionality have improved performance by multi-threaded implementation.
MPI is the Message Passing Interface. MPI is a widely-used point-to-point and collective message-passing communication library designed for parallel computing in distributed memory environments.

Online reference: man mpi
MPT is the Message Passing Toolkit from Cray Research. MPT is built on PVM and MPI, two widely-used point-to-point message-passing communication libraries especially designed for parallel computing in distributed memory environments which use hardware ranging from clusters of workstations to massively parallel processors (MPPs). Cray's Message Passing Toolkit contains PVM and MPI implementations tuned for its parallel vector processor (PVP) systems with shared memory that offer 45 times the bandwidth at one-quarter the latency of the public domain versions.

Online reference: PVM manual pages, mpirun, MPI, modules.
NCSA HDF was developed by the National Center for Supercomputing Applications and is part of the NCSA Visualization Suite. NCSA HDF (for Hierarchical Data Format) is a multi-object file format that facilitates the transfer of scientific data between various operating systems and platforms including Cray, Sun, Convex, Connection Machine, DEC, Silicon Graphics, Macintosh, and IBM PC computers. HDF allows self-definitions of data content and easy extensibility for future enhancements and is compatible with standard formats, including FORTRAN and C calling interfaces.

Online reference: man hdf.
OpenDX stands for IBM Open Visualization Data Explorer (OpenDX). OpenDX is an application and development system for visualizing data, especially 3D data from simulations or acquired from observations. It uses a graphical user interface, and features a complete set of standard visualization algorithms. These include cutting planes, vector line traces, volume rendering, and isosurfacing/ isocontouring. OpenDX is based on code and ideas formerly found in the IBM Visualization Data Explorer program product.
ParMETIS is an MPI based library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS is built on top of METIS and can be used to perform dynamic graph repartitioning for adaptively refined meshes in addition to decomposition for multi-phase and multi-physics computations.

More info including FAQs and tutorials can be found at: ParMETIS
For online library linking information, see: module help pmetis
SPRNG SPRNG is a library of scalable pseudorandom number generators. The library was specifically designed for parallel calculations and provides reproducible streams of parallel pseudorandom numbers, independent of the number of processors.

Online reference: man sprng.

SPRNG User's Guide
VML is a set of functions collectively known as the "Vector Math Library" (VML). VML is a set of vectorized transcendental functions that offer both high performance and excellent accuracy compared to the libm functions for most of the processors. For the Pentium 3 processor, the accuracy of these functions approaches that of libm, but these vectorized functions are considerably faster for vectors longer than a few elements.
  • The VML routines are in the MKL libraries.
  • The list of functions and a usage document are available on the VML web page
Online reference: http://www.tacc.utexas.edu/services/userguides/mkl/VMLnotes.php
ZETALIB is a set of 11 industry-standard and over 20 extended subroutines developed by Nicolet, Computer Graphics Division. The ZETA library is a more recent release of this package and is compatible for Nicolet ZETA plotters with level 5.4 or better firmware. If you generate ZETA plots on the SV1 for plotting at UT Austin RJO sites, you should use the RJOZETA library instead of this library.

Online reference: man zeta.
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