Exploring New Uses, New Communities, New Knowledge ...
Cyber-enabled Collaborative Research: The availability of a regional cyberinfrastructure enhances research by providing access to resources beyond those available on a single campus. SURAgrid supports regional research initiatives by:
- encouraging and facilitating research collaborations and collaborative proposal development
- enabling access to distributed HPC resources capable of supporting a variety of modeling and simulation applications
- providing access to shared data and visualization tools
- simplifying access to and use of regional and national cyberinfrastructure services
For more information on the status of application deployment on SURAgrid, contact Linda Akli, SURA IT Application and Outreach Specialist or see "Running Applications on SURAgrid" under the "Join SURAgrid" tab for guidance on how to submit your request and get started.
Applications Deployed in SURAgrid
The following applications are deployed on SURAgrid:
UNC Storm Surge Modeling with ADCIRC
ADCIRC is a finite element method shallow water model for computing tidal and storm surge water level and depth-averaged currents associated with these phenomena. Grid environments such as SURAgrid are ideal for the ensembles in applications like ADCIRC, which is one of a set included under SCOOP (SURA Coastal Ocean Observing and Prediction) program that is focused on improving predictions of coastal phenomena. Project Partners: University of North Carolina Marine Science, Renaissance Computing Institute (RENCI), MCNC, SAIC.
Handout (PDF) * Poster (PDF) * Application Description (PDF) * Resource Set-Up Instructions
GSU Multiple Genome Alignment on the Grid
This multiple sequence alignment algorithm application takes a number of genome sequences as input and gives aligned sequence based on their structure by using a pairwise alignment algorithm. When run on grids like SURAgrid, carefully designed, grid-enabled algorithms like this, which implement a memory efficient method for computation and are also parallelized efficiently so that the workload is well distributed on grids, afford bioinformatics users a performance comparable to cluster environments while giving them added flexibility and scalability.
Handout (PDF) * Poster (PDF) * Application Description (PDF) *
NCSU Simulation-Optimization for Threat Management in Urban Water Systems
NCSU threat Management in Urban Water Systems incorporates dynamic demand data, in real-time, into a simulation-optimization process for contamination threat management in drinking water distribution systems. The nature of this work is highly compute-intensive and requires multi-level parallel processing via computer clusters and high-performance computing architectures such as SURAgrid. Simulation-Optimization with EPANET is part of a multi-disciplinary, three-year NSF-funded DDDAS (Dynamic Data-Driven Application Systems) research project to develop a cyberinfrastructure system that will both adapt to and control changing needs in data, models, computer resources and management choices facilitated by a dynamic workflow design. Project Partners: North Carolina State University; University of Chicago; University of Cincinnati; University of South Carolina.
Handout (PDF) * Poster (PDF) * Application Description (PDF)
ODU Bio-Sim: Bio-electric Simulator for Whole Body Tissues
ODU Bio-Sim is designed to simulate the response of a "whole body tissue" model to potential/current stimulus through direct electrode contact. The Electrical and Computer Engineering and Office of Computing and Communications Services departments at Old Dominion University are using SURAgrid to grid-enable this application to utilize concepts such as workflow and virtual data methods. The Bio-electric Simulator, which is both computation and data intensive, has been demonstrated to scale with the number of processors and can thus benefit from the accessibility to the additional computational resources of SURAgrid.
Handout (PDF) * Poster (PDF) * Application Description (PDF) *
UABgrid Dynamic BLAST
BLAST is a database search application for matching protein and nucleotide sequences. Maximizing the throughput of searches is critical to improving research results. This distributed implementation of BLAST uses the Dynamic BLAST Meta-scheduler to select appropriate grid resources for select query strings. Globus is used for job staging, submission and retrieval. ncbiBLAST performs the computations. Jobs are submitted using a web-based interface that leverages campus identity credentials via Pubcookie and manages grid authentication on behalf of the user via MyProxy, providing a simplified user authentication experience. Handout (PDF) * Poster (PDF) * Application Description (PDF) *
SURA: SURAgrid Teaching Environment
The SURAgrid Teaching Environment is a multi-organization project that is addressing the development of teaching
grid technology and teaching with grids. Effective teaching about grids, within Computer Science as well as other disciplines, is greatly enhanced by students and instructors having hands-on access to a stable grid environment. Through coordinated commitment, operation and support across a subset of SURAgrid resources, SURAgrid is developing a predictable, secure and reliable grid-based teaching facility for use by SURAgrid sites in their grid course development and/or delivery.
Application Description (PDF) *
LSU Wave Watch 3 for SCOOP
WAVEWATCH III solves the spectral action density balance
equation for wavenumber-direction spectra. Grids such as SURAgrid have the potential to greatly improve the ability to distribute Event Driven Wave Watch 3 instances across geographical domains and take advantage of supercomputing resources to process wave model for Hurricane events. Project Partners: Center for Computation and Technology (CCT), Louisiana State University; SCOOP; Bedford Institute of Oceanography.
Application Description (PDF) *
UFL CH3D Storm Surge Monitoring System with Grid Appliance
The Curvilinear Hydrodynamics in Three Dimensions (CH3D) application is used to model physical processes in bays, rivers, lakes, and estuaries. CH3D is a circulation model that aids storm surge forecasting and is one of a set of applications included under the SCOOP program. On SURAgrid, CH3D is implemented in combination with the Grid Appliance application, which is a self-configuring virtual machine that contains the IPOP virtual networking package and the NSF/NMI Condor middleware. The retrospective analysis the application duo is used for requires high-throughput, is computationally intensive, and can thus take advantage of the resources available on SURAgrid .
Application Description (PDF) *
University of Delaware Climate Modeling with CAM3
University of Delaware (UDel) is in the process of deploying a climate modeling application on SURAgrid. UDel is currently running the Community Atmosphere Model (CAM3) on a department Linux box which is a single processor 1.5 GHz box. One year of model output from the CAM takes approximately 5-6 days real time. The use of a multi-prcoessor machine will greatly broaden the scope of the study and allow for the use of an additional model called the SLAB Ocean Model (SOM). Most of the improvement in calculation time would come from the ability to implement multi-processor capabilities.
Application Description (PDF) *
VCU Virtual Parasite
The VPP is housed in the Center for the Study of Biological Complexity at VCU, and allows researchers to select the parameters they would like to specifically test. For example, what would happen if gravity was turned off? Could the parasites swim? Would they know where they are? How would they react? Would the parasites still swim downward toward the host cells, as they do now? Deployment on SURAgrid provides the computational resources necessary to carry out the large amount of calculations needed and access to the large amount of memory and disk space needed to generate the simulations.
Application Description (PDF) *
GSU Virtual Screening for Chemistry
Virtual screening is a computational technique used in drug design research. To shorten the time-consuming drug design & discovery procedure, in the current project, millions of molecules will be docked into the receptor for the evaluation of receptor-based potency by molecular docking program DOCK 6.1.
Application Description (PDF) *
Applications Being Ported to SURAgrid
The SURAgrid community is actively identifying and porting applications, and currently the following applications are being ported to SURAgrid:
Hampton University Tokamak Divertor Map
Hampton University's Center for Fusion Research and Training (CFRT) main area of research is mathematical maps to calculate trajectories of magnetic field lines in divertor tokamaks. The purpose is to calculate the footprint of magnetic field lines on collector plates of tokamaks. Mathematical maps preserve topological invariants, and have the advantage of computational efficiency. Evolution of each field line is independent of other field lines. So, each processor can independently calculate trajectory (or path) of one field line. When paths of all field lines are calculated, their accumulative statistical behavior can then be determined. This research is ideally suited to run on a large number of processors in a parallel fashion.
Handout (PDF) * Application Description (PDF) *
NCAT Protein Loop Structure Prediction
NCAT is developing a new protein loop structure prediction software package based on the residue triplet scoring function and distance-based atom interaction scoring function. The software package has already shown resolution improvement in various difficult protein loops. SURAgrid will be used to benchmark the protein loop structure prediction package on a large protein loops and tune the performance of the protein loop structure prediction package.
* Application Description (PDF) *
ODU Options Pricing
This project focuses on specialized implementations for binomial tree option price valuations. In particular, it will exploit the memory hierarchy, as well as communication systems in a parallel system. It will also attempt to solve a two-dimensional space of number of problems and the problem size that will exploit the topology of a grid to maximize throughput.
* Application Description (PDF) *
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