On IU's TeraGrid-enabled system Big Red, what software is available to researchers with TeraGrid accounts?

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Following is a list of software available on Indiana University's Big Red system to researchers with TeraGrid accounts.

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Compilers and support

Boost: Boost is a set of peer-reviewed portable C++ source libraries.
CHARM++: CHARM++ is an object-oriented portable parallel programming language based on C++ (only 64-bit addressing is available).
FDPR: FDPR-Pro is a feedback-based post-link optimization tool. It optimizes the executable image of a program by collecting information on the behavior of the program while the program is used for some typical workload and then creating a new version of the program optimized for that workload.
Ruby: Ruby is an object-oriented programming language.
SWIG: SWIG is a Simplified Wrapper and Interface Generator.
Xerces: Xerces-C++ is a validating XML parser written in a portable subset of C++.

Debugging and performance packages

DDD: DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger, or the Python debugger.
Totalview: This is a source code debugger.
Vampir: Vampir is a graphical tool for analyzing the performance and message passing characteristics of parallel programs that use the MPI message-passing library.
Vampir-trace: Vampir-trace is a library you can link into your application. It will produce a trace file that can be viewed by Vampir (both 32- and 64-bit addressing are available).

Mathematical packages

ATLAS: Automatically Tuned Linear Algebra Software (ATLAS) is a research effort to deploy empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK (both 32- and 64-bit addressing are available).
BLACS: Basic Linear Algebra Communication Subprograms (BLACS) create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms (both 32- and 64-bit addressing are available).
BLAS: Basic Linear Algebra Subprograms (BLAS) are routines that provide standard building blocks for performing basic vector and matrix operations (both 32- and 64-bit addressing are available).
CERN-2005: The CERN Program Library is a large collection of general purpose libraries and modules maintained and offered from the CERN central computers.
DRSEED: DRSEED is a random seed generator package.
FFTW2 (MPI version) and FFTW3: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions of arbitrary input size, and of both real and complex data (as well as of even/odd data, e.g., the discrete cosine/sine transforms or DCT/DST). (FFTW2 features 64-bit addressing and single precision. For FFTW3, both 32- and 64-bit addressing and both single and double precision are available.)
GMP: GMP is a library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers (only 64-bit addressing is available).
GSL: These are the GNU Scientific Math Libraries (only 64-bit addressing is available).
LAPACK: Linear Algebra PACKage (LAPACK) provides serial routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems (both 32- and 64-bit addressing are available).
MPFR: The MPFR library is a C library for multiple-precision floating-point computations with exact rounding (also called correct rounding). It is based on the GMP multiple-precision library.
Scalapack: Scalable LAPACK provides parallel routines for distributed clusters to solve systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems (both 32- and 64-bit addressing are available).
SPRNG2: SPRNG is a set of libraries for scalable and portable pseudorandom number generation; it was developed with the requirements of users involved in parallel Monte Carlo simulations in mind (only 32-bit addressing is available).
SVDPACK: SVDPACK comprises four numerical (iterative) methods for computing the singular value decomposition (SVD) of large sparse matrices (only 64-bit addressing is available).

Science packages

Amber9: Assisted Model Building with Energy Refinement (Amber) is a set of molecular mechanical force fields for the simulation of biomolecules, and a package of molecular simulation programs that includes source code and demos.
AutoDock: AutoDock is a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
BLASTZ: BLASTZ is a multiple sequence alignment program for the whole-genome human-mouse alignments.
Boxshade: Boxshade creates shaded or colored printouts from multiple-aligned DNA or protein sequences. The program does not align sequences but stylizes multiple alignments.
CPMD: CPMD code is a parallelized plane wave/pseudopotential implementation of density functional theory, particularly designed for ab initio molecular dynamics (Car-Parrinello Molecular Dynamics with MPI and SMP).
Cri-map: Cri-map performs largely automated construction of multilocus linkage maps (and facilitates the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors).
DOCK5 and DOCK6: DOCK is a parallel package that identifies molecules "docking" to each other. In general, docking is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known.
Note: You must hold an external license to use this software.
ESPRESSO: Quantum ESPRESSO is an integrated suite of computer codes for electronic structure calculations and materials modeling at the nanoscale. It is based on density functional theory, plane waves, and pseudopotentials (both 32- and 64-bit addressing are available).
Finale: Finale collects the results of a SimWalk2 analysis into a single IBD file that is ready for input into the QTDT program.
GAMESS: General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package (both 32- and 64-bit addressing are available).
GROMACS: GROMACS is a versatile package for performing molecular dynamics, i.e., simulating the Newtonian equations of motion for systems with hundreds to millions of particles (both serial and MPI versions are available with 64-bit addressing).
Mapmaker2 and SIBS: Mapmaker 2 and SIBS are unified programs for genetic linkage analysis of simple markers (MAPMAKER) and complex traits.
MERLIN: MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages available.
MERLIN-REGRESS: MERLIN-REGRESS implements an extension of the Haseman-Elston quantitative trait linkage analysis procedure, which extracts linkage information from trait squared-sums and differences from all non-inbred relative pairs.
MINX: MINX implements X-chromosome-specific versions of the functions provided by the standard MERLIN implementation.
NAMD: NAMD is parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NCBI: BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between nucleotide or protein sequences and sequence databases and calculates the statistical significance of matches.
PAML: Phylogenetic Analysis by Maximum Likelihood (PAML) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
PedMerge: PedMerge is a program that merges extended pedigrees.
PedStats: The PedStats utility summarizes the contents of pedigree files and can produce graphical output in PDF format.
Pedwipe: Pedwipe retrieves a list of unlikely genotypes from the merlin.err file and removes them from the data.
Phylip: Phylip is a set of Phylogeny Inference Package programs for inferring phylogenies.
Prelude: Prelude prepares data and pedigree files in QTDT format to be analyzed by SimWalk2 or Genehunter.
PROCHECK: PROCHECK is a suite of programs for assessing the stereochemical quality of a given protein structure.
QTD: A QTDT interface for family based tests of linkage disequilibrium that can be used to analyze quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested.
SHELX: SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. SHELXH has been modified for huge data.
SimWalk2: SimWalk2 is a statistical genetics application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD), and mistyping analyses on any size of pedigree.

VIZ packages

ImageMagick: ImageMagick is a software suite for creating, editing, and composing bitmap images. It can read, convert, and write images in approximately 100 formats (both 32- and 64-bit addressing are available).

For more information about TeraGrid software, see the following pages in the TeraGrid User Support documentation:

This document was developed with support from the National Science Foundation (NSF) under Grant No. 0503697 to the University of Chicago and subcontracted to Indiana University. Additional support was provided by IU through its participation in the TeraGrid, which is supported by the NSF under Grants No. 0833618, SCI451237, SCI535258, and SCI504075. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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Last modified on November 05, 2009.