RESEARCH
COMPUTING

Useful Links for the Research Community

General

Internet2

Case is a member of Internet2 . Internet2 leases optical fiber pathways from commercial providers and makes the resulting bandwidth available to its members. Routing set up by Case causes outward bound network traffic to another Internet2 member to automatically be sent via Internet2; all outward traffic to non-Internet2 members is sent over the commodity Internet. The Case connection to Internet2 is currently at 45 Mbps with plans to increase to 155 Mbps; the Case connection to the commodity Internet is currently at 150 Mbps with plans to increase to 200 Mbps. The Abilene Observatory of Internet2 is a program that supports the collection and dissemination of network data associated with the Abilene Network, the backbone of Internet2. At present, there are several research projects that make use of data provided by the Abilene Observatory. A project proposal is required to use Abilene Observatory data in research. Internet2 supports several initiatives that may be of interest to Case researchers. For additional information on Internet2, including research opportunities related to Internet2, please consult their web site www.internet2.edu or contact them at info@internet2.edu .

National LambdaRail

Case has recently joined the National LambdaRail . NLR is purchasing optical fiber to build a 320 Gbps backbone for use by its members. Case will be connected to an existing NLR point of presence located off-campus in Cleveland . The NLR is designed to permit experimentation. Case researchers who are interested in beginning to plan experiments using NLR should contact the Experiments Support Services at ess@nlr.net . For other information on NLR, please contact info@nlr.net .

OSCnet

GENI: Global Environment for Network Investigations

GENI is an experimental facility being planned by the National Science Foundation, in collaboration with the research community. Its goal is to enable the research community to invent and demonstrate a global communications network and related services that will be qualitatively better than today's Internet. The research community is encouraged to participate in its design. See www.geni.net for complete details.

Cyberinfrastructure Technology Watch

"Cyberinfrastructure Technology Watch ( www.CTWatch.org ) is an online venue designed to engage the science and engineering research community in the news, ideas, and information surrounding the emergence of cyberinfrastructure as the essential foundation for advanced scientific inquiry.

CTWatch is a joint effort of the new NSF funded Cyberinfrastructure Partnership (CIP) between the San Diego Supercomputer Center (SDSC) and the National Center for Supercomputing Applications (NCSA), and it is being carried out in collaboration with the Innovative Computing Laboratory (ICL) at the University of Tennessee . It will serve both as a forum for opinion and analysis on issues related to cyberinfrastructure generally, and as an ongoing news and information source concerning the latest innovations in cyberinfrastructure technology. As a forum, the goal of CTWatch is to present thoughtful opinion and analysis on cyberinfrastructure in all its myriad aspects, including its impact on research, education, and practice; its implications for science and technology policy; its evolution at the hands of engineering research and innovative technology; and its critical role in increasing the nation's industrial capacity and economic competitiveness. Our intent is to stimulate the kind of productive debate and dialogue, both within the research community and outside it, which we believe the advent of this powerful new era of shared cyberinfrastructure requires." - from www.CTWatch.org

The Ohio Supercomputer Center (OSC)

The Ohio Supercomputer Center (OSC), in cooperation with the Ohio Board of Regents and the Ohio Department of Development, is sponsoring the Ohio Computational Science Initiative, whose main components are education ( The Ralph Regula School of Computational Science ), service to business ( Blue Collar Computing ), and research ( computational science research ). Please see http://www.osc.edu/supercomputing/csi/index.shtml for more information.

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High Performance Computing

Advanced Scientific Computing Research (DoE): www.science.doe.gov/feature/ASCR.htm

National Energy Research Scientific Computing Center (DoE / LBNL): www.nersc.gov

NASA Advanced Supercomputing (NAS) Division: marsoweb.arc.nasa.gov

NIH National Center for Biotechnology Information: www.ncbi.nih.gov

Computational Molecular Biology at NIH: molbio.info.nih.gov/molbio/Index.htm

NIH Center for Molecular Modeling: cmm.info.nih.gov/modeling

NIH Research and Scientific Support: www.cit.nih.gov/science.html

Scientific Computing at the National Center for Atmospheric Research: www.scd.ucar.edu

National Center for Supercomputing Applications: www.ncsa.uiuc.edu

San Diego Supercomputer Center: www.sdsc.edu

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Cluster Computing

What is a cluster?

A cluster is most often implemented as a collection of identical servers with a separate network interconnecting them for the purpose of exchanging data related to the applications they are running. Some helpful links for gaining an overview: www.beowulf.org , www.ieeetcsc.org , www.openclustergroup.org , and www.ram.org/computing/linux/linux_cluster.html .

Parallel Programming Using MPI

MPI (message passing interface) is a popular way for parts of a computation running in different processors in a cluster to communicate. MPI libraries are available for programming languages such as C/C++ and FORTRAN that are typically used in parallel applications. The links below provide information on MPI programming and related topics.

Tutorial on MPI programming from OSC

Tutorial on MPI programming from the Mathematics and Computer Science Division of the Argonne National Laboratories

Workshop I on MPI programming from the Maui High Performance Computing Center

Workshop II on MPI performance from the Maui High Performance Computing Center

from the Research Computing Core Facility at the U of South Florida

MPI: The Complete Reference (by Marc Snir, Steve Otto, Steven Huss-Lederman, David Walker, Jack Dongarra) - full text online

MPICH - a portable MPI implementation from the Mathematics and Computer Science Division of the Argonne National Laboratories

Optimizing MPI code from the Maui High Performance Computing Center

Tuning MPI applications for peak performance from the Mathematics and Computer Science Division of the Argonne National Laboratories

Programming on Linux

Linux programming tutorial from the Mathematics and Computer Science Division of the Argonne National Laboratories

C/C++ Programming

C programming tutorial from the Mathematics and Computer Science Division of the Argonne National Laboratories

Using the Case cluster

Please refer to the Case wiki pages for information on the cluster.

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Grid Computing

General

What is a grid? Although you are likely to get a different definition from everyone you ask, The Anatomy of the Grid (2001) and What is the Grid? A Three Point Checklist (2002) address the definitional issue.

The SURA Grid Application Planning and Implementation Workshop was held on January 5-7, 2005 at Georgia State University . Nearly all presentations and notes from the breakouts sessions are now available on the workshop web page at www2.gsu.edu/~wwwacs/suragridconf .

Descriptions of various grid project and deployments are available at www.grid.org .

Sun Grid Computing Community of Interest

The Sun Grid Computing Community of Interest is a special interest group devoted to grid computing. See http://www.sun.com/products-n-solutions/edu/commofinterest/gridcomp/ for subscription information and archives of their newsletters.

Project-specific and discipline-specific grids

GriPhyN, the Grid Physics Network: www.griphyn.org

The International Virtual Grid Laboratory / Grid 3 Collaboration: www.ivdgl.org/grid2003

The Particle Physics Data Grid: www.ppdg.net

European Collaborative National Grid project: www.crossgrid.org

EU DataTAG project: datatag.web.cern.ch/datatag/index.html

European Datagrid project: datagrid.cnr.it

Grid for UK Particle Physics: www.gridpp.ac.uk

LHC Computing Grid project: lhcgrid.web.cern.ch/LHCgrid

Open Science Grid: www.opensciencegrid.org/

Open Geospatial Consortium: www.opengis.org

Intelligent Robotic Telescope Network project: a collaboration of the Astrophysics Research Institute at Liverpool John Moores University and the Astrophysics Research Group of the School of Physics at the University of Exeter is described at www.estar.org.uk/ .

Petroleum engineering: www.ucoms.org

The National Office for Integrated and Sustained Ocean Observations: www.ocean.us and www.usnfra.org

Integrated Ocean Observing System: www.openioos.org

The National Oceanographic Partnership Program: www.nopp.org

The Ocean Research Interactive Observatory Networks: www.joiscience.org/ocean_observing

The Marine Metadata Interoperability Project: www.marinemetadata.org

SURA Coastal Ocean Observing and Prediction Program: www1.sura.org/3000/3300_Coastal.html

NASA Information Power Grid: www.nas.nasa.gov/sc2000/ARC/launchpad.html

Healthgrid: www.community.healthgrid.org

The NIH Cancer Biomedical Informatics Grid: caBig.nci.nih.gov

National and International Grid Computing Efforts

The World Community Grid's mission is to create the largest public computing grid benefiting humanity. There are opportunities for individuals to contribute unused time on their personal computers toward their efforts, and there are opportunities to submit a research project that can benefit from grid technology. IBM is a major partner in this effort.

TeraGrid is a multi-year effort to build and deploy the world's largest, most comprehensive, distributed infrastructure for open scientific research. Researchers at Case can apply for access to the TeraGrid. Get started reading about the TeraGrid here and here .

International Lattice DataGrid: www.lqcd.org/ildg/

The Open Science Grid Consortium: www.opensciencegrid.org

The OptIPuter: www.optiputer.net

The NSF Middleware Initiative: archive.nsf-middleware.org/

NSF Middleware Initiative testbed status: archive.nsf-middleware.org/testbed/testbed_status.asp

Regional Grid Computing Efforts

The High Performance Computing Across Texas consortium: www.hipcat.net

The North Carolina Research and Education Network: http://www.mcnc.org

Grid Computing Efforts at Universities

Georgetown University : http://www.gridswatch.com/

Georgia State University : www2.gsu.edu/~wwwacs/GRIDGroup/GRID_Group_GSU.htm

University of Alabama at Birmingham UABgrid: uabgrid.uab.edu

University of Arkansas : archie.csce.uark.edu/middleware.html

University of Florida : at.ufl.edu/grid

University of Michigan MGRID : www.mgrid.umich.edu

University of North Carolina at Wilmington : www.gridnexus.org

University of Southern California : www.usc.edu/hpcc

University of Texas Grid project: www.utgrid.utexas.edu

Grid Standards

The Globus Consortium: www.globusconsortium.com/index.html

Open Grid Forum: www.gridforum.org

The Enterprise Grid Requirements Research Group: forge.gridforum.org/projects/egr-rg

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Geographic Information Systems

There is a comprehensive list of links of interest to the GIS community at www.geo.ed.ac.uk/home/giswww.html .

A FAQ for LandView 6 from the Census Bureau is available at www.census.gov/geo/landview/lv6help/lv6_faq.html .

A beginner's guide is available at www.umich.edu/~ipcaa/GIS/Home.htm .

Another resource on GIS is www.compinfo.co.uk/cad/gis.htm .

Information on using GIS at Kelvin Smith Library at Case: library.case.edu/ksl/csgd

Visualization

Visualization of Complex Networks: www.visualcomplexity.com

Purdue University: www.envision.purdue.edu

University of Florida: invigo.acis.ufl.edu/docs/aboutInVigo.html

Data Visualization Research Lab at UNH: www.ccom.unh.edu/vislab

Visualization of Remote Sensing Data at NASA: rsd.gsfc.nasa.gov/rsd

Great Cities Urban Data Visualization Lab: www.uic.edu/cuppa/udv

OCLC Data Visualization Demo: www.resourceshelf.com/2005/01/12/demo-now-available-oclcs-data-visualization-pilot-with-antarctica-systems-inc/

Data Visualization at Sandia National Laboratories: www.cs.sandia.gov/analysis_visualization/

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Data Mining

University of Alabama at Huntsville : datamining.itsc.uah.edu

Microsoft Research: research.microsoft.com/dmx/DataMining/default.aspx

Statistics and Data Mining Research at Bell Labs: cm.bell-labs.com/cm/ms/departments/sia

NCBI Tools for Data Mining: www.ncbi.nlm.nih.gov/Tools

IBM Almaden Research Center : www.almaden.ibm.com/software/quest/index.shtml

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Software

Statistical and mathematical software

The R Project for Statistical Computing: www.r-project.org

Scientific computing with Python: www.python.org/moin/NumericAndScientific

SAS, SPSS, Mathematica, Matlab, Minitab, S-Plus, Origin, and MathType are all available at the Case Software Center : softwarecenter.case.edu

Please see help.case.edu/key/softwarecenter for more information on the Software Center , including information on statistical software licensing for UNIX, Linux, Solaris, etc.

Software for high performance clusters

Rocks Cluster Distribution: www.rocksclusters.org

The OpenScience project is dedicated to writing and releasing free and Open Source scientific software.

Cluster Resources: www.clusterresources.com/

Grid Software

The Globus Alliance : www.globus.org

Condor: www.cs.wisc.edu/condor

The GRIDS Center : www.grids-center.org

GridLab: www.gridlab.org

Open Grid Computing Environment: www.collab-ogce.org/nmi

Visualization Software

XGobi: www.research.att.com/areas/stat/xgobi

GGobi Data Visualization System: www.ggobi.org

Data visualization toolbox for Matlab: www.datatool.com

AVS Advanced Visual Systems: www.avs.com/index_wf.html

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