High Performance Computing

A High Performance Computing (HPC) cluster is a massively parallel computer that performs similarly to a supercomputer by connecting a group of computers (nodes) through a high-speed network in order to perform intense computing tasks. The cluster works in tandem to complete the tasks by dividing the work among the cluster nodes, reassembling the results, and presenting them to the client as if a single system did the work. HPC clusters provide a platform for support of research activities for University faculty who require more resources than can be accommodated with a single user's workstation. ISU's high performance computing environment supports research across a wide range of academic fields including Life Sciences, Bioinformatics, Computational Chemistry and Mathematics.

CIRT is working with computational chemists and physicists on campus to support Gaussin, MOLPRO, GAMESS, NWChem, as well as a range of bioinformatics and life science applications such as BLAT, EMBOSS, HMMer, and MATLAB.

CIRT provides academic programming services as well as software tools and techniques to effectively make use of clusters for computational science research. In addition, CIRT provides a wide-range of training opportunities for faculty and graduate students on the uses of HPC in research activities. These HPC systems will also act as a platform for development and testing of applications that may later migrate to national supercomputer centers for high-end production work. This initiative was implemented to maintain a level of institutional computational capability that is consistent with peer institutions.

You may apply for an account here. Make sure you select High Performance Computing under CIRT Provided Services. For details on how to use HPC, read this tutorial.

Hardware

In June of 2004 a 48-node / 64-processor AMD-based system was purchased from Aspen Computing (Slotnick).  Slotnick has since been upgraded and is now comprised of 64 nodes and 138 processors connected through an Infiniband backbone and Gigabit Ethernet.  Onyx 2 was acquired in the summer of 2006.  Also, in the summer of 2006 a 16-node / 32-processor Intel-based was purchased as a rendering farm for the Center for Visualization.

Gallery - Arrival Day 9/30/04

Software

MATLAB

Additional information on MATLAB.
Disciplines / Categories: Data Analysis and Visualization, Mathematics and Statistics
Software Support Homepage (External Link).

Gaussian

Gaussian is the latest in electronic structure programs. Gaussian is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

Disciplines / Categories: Chemical Engineering, Computational Biology, Computational Chemistry, Materials Science

MOLPRO

A system of ab initio programs for molecular electronic structure calculations, with the emphasis on highly accurate computations. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

Disciplines / Categories: Chemical Engineering, Computational Chemistry
Software Support Homepage - User Manual (External Link)

GAMESS

GAMESS is a program for ab initio quantum chemistry. Briefly, GAMESS can compute SCF wave functions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wave functions include Configuration Interaction, second order perturbation theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Analytic gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, and together with effective core potentials, all elements up to Radon may be included in molecules. Several graphics programs are available for viewing of the final results. Many of the computational functions can be performed using direct techniques, or in parallel on appropriate hardware.

Disciplines / Categories: Chemical Engineering, Computational Chemistry, Materials Science
Software Support Homepage - User Manual (External Link)

NWChem

NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Theory, Modeling & Simulation program of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction.

Disciplines / Categories: Chemical Engineering, Computational Chemistry
Software Support Homepage (External Link)

BLAT

BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT -- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.) BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory.

EMBOSS

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

HMMRE

HMMRE is a software suite for making and using Hidden Markov Models (HMMs) of biological sequences.

XCRYSDEN

XCrySDen is a crystalline- and molecular-structure visualization program. The name of the program stands for Crystalline Structures and Densities and X because it runs under the X-Window environment. It facilitates a display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualization of Fermi surfaces (experimental). It can run on most UNIX platforms, without any special hardware requirements.

MUPAD

MuPAD is a modern, full-featured computer algebra system in an integrated and open environment for symbolic and numeric computing. It may be the solution for a wide range of mathematical problems in various sectors like; Basic education in schools, Higher education and research,Engineering and technical sciences. Furthermore, MuPAD comes with VCam, a powerful visualization tool for high quality 2D and 3D graphics. Beside using the built-in features you will be able to extend MuPADs capabilities by writing you own MuPAD procedures. The MuPAD language has a Pascal-like syntax and allows imperative, functional, and object-oriented programming. Its domains and categories are object-oriented classes that allow overriding and overloading methods and operators, inheritance, and generic algorithms. MuPAD also supports compiling and linking existing C/C++-code as Dynamic Modules at runtime.

VTK

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. Professional support and products for VTK are provided by Kitware, Inc. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data. The design and implementation of the library has been strongly influenced by object-oriented principles.

POV-Ray

POV-Ray is short for the Persistence of Vision Raytracer, a tool for producing high-quality computer graphics.

Other Applications

Many other titles are available as well as custom applications and software requests.

Compilers

The following compilers are available:

Cluster Management

Aspen Beowulf Cluster Management (ABC)

Aspen Beowulf Cluster (ABC) Management Software is a comprehensive management environment that supports the installation, configuration, and day-to-day operations of any node or supported device within a Linux-based Beowulf cluster. The functions of ABC empower an administrator with the ability to install and clone nodes, upgrade software packages, define alarm thresholds and actions, run programs across the cluster, and create historical graphs of monitored data . . . all from a single, browser-based, integrated application accessed via a secure, encrypted connection.

Bioteam Inquiry

Inquiry is a ready-to-use cluster and web portal optimized for use in life science informatics settings. It comes preconfigured with hundreds of open source scientific applications and can easily be extended to support additional commercial, open-source or internally developed applications. The end result is a powerful and scalable in-house informatics resource that installs rapidly and is ready to use --no expensive professional services fees or long weeks of setup, configuration and tuning.

Sun Grid Engine

Grid Engine is Distributed Resource Management (DRM) software. DRM software aggregates compute power and delivers it as a network service. Grid Engine software is used with a set of computers to create powerful compute farms, which are used in a wide range of technical computing applications such as the development of semiconductors, bioinformatics, mechanical design, software development, oil/gas exploration, and financial analysis; additionally, massively scaling supercomputers use Grid Engine software in a variety of academic and research pursuits. Users enjoy access to large computing capability and organizations enjoy effective utilization of their computing resource investments approaching 100%.