- 1
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OpenMP: A Proposed Standard API for Shared Memory Programming.
white paper, October 1997.
http://www.openmp.org/specs/mp-documents/paper/paper.ps cache: ../../archive/openmp-whitepaper.ps.gz.
- 2
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IPDPS 2000: 14th International Parallel and Distributed Processing
Symposium 1-5 May 2000 Cancun, Mexico: Proceedings. IEEE Computer Society,
August 2000.
ISBN: 0769505740,
http://ieeexplore.ieee.org/xpl/RecentCon.jsp?puNumber=6818.
http://www.ipdps.org/ipdps2000/ipdps2000.htm
- 3
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Multi-Threading in IDL.
white paper, 2001.
http://www.researchsystems.com/idl/mthread56.pdf cache: ../../archive/mthread56.pdf.
- 4
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Proceedings of the ACM/IEEE SC2003 Conference, Phoenix, Arizona, November
2003.
http://www.sc-conference.org/sc2003/tech_papers.php.
- 5
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Chapel Specification (version 0.4).
draft, February 2005.
http://chapel.cs.washington.edu/specification.pdf cache: ../../chapel_specification_0.4.pdf.
See the chapel website:
http://chapel.cs.washington.edu/
- 6
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David Abramson, Jon Giddy, and Lew Kotler.
High Performance Parametric Modeling with Nimrod/G:
Killer Application for the Global Grid?
[2], pages 520-528.
http://www.csse.monash.edu.au/~davida/papers/ipdps.pdf cache: ../../archive/ipdps.pdf.
Nimrod is a parametric modeling system, which uses
a declarative language to describe parametric experiments. Nimrod takes this
description and automates the running of various formulations of the
experiment, and collates the results. A scheduler distributes tasks to idle
cluster nodes. Shortcomings for the use of Nimrod on global grids include the
lack of dynamic discovery of resources, the lack of a user deadline notion,
the reliance on the standard UNIX security model, and the lack of support for
a wide range of access mechanisms/queue managers. The paper describes a new
version of Nimrod, named Nimrod/G which aims at overcoming these problems.
- 7
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David Abramson, Andrew Lewis, and Tom Peachey.
Nimrod/O: A Tool for Automatic Design Optimization.
In Goscinski et al. [81].
http://www.csse.monash.edu.au/~davida/papers/nimrodo.pdf cache: ../../archive/nimrodo.pdf.
Nimrod/O is a front-end which uses the Nimrod API,
adding support for non-exhaustive optimization algorithms.
- 8
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W. Allcock, J. Bester, J. Bresnahan, S. Meder, P. Plaszczak, and S. Tuecke.
GridFTP: Protocol Extensions to FTP for the Grid.
Technical Report GFD.20, Argonne National Laboratory, April 2003.
http://www.ggf.org/documents/GWD-R/GFD-R.020.pdf cache: ../../archive/GFD-R.020.pdf.
This document describes and defines the GridFTP
protocol, a file transfer protocol that aims to satisfy the specific
requirements of grid applications, which aren't met by standard protocols
(HTTP/FTP). As the name implies, GridFTP is an extension of FTP. Extensions
over standard FTP include secure authentication, parallel transfers (multiple
streams between the two endpoints of, communication), striped transfers
("many to many" streams of data transfer).
- 9
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Eric Allen, David Chase, Victor Luchangco, Jan-Willem Maessen, Sukyoung Ryu,
Guy L. Steele Jr., and Sam Tobin-Hochstadt.
The Fortress Language Specification.
Technical Report 0.618, Sun Microsystems, April 2005.
http://research.sun.com/projects/plrg/fortress0618.pdf cache: ../../archive/fortress0618.pdf.
- 10
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P.V. Artigas, M. Gupta, S.P. Midkiff, and J.E. Moreira.
High Performance Computing in Java: Language and Compiler
Issues.
Technical Report RC21482, IBM T.J. Watson Research Center, May 1999.
http://domino.watson.ibm.com/library/CyberDig.nsf/a3807c5b4823c53f85256561006324be/145d6feb247a35048525678600678a92?OpenDocument cache: ../../archive/RC21482.ps.gz.
IBM's implementation of efficient true
multi-dimensional arrays, with discussion of compiler techniques required to
retain this efficiency and also how to create exception-free regions of code
that can be heavily optimized. In four benchmarks this gives a large
improvement in efficiency compared to all other Java implementations.
- 11
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Calvin Austin.
J2SE 1.5 in a Nutshell.
Sun Developer Network, February 2004.
accessed wed 21/4/2004 11am,
http://java.sun.com/developer/technicalArticles/releases/j2se15/ cache: ../../archive/j2se_1.5_in_a_nutshell.html.
Examples of some of the new features in Java 1.5.
- 12
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John Baker, Carsten Gundlach, Ginny Hudak-David, Sai Iyer, Paul Lamping, Nancy
Tran, and Ed Seidel.
Cactus 4.0 Users' Guide.
Albert Einstein Institute, Max Planck Institute for Gravitational
Physics, revision 1.45 edition, January 2004.
http://www.cactuscode.org/Guides/Stable/UsersGuide/UsersGuideStable.ps cache: ../../archive/cactuscode_UsersGuideStable.ps.gz.
- 13
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Mark Baker, Rajkumar Buyya, and Domenico Laforenza.
The Grid: International Efforts in Global Computing.
In Proceedings of SSGRR 2000, August 2000.
http://www.cs.mu.oz.au/~raj/papers/TheGrid.pdf cache: ../../archive/TheGrid.pdf.
Introduction to Grid computing and some of the
various groups involved in the area.
- 14
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Mark Baker and Bryan Carpenter.
MPJ: A Proposed Java Message Passing API and
Environment for High Performance Computing.
In IPDPS Workshops, pages 552-559, 2000.
http://dsg.port.ac.uk/~mab/Papers/IPDPS00/Java/paper.ps cache: ../../archive/mpj_paper.ps.gz.
The authors of mpiJava describe their attempt at a
reference implementation of MPJ. Significant future work is expected to take
place in MPJ instead of mpiJava.
- 15
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Mark Baker, Bryan Carpenter, Geoffrey Fox, Sung Hoon Ko, and Sang Lim.
mpiJava: An Object-Oriented Java interface to MPI.
In International Workshop on Java for Parallel and Distributed
Computing, IPPS/SPDP, San Juan, Puerto Rico, April 1999.
http://www.hpjava.org/papers/ipps99/paper.ps cache: ../../archive/ipps99-paper.ps.
- 16
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Mark Baker, Bryan Carpenter, and Aamir Shafi.
MPJ: Enabling Parallel Simulations in Java.
Technical report, Distributed Systems Group, University of
Portsmouth, June 2005.
http://dsg.port.ac.uk/projects/mpj/docs/res/mpj-parsim.pdf cache: ../../archive/mpj-parsim.pdf.
- 17
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Mark A. Baker, Hong Ong, and Aamir Shafi.
A Status Report: Early Experiences with the implementation
of a Message Passing System using Java NIO.
Technical report, Distributed Systems Group, University of
Portsmouth, UK, October 2004.
http://dsg.port.ac.uk/~shafia/res/papers/DSG_2.pdf cache: ../../archive/DSG_2.pdf.
The reference MPJ implementation appears to be
relatively efficient- in the layers of the implementation that have been
completed, at least. MPJ is not ready for production use, at this stage.
- 18
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Henri Bal, Henri Casanova, Jack Dongarra, and Satoshi Matsuoka.
Application-Level Tools, chapter 24, pages 463-489.
In Foster and Kesselman [70], November 2003.
ISBN: 1-55860-933-4
http://books.elsevier.com/uk/mk/uk/subindex.asp?isbn=1558609334.
Grid application developers often do not like
working with grid middleware directly, and prefer higher level abstractions.
There is an obvious need for tools to suit these people (such as application
scientists) in order for them to make effective use of grid technologies.
This paper defines the requirements of these tools, and summarises existing
solutions that aim to achieve those requirements.
- 19
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David M. Beazley.
Advanced Python Programming.
In O'Reilly OSCON, July 2000.
http://systems.cs.uchicago.edu/~beazley/tutorial/beazley_advanced_python/advpy.pdf cache: ../../archive/advpy.pdf.
- 20
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Brett Beeson, David G. Barnes, and Paul D. Bourke.
A distributed-data implementation of the perspective shear-warp
volume rendering algorithm for visualisation of large astronomical cubes.
Publications of the Astronomical Society of Australia,
20(3):300-313, 2003.
http://www.publish.csiro.au/nid/139/issue/701.htm http://www.aus-vo.org/papertrail/papers/pasa.pdf cache: ../../archive/pasa.pdf.
The perspective shear-warp volume rendering
algorithm is implemented with distributed data on a beowulf cluster. Previous
distributed implementations of VR rely on all compute nodes having access to
the entire input dataset.
- 21
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Tom Bellwood, Luc Clément, David Ehnebuske, Andrew Hately, Maryann Hondo,
Yin Leng Husband, Karsten Januszewski, Sam Lee, Barbara McKee, Joel Munter,
and Claus von Riegen.
UDDI Version 3.0: UDDI Spec Technical Committee
Specification.
Technical report, OASIS, July 2002.
http://uddi.org/pubs/uddi-v3.00-published-20020719.htm cache: ../../archive/uddi-v3.00-published-20020719.htm http://uddi.org/pubs/uddi-v3.00-published-20020719.pdf cache: ../../archive/uddi-v3.00-published-20020719.pdf.
UDDI is a method for describing and finding web
service providers, web services and the technical interfaces for those
services.
- 22
-
Rob H. Bisseling.
Parallel Scientific Computation: A structured approach
using BSP and MPI.
Oxford University Press, 2004.
http://www.oup.co.uk/isbn/0-19-852939-2 ISBN: 0 19 852939 2.
Programming examples using both BSPlib and BSP
style MPI.
- 23
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Guy E. Blelloch.
NESL: A Nested Data-Parallel Language.
Technical Report CMU-CS-95-170, CMU, September 1995.
http://www-2.cs.cmu.edu/afs/cs.cmu.edu/project/scandal/public/papers/CMU-CS-95-170.ps.gz cache: ../../archive/CMU-CS-95-170.ps.gz.
- 24
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Guy E. Blelloch, Jonathan C. Hardwick, Jay Sipelstein, Marco Zagha, and
Siddhartha Chatterjee.
Implementation of a portable nested data-parallel language.
Journal of Parallel and Distributed Computing, 21(1):4-14,
1994.
http://citeseer.ist.psu.edu/blelloch94implementation.html cache: ../../archive/CMU-CS-93-112.ps.gz.
- 25
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Brian Blount and Siddhartha Chatterjee.
An Evaluation of Java for Numerical Computing.
In International Symposium on Computing in Object-oriented,
pages 35-46, 1998.
ftp://ftp.cs.unc.edu/pub/users/sc/papers/sp-java.pdf cache: ../../archive/sp-java.pdf.
Java is observed to be approaching traditional high
performance computing languages in terms of speed. Differences between using
primitive and programmer-defined types for complex numbers are quantified,
suggesting that a new primitive is needed.
- 26
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Blue Marsh Softworks.
JSwat 2.x Tutorial.
http://www.bluemarsh.com/java/jswat/docs/tutorial.html cache: ../../archive/jswat_tutorial.html.
- 27
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Gilad Bracha, Martin Odersky, David Stoutamire, and Philip Wadler.
Making the future safe for the past: Adding Genericity to the
Java Programming Language.
In 13th Annual ACM SIGPLAN Conference on
Object-Oriented Programming Systems, Languages, and Applications
(OOPSLA`98), October 1998.
http://homepages.inf.ed.ac.uk/wadler/gj/Documents/gj-oopsla-a4.ps.gz cache: ../../archive/gj-oopsla-a4.ps.gz.
GJ is a Java extesion providing generic types and
methods. This is now a part of Java itself as of version 1.5.0 aka Java2 5.0.
The implementation described is applied by translating from the
extended language to standard Java, making it trivial to mix GJ code with
regular Java code.
- 28
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Silvia Breitinger, Rita Loogen, Yolanda Ortega-Mallén, and Ricardo Peña.
Eden - Language Definition and Operational Semantics.
Technical Report 96-10, Reihe Informatik, Fachbereich Mathematik und
Informatik, Philipps Universität Marburg, 1998.
http://www.mathematik.uni-marburg.de/~eden/paper/edenReport98.ps cache: ../../archive/edenReport98.ps.gz.
- 29
-
J. M. Bull and M. E. Kambites.
JOMP an OpenMP-like interface for Java.
In Proceedings of the ACM 2000 conference on Java Grande, pages
44-53, June 2000.
ISBN: 1-58113-288-3
http://portal.acm.org/citation.cfm?id=337466.
- 30
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Mark Burgess.
Cluster Management with GNU cfengine.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 4(1), Fall 2002.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-4-1-burgess.shtml cache: ../../archive/cfengine.html.
A cluster management system for configuring and
maintaining distributed systems.
- 31
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William Joseph Butera.
Programming a Paintable Computer.
PhD thesis, Media Arts and Sciences, School of Architecture and
Planning, February 2002.
http://www.swiss.ai.mit.edu/projects/amorphous/papers/butera-phd.pdf cache: ../../archive/butera-phd.pdf.
- 32
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Rajkumar Buyya, Kim Branson, Jon Giddy, and David Abramson.
The Virtual Laboratory: Enabling On Demand Drug
Design with the Worldwide Grid.
Concurrency and Computation: Practice and Experience,
15(1):1-25, January 2003.
http://www3.interscience.wiley.com/cgi-bin/jissue/102522535 http://www.csse.monash.edu.au/~davida/papers/vlab-drug-design.pdf cache: ../../archive/vlab-drug-design.pdf.
Nimrod/G is applied to molecular modeling for drug
design, a task which is both data and compute intensive. Fortunately, this
task has a high computation : communication ratio, making it suitable for
distributed grid-like systems. A program is written that takes a molecule as
input (the parameter), and searching for ways it might bind easily to another
molecule. A declarative "plan file" describes how the parameter varies, and
a computational broker decides to outsource versions of the computation with
different parameter values. The grid service providers that execute this
computation contact a database broker to find out where to get a copy of the
input molecule they require (dynamic data discovery [6]). The
compute node then performs the computation and resturns the result to the
computation broker, which tallies up the results.
- 33
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Rajkumar Buyya and Srikumar Venugopal.
Gridbus: A toolkit for service-oriented grid computing.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 4(2), Spring 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-4-2-buyya.shtml cache: ../../archive/gridbus.html.
Gridbus is an open-source framework that aids
support of distributed computational economies.
- 34
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L.W. Cannon, R.A. Elliott, L.W. Kirchhoff, J.H. Miller, J.M. Milner, R.W.
Mitze, E.P. Schan, N.O. Whittington, Henry Spencer, David Keppel, and Mark
Brader.
Indian Hill C Style and Coding Standards, volume Revision: 6.0.
1990.
http://www.psgd.org/paul/docs/cstyle/cstyle.htm cache: ../../archive/indhill-cstyle.pdf.
- 35
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Bryan Carpenter, Geoffrey Fox, Sung Hoon Ko, and Sang Lim.
Object Serialization for Marshalling Data in a Java
Interface to MPI.
In Java Grande, pages 66-71, 1999.
http://citeseer.ist.psu.edu/article/carpenter99object.html cache: ../../archive/carpenter99object.ps.gz.
- 36
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Bryan Carpenter, Vladimir Getov, Glenn Judd, Tony Skjellum, and Geoffrey Fox.
MPI for Java - Position Document and Draft API
Specification.
Technical Report JGF-TR-03, Java Grande Forum, November 1998.
http://www.hpjava.org/reports/MPIposition/position.ps cache: ../../archive/position.ps.gz.
mpiJava is an (unofficial) MPI binding for Java,
which follows the style of the official C++ MPI 2.0 binding. It uses JNI to
interface with a native MPI installation (typically MPICH).
- 37
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Bryan Carpenter, Vladimir Getov, Glenn Judd, Tony Skjellum, and Geoffrey Fox.
MPJ: MPI-like Message Passing for Java.
Concurrency: Practice and Experience, 12(11):1019-1038,
September 2000.
http://www.hpjava.org/papers/MPJ-CPE/cpempi.ps cache: ../../archive/cpempi.ps.gz.
Begins with a summary of a number of Java MPI
bindings (or approximations), and describes the Java Grande Message Passing
working group's standardised MPI-like binding- named MPJ.
http://dsg.port.ac.uk/projects/mpj/
- 38
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Bryan Carpenter, Guansong Zhang, Geoffrey Fox, Xiaoming Li, Xinying Li, and
Yuhong Wen.
Towards a Java Environment for SPMD Programming.
Volume 1470 of Pritchard and Reeve [128], September 1998.
http://www.hpjava.org/papers/europar98/europar.ps cache: ../../archive/europar.ps.gz.
This paper suggests steps towards a high
performance Java, with some similar characteristics high performance fortran
(HPF). True multidimensional arrays are added as new language primitives to
Java, distinct from regular Java arrays. Distributed arrays are defined as
multidimensional arrays with one or more dimensions declared to be
distributed. with explicit non-local communication. This is justified as
encouraging the programmer to write algorithms that exploit locality. This
reduces the effort of the compiler writer, while increasing the effort of the
programmer.
- 39
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Bryan Carpenter, Guansong Zhang, Geoffrey Fox, Yuhong Wen, and Xinying Li.
Hpjava: data parallel extensions to Java, December 1997.
http://www.npac.syr.edu/projects/pcrc/doc/DOC/Java/Java98.ps cache: ../../archive/Java98.ps.
- 40
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Brad Chamberlain.
An Introduction to Chapel: Cray Cascade's
High-Productivity Language.
In AHPCRC/DARPA PGAS Conference, September 2005.
http://chapel.cs.washington.edu/ChapelForAHPCRC.pdf cache: ../../ChapelForAHPCRC.pdf.
- 41
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Bradford L. Chamberlain.
The Design and Implementation of a Region-Based Parallel
Programming Language.
PhD thesis, University of Washington, November 2001.
http://www.cs.washington.edu/research/zpl/papers/data/Chamberlain01Design.pdf http://www.cs.washington.edu/research/zpl/papers/data/Chamberlain01Design.ps cache: ../../archive/Chamberlain01Design.pdf.
A detailed look at the difficulties of producing
programs for parallel computation, and at the design decisions made in ZPL-
an array programming language. The basis of the design is the concept of
"regions"- a set of indices over which data is mapped. The data itself may
be mapped over a set of processor nodes, producing a parallel interpretation
of a program.
The rules for the distribution of regions begin on page
112.
The syntax is similar to Modula-2, with justification being that
it may be beneficial for C/Fortran users to learn the language from scratch
so that they're less likely to write ZPL programs in a sequential style
they're familiar with (page 29).
ZPL
homepage: http://www.cs.washington.edu/research/zpl/home/index.html
- 42
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Bradford L. Chamberlain, Sung-Eun Choi, E Christopher Lewis, Calvin Lin,
Lawrence Snyder, and W. Derrick Weathersby.
ZPL's WYSIWYG Performance Model.
In Proceedings of the IEEE Workshop on High-Level Parallel
Programming Models and Supportive Environments, page 50. IEEE Computer
Society, 1998.
http://www.cs.washington.edu/homes/brad/cv/pubs/reports/tr971202.pdf cache: ../../archive/tr971202.pdf, ISBN: 0-8186-8412-7.
Third International Workshop on High-Level Parallel
Programming Models and Supportive Environments (HIPS'98) website:
http://ipdps.eece.unm.edu/1998/hips/ http://portal.acm.org/citation.cfm?id=822265,
- 43
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Bradford L. Chamberlain, Sung-Eun Choi, E. Christopher Lewis, Calvin Lin,
Lawrence Snyder, and W. Derrick Weathersby.
ZPL: A Machine Independent Programming Language for
Parallel Computers.
IEEE Transactions on Software Engineering, 26(3):197-211,
March 2000.
http://csdl.computer.org/comp/trans/ts/2000/03/e0197abs.htm cache: ../../archive/tse99.pdf.
This paper describes the "CTA" abstract parallel
machine model used by ZPL, the concept of Regions, and gives some benchmarks
suggesting that it is efficient and portable.
- 44
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Philip Chan and David Abramson.
NetFiles: A Novel Approach to Parallel Programming of
Master/Worker Applications.
In Proc. of the 5th International Conference and Exhibition on
High-Performance Computing in the Asia-Pacific Region (HPCAsia 2001),
September 2001.
http://www.griffith.edu.au/conference/hpcasia2001/ http://www.csse.monash.edu.au/~pchan/cgi-bin/get.py.cgi?name=hpcasia2001&inc=1&fname=n&p=pubs-data cache: ../../archive/hpcasia2001.pdf.
- 45
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Siddhartha Chatterjee.
Compiling Nested Data-Parallel Programs for
Shared-Memory Multiprocessors.
ACM Transactions on Programming Languages and Systems,
15(3):400-462, July 1993.
ftp://ftp.cs.unc.edu/pub/users/sc/papers/toplas-vcode.pdf cache: ../../archive/toplas-vcode.pdf.
- 46
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James Cheetham, Frank Dehne, Sylvain Pitre, Andrew Rau-Chaplin, and Peter J.
Taillon.
Parallel CLUSTAL W for PC Clusters.
In Vipin Kumar, Marina L. Gavrilova, C.J. Kenneth Tan, and Pierre
L'Ecuyer, editors, Proceedings of the International Conference on
Computational Science and Its Applications (ICCSA 2003), pages 300-309,
Montreal, Canada, May 2003. Springer-Verlag.
http://132.234.86.15/www/research/cgm-lab/software/clustalxp/paper1.pdf cache: ../../archive/pclustal.pdf.
pCLUSTAL is a parallel implementation of CLUSTAL W,
an algorithm for highlighting similar arrangements of two or more sequences
(used in biological sciences to study evolution of proten/DNA sequences).
- 47
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Ming Chen, Guangwen Yang, and Xuezheng Liu.
Gridmarket: A Practical, Efficient Market Balancing
Resource for Grid and P2P Computing.
In Li et al. [110], pages 612-619.
http://www.springerlink.com/link.asp?id=xgjmmcecr6kqctpc cache: https://bubble.csse.monash.edu.au/archive/lncs3033/p612-619.pdf.
An economic model of computational grids is
suggested, as this may be a good model for cooperative systems which are
based on the "fickle concept of goodwill". A double
auction is used, mimicking the process used by many stock markets (NASDAQ,
Shanghai Stock Exchange, Shenzhen Stock Exchange).
- 48
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Ron Choy.
Parallel Matlab survey.
WWW, October 2003.
http://supertech.lcs.mit.edu/~cly/survey.html cache: ../../archive/parallel_matlab_survey.html.
- 49
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Ron Choy and Alan Edelman.
Parallel MATLAB: Doing it Right.
http://www-math.mit.edu/~edelman/homepage/papers/pmatlab.pdf cache: ../../archive/pmatlab.pdf, November 2003.
- 50
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Erik Christensen, Francisco Curbera, Greg Meredith, and Sanjiva Weerawarana.
Web Services Description Language (WSDL) 1.1.
Technical report, World Wide Web Consortium (W3C), March 2001.
http://www.w3.org/TR/2001/NOTE-wsdl-20010315 cache: ../../archive/NOTE-wsdl-20010315.htm.
WSDL is an attempt to standardize the documentation
of web-based communication protocols and message formats.
- 51
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Michael Philippsen Christian Nester and Bernhard Haumacher.
A More Efficient RMI for Java.
In Proceedings of the ACM 1999 Conference on Java Grande, pages
152-159, San Francisco, June 1999. ACM Press.
ISBN: 1-58113-161-5
http://portal.acm.org/citation.cfm?doid=304065.304117 cache: ../../archive/p103.pdf.
Java's RMI was designed for wide-area high-latency
networks. This paper presents a drop-in replacement, KaRMI, which is much
faster, and also written in pure Java.
- 52
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editor Claus Reinke.
Haskell Communities and Activities Report.
Technical Report 5, http://www.haskell.org/communities/,
November 2003.
http://www.haskell.org/communities/11-2003/html/report.html.
- 53
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Bernard Daines.
Cluster Opinion: The Ethernet Opportunity for Linux
Clusters.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 5(2), September/October 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-5-2-daines.shtml cache: ../../archive/new_ethernet.html.
Comments on the need for high throughput, low
latency cluster interconnects based upon open standards, in order for Linux
clusters to become more useful in the enterprise and high availability areas.
- 54
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Frank Dehne, Andreas Fabri, and Andrew Rau-Chaplin.
Scalable Parallel Geometric Algorithms for Coarse Grained
Multicomputers.
In Proceedings of the ACM Symposium on Computational Geometry,
pages 298-307, 1993.
http://132.234.86.15/www/publications/publ/2-36/paper.pdf cache: ../../archive/paper93.pdf.
This paper studies the design of algorithms for the
Coarse Grained Multicomputer ("CGM") model for parallel computation. In
this model, the multicomputer contains p processors, each with
local memory, connected by an arbitrary network and
is assumed to be large, ie . This model is said to
accurately compare with real-world parallel machines.
- 55
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Dr. Charles R. Denham.
Macintosh Matlab Survival Toolkit.
WWW, June 2004.
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/snackbar/mac-matlab-survival.html cache: ../../archive/mac-matlab-survival.html.
- 56
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Bill Devlin, Jim Gray, Bill Laing, and George Spix.
Farms, clones, partitions, packs, RACS, and RAPS Improve your
scalability vocabulary.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 4(1), Fall 2002.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-4-1-gray.shtml cache: ../../archive/vocab.html.
Definitions for common terms and phrases in
relation to highly scalable computer systems.
- 57
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Ellie D'Hondt.
Exploring the Amorphous Computing Paradigm.
Master's thesis, Vrije Universiteit Brussel, Faculteit van de
Wetenschappen, Departement Informatica, August 2000.
http://www.vub.ac.be/CLEA/ellie/homepage/PDFdirectory/thesisAmorphous.pdf cache: ../../archive/thesisAmorphous.pdf.
Amorphous computing is a new programming paradigm
which aims to be useful for systems with enormous numbers of small units of
computation with limited power. This masters thesis classifies existing
amorphous algorithms, hardware implementations (and simulations thereof),
gives an overview of the Growing Point Language (GPL), and finally introduces
some amorphous solutions to computational geometry problems.
- 58
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Satheesh A. Donthy.
Java Tip 56: How to eliminate debugging problems for
RMI-based applications.
WWW, July 1998.
http://www.javaworld.com/javaworld/javatips/jw-javatip56.html cache: ../../archive/rmi_debugging/jw-javatip56.html.
- 59
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Sean Dorward, Rob Pike, David Leo Presotto, Dennis Ritchie, Howard Trickey, and
Phil Winterbottom.
Inferno.
In Proceedings of COMPCON 97, pages 241-244. Bell Labs -
Lucent Technologies, February 1997.
http://www.vitanuova.com/inferno/papers/hotchips.html cache: ../../archive/00584718.pdf.
Overview of the Inferno operating system, a
descendant of Plan 9 and Unix. It is capable of running as a user application
in a range of host operating systems, or as a standalone operating system.
Inferno applications (written in a language named Limbo) are capable of
running on any of these systems without modification, by way of a virtual
machine. The Styx communication protocol allows remote resources to be
accessed as though they were local, making distributed computing easier.
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Sean Dorward, Rob Pike, and Phil Winterbottom.
Programming in Limbo.
In Proceedings of COMPCON 97, pages 245-250. Bell Labs -
Lucent Technologies, February 1997.
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Limbo is the application programming language for
the Inferno operating system. It uses a C-like syntax, but contains many
features that make it safer and easier to use in distributed/heterogeneous
environments. These include garbage collection, concurrency, and modules.
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Wei Du, Renato Ferreira, and Gagan Agrawal.
Compiler Support for Exploiting Coarse-Grained Pipelined
Parallelism.
[4].
http://www.sc-conference.org/sc2003/paperpdfs/pap133.pdf cache: ../../archive/pap133.pdf.
This paper proposes a pipeline model for grid
computation: the first stage involves the site hosting the input data, the
last stage involves the user's local machine (where results are to be
examined), normally other nodes will house intermediate stages.
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Scott Farrand.
The Case for Blades in High-Performance Computing.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 5(3), November/December 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-5-3-farrand.shtml cache: ../../archive/blade.html.
An argument for the use of blade server clusters
(multiple compute nodes living in a single enclosure) in high performance
cluster computing.
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Donal K. Fellows.
Getting Java RMI Working.
WWW, September 2004.
http://www.cs.man.ac.uk/~fellowsd/work/usingRMI.html cache: ../../archive/rmi_debugging/usingRMI.html.
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David Flanagan.
Java in a Nutshell.
O'Reilly, third edition, November 1999.
ISBN: 1-56592-487-8 http://www.oreilly.com/catalog/javanut3/.
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David Flanagan.
Java in a Nutshell, chapter 4, pages 149-152.
In [64], third edition, November 1999.
ISBN: 1-56592-487-8 http://www.oreilly.com/catalog/javanut3/.
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Message Passing Interface Forum.
MPI: A Message-Passing Interface Standard, June 1995.
http://www.mpi-forum.org/docs/mpi-11.ps.Z cache: ../../archive/mpi-11.ps.Z.
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Message Passing Interface Forum.
MPI-2: Extensions to the Message-Passing Interface, July
1997.
http://www.mpi-forum.org/docs/mpi-20.ps.Z cache: ../../archive/mpi-20.ps.Z.
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Ian Foster.
The Grid: A New Infrastructure for 21st Century Science.
Physics Today, 55, February 2002.
http://www.physicstoday.org/vol-55/iss-2/p42.html cache: ../../archive/ian_foster-aip_today.html.
Brief introduction to Grid computing- a scalable,
secure, high-performance infrastructure for utilizing global resources.
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Ian Foster and Tom Garritano.
The GRIDS software suite: Toward a national middleware
infrastructure.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 4(2), Spring 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-4-2-foster.shtml cache: ../../archive/grids_software_suite.html.
Overview of the GRIDS software suite, which
includes Globus (de facto standard for grid computing), Condor-G (software
for managing "high throughput computing", for enabling high processing
capacity over extended periods of time), the Network Weather Service (NWS for
short, used for monitoring and forecasting performance of network and
computational resources) and KX.509. New inclusions are GSI-OpenSSH (a
version of OpenSSH with support for Grid Services Infrastructure
authentication), Grid Packaging Tools (GPT for short, is a collection of
packaging tools for software packages, using an XML data format) and
GridConfig (tools for managing GRIDS software components).
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Ian Foster and Carl Kesselman, editors.
The Grid 2: Blueprint for a New Computing Infrastructure.
Morgan Kaufmann Publishers, November 2003.
ISBN: 1-55860-933-4
http://books.elsevier.com/uk/mk/uk/subindex.asp?isbn=1558609334.
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Ian Foster, Carl Kesselman, Jeffry M. Nick, and Steven Tuecke.
The Physiology of the Grid.
June 2002.
Draft document, last modified: 22/6/2002.
http://www.globus.org/research/papers/ogsa.pdf cache: ../../archive/ogsa-physiology.pdf.
Succesor to the "Anatomy of the grid"
[72].
(Summary:
http://carol.science.uva.nl/~zegerh/globus/OGSAsummary.html cache: ../../archive/OGSAsummary.html)
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Ian Foster, Carl Kesselman, and Steven Tuecke.
The Anatomy of the Grid: Enabling Scalable Virtual
Organizations.
Lecture Notes in Computer Science, 2150, 2001.
http://citeseer.ist.psu.edu/foster01anatomy.html cache: ../../archive/grid-anatomy.pdf.
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Ian Foster and Steven Tuecke.
Enabling Technologies for Web-Based Ubiquitous
Supercomputing.
In Proceedings of the 5th IEEE Symp. on High Performance
Distributed Computing, (to appear).
ftp://ftp.mcs.anl.gov/pub/nexus/reports/hpdc_java.ps.gz cache: ../../archive/hpdc_java.ps.gz.
Nexus is a communications library for asynchronous
communicatoin, multithreading and dynamic resource management in
heterogeneous (grid?) environments. A java binding, NexusJava has been
written.
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Geoffrey C. Fox, editor.
Concurrency and Computation: Practice and Experience. Special
Issue: ACM 2001 Java Grande-ISCOPE (JGI2001) Conference, volume 15 of Concurrency and Computation: Practice and Experience.
Wiley InterScience, 2003.
http://www3.interscience.wiley.com/cgi-bin/jissue/102530974.
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Edgar Gabriel, Graham E. Fagg, George Bosilca, Thara Angskun, Jack J. Dongarra,
Jeffrey M. Squyres, Vishal Sahay, Prabhanjan Kambadur, Brian Barrett, Andrew
Lumsdaine, Ralph H. Castain, David J. Daniel, Richard L. Graham, and
Timothy S. Woodall.
Open MPI: Goals, Concept, and Design of a Next
Generation MPI Implementation.
In 11th European PVM/MPI Users' Group Meeting, pages 97-104,
Budapest, Hungary, September 2004.
http://www.open-mpi.org/papers/euro-pvmmpi-2004-overview/euro-pvmmpi-2004-overview.pdf cache: ../../archive/euro-pvmmpi-2004-overview/euro-pvmmpi-2004-overview.pdf.
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G.A. Geist, J.A. Kohl, and P.M. Papadopoulos.
PVM and MPI: A Comparison of Features.
Calculateurs Paralleles, 8(2), May 1996.
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Vladimir Getov, Susan Flynn-Hummel, and Sava Mintchev.
High-Performance Parallel Programming in Java: Exploiting
Native Libraries.
Concurrency: Practice and Experience, 10(11-13):863-872,
1998.
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This paper describes the issues in binding native
libraries to Java, and introduce a tool for generating C interface code,
named JCI. JCI reads C header files and produces the code necessary to call
this code from Java. It has been successfully used to create binding for MPI,
with over 120 functions.
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Vladimir Getov, Paul Gray, and Vaidy Sunderam.
MPI and Java-MPI: Contrasts and Comparisons of Low-Level
Communication Performance.
In Proceedings of the 1999 ACM/IEEE conference on
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Sushant Goel, Hema Sharda, and David Taniar.
Preserving Data Consistency in Grid Databases with Multiple
Transactions.
In Li et al. [110], pages 847-854.
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Papers presented at the 2nd International Workshop
on Grid and Cooperative Computing, GCC 2003, held in Shanghai, P.R. China.
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Tom Goodale, Gabrielle Allen, Gerd Lanfermann, Joan Masso, Thomas Radke, Edward
Seidel, and John Shalf.
The Cactus Framework and Toolkit: Design and Applications.
In J.M.L.M. Palma, J. Dongarra, V. Hernández, and A. Augusto Sousa,
editors, High Performance Computing for Computational Science - VECPAR
2002: 5th International Conference, Porto, Portugal, June 26-28, 2002.
Selected Papers and Invited Talks, pages 197-227. Springer-Verlag
Heidelberg, 2003.
http://springerlink.metapress.com/app/home/issue.asp?wasp=012cyjuhwq3ju2rlfray&referrer=parent&backto=journal,755,1867;linkingpublicationresults,1:105633,1.
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Andezej Goscinski, Horace H.S. Ip, Weijia Jia, and Wanlei Zhou, editors.
International Conference on Algorithms & Architectures for
Parallel Processing, Hong Kong, December 2000. World Scientific Publishing
Company, Inc.
http://www.cs.cityu.edu.hk/~ica3pp2k/ ISBN: 981-02-4481-9.
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James Gosling and Henry McGilton.
The Java Language Environment.
White Paper, May 1996.
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Introduction to Java, mentions design goals, and
asserts that Java performs better than other languages with similar
capabilities (smalltalk, perl).
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Richard L. Graham, Timothy S. Woodall, and Jeffrey M. Squyres.
Open MPI: A Flexible High Performance MPI.
In Proceedings, 6th Annual International Conference on Parallel
Processing and Applied Mathematics, Poznan, Poland, September 2005.
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Jim Gray.
Distributed Computing Economics.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 5(1), July/August 2003.
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This article compares the relative cost of various
computing resources, and suggests what types of computation are viable and
desirable for grid computing, and other situations such as cluster computing.
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Perry Greenfield, Jay Todd Miller, Jin chung Hsu, and Richard L. White.
numarray: A New Scientific Array Package for Python.
In PyCon DC2003, 2003.
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One method of allowing interpreted languages such
as python to operate efficiently on large sets of data is to allow array
programming operations, which typically executed by efficient libraries.
(Matlab and IDL are well known examples of this). The numarray package for
python is a replacement for the old numeric package.
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William Gropp, Ewing Lusk, Nathan Doss, and Anthony Skjellum.
A High-Performance, Portable Implementation of the MPI
Message Passing Interface Standard.
Parallel Computing, 22(6):789-828, September 1996.
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William Gropp, Ewing Lusk, and Anthony Skjellum.
Using MPI: Portable Parallel Programming with the
Message-Passing Interface.
MIT Press, second edition, 1999.
ISBN: 0-262-57134-3.
An introduction to the message-passing model of
parallel computation, and MPI- the most widely used instance of this model.
Some features of MPI-2 are included, MPI datatypes and collective operations.
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William Gropp, Ewing Lusk, and Rajeev Thakur.
Using MPI-2: Advanced Features of the Message-Passing
Interface.
Scientific and Engineering Computation. MIT Press, November 1999.
ISBN: 0-262-57133-1.
Following on from [87], this book
covers the extensions to MPI-1.
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William D. Gropp and Ewing Lusk.
User's Guide for mpich, a Portable Implementation of
MPI.
Mathematics and Computer Science Division, Argonne National
Laboratory, 1996.
ANL-96/6
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W. Gu, N.A. Burns, M.T. Collins, and W.Y.P. Wong.
The evolution of a high-performing Java virtual machine.
IBM Systems Journal, 39(1):135-150, 2000.
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How IBM identified and eliminated or minimized
various bottlenecks present in early JVM's.
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Duane Hanselman and Bruce Littlefield.
Mastering MATLAB 7.
Pearson/Prentice Hall, 2005.
ISBN: 0-13-143018-1 http://www.eece.maine.edu/mm/mm7.html.
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Yasushi Hayashi.
Shape-based Cost Analysis of Skeletal Parallel
Programs.
PhD thesis, Institute for Computing Systems Architecture, Division of
Informatics, University of Edinburgh, 2001.
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Janice J. Heiss.
New Language Features for Ease of Development in the Java 2
Platform, Standard Edition 1.5: A Conversation with Joshua Bloch.
Sun Developer Network, May 2003.
accessed wed 21/4/2004 11am,
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Simple examples of the new features in Java 1.5.
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H. Hellerman.
Experimental Personalized Array Translator System.
Communications of the ACM, 7(7):433-438, July 1964.
ISSN: 0001-0782
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PAT was the first implementation of Iverson's
programming notation [99].
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Johnathan M.D. Hill, Bill McColl, Dan C. Stefanescu, Mark W. Goudreau, Kevin
Lang, Satish B. Rao, Torsten Suel, Thanasis Tsantilas, and Rob Bisseling.
BSPlib - The BSP Programming Library.
Technical Report TR-29-97, Oxford University Computing Laboratory,
Programming Research Group, May 1997.
ftp://ftp.comlab.ox.ac.uk/pub/Documents/techreports/TR-29-97.ps.Z cache: ../../archive/TR-29-97.ps.Z.
Examples of how to use BSPlib.
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W. Daniel Hillis and Guy L. Steele Jr.
Data Parallel Algorithms.
Communications of the ACM, 29(12):1170-1183, December 1986.
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Examples of fine-grained algorithms written in a
data parallel style suitable for parallel machines with large numbers of
processors (thousands or even millions- the Connection Machine architecture
in particular).
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John Hunt.
Smalltalk and Object Orientation: an Introduction.
Springer-Verlag, 1997.
ISBN: 3-540-76115-2
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Link: Stéphane Ducasse's free online smalltalk
books, http://www.iam.unibe.ch/~ducasse/FreeBooks.html
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Atshushi Igarashi, Benjamin Pierce, and Philip Wadler.
Featherweight Java: A Minimal Core Calculus for Java
and GJ.
In Loren Meissner, editor, Proceedings of the 1999 ACM
SIGPLAN Conference on Object-Oriented Programming, Systems, Languages &
Applications (OOPSLA`99), pages 132-146.
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Featherweight Java is a cut-down version of the
Java language, with features removed to make reasoning about key properties
easier. (The relationship to Java is like that between lambda calculus and
practical functional programming languages.) By starting with such a small
model, it may be possible (hopefully simple) to form a model of an extension
to java.
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Kenneth E. Iverson.
A Programming Language.
John Wiley & Sons, New York, January 1962.
ISBN: 0471430145.
This programming notation allowed arrays to be
specified as operands to functions and other operations, and is the ancestor
of programming languages such as Matlab and IDL.
The APL language,
which was based upon this notation was implemented by IBM in the 60's.
This book is available at the melbourne uni maths library, call number
001.6424 Iv3.
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C. Barry Jay.
Shape Analysis for Parallel Computing.
In International Parallel Computing Workshop, pages 287-295,
September 1995.
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Sheng Jiang, Piers O'Hanlon, and Peter Kirstein.
Moving Grid Systems into the IPv6 Era.
In Li et al. [110], pages 490-499.
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Notes on porting GT3 (Globus Toolkit 3) to use
IPv6, which is set to replace the (now quite old) IPv4. Potential advantages
of the use of IPv6 are mentioned, three of these are examined in detail: the
increase of available address space, support for mobile computer systems, and
network-layer security. A walkthrough for setting up an IPv6 environment on
Linux systems (chosen since GT3 is currently only fully supported in Linux)
is given, followed by a guide for porting GT3 to make use of IPv6 instead of
IPv4.
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Simon Peyton Jones, editor.
Haskell 98 language and libraries: the Revised Report.
Cambridge University Press, April 2003.
ISBN: 0521826144,
http://titles.cambridge.org/catalogue.asp?isbn=0521826144.
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Zoltan Juhasz.
JGrid: Jini as a Grid Technology.
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 5(3), November/December 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-5-3-juhasz.shtml cache: ../../archive/jgrid.html.
An investigation of the use of Jini and the JGrid
project as a potential infrastructure for future grids.
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Nicholas T. Karonis, Brian Toonen, and Ian Foster.
MPICH-G2: A Grid-Enabled Implementation of the Message
Passing Interface.
Journal of Parallel and Distributed Computing, 63(5):551-563,
November 2002.
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Ken Kennedy.
Languages, Compilers, and Run-Time Systems, chapter 25, pages
491-512.
In Foster and Kesselman [70], November 2003.
ISBN: 1-55860-933-4
http://books.elsevier.com/uk/mk/uk/subindex.asp?isbn=1558609334.
This paper explores the use of application
development tools and libraries for use on the grid, beginning with software
originally designed for clusters and parallel computers.
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Han-Ku Lee.
Towards Efficient Compilation of the HPJava Language
for High Performance Computing.
PhD thesis, Florida State University, June 2003.
http://www.hpjava.org/theses/hkl/dissertation/dissertation.pdf cache: ../../archive/hkl-dissertation.pdf.
This thesis introduces the HPspmd programming
model, which is a mix of HPF style data-parallel features with the SPMD
style.
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Paul Leszek.
Debugging with the Eclipse Platform.
WWW, May 2003.
http://www-106.ibm.com/developerworks/java/library/os-ecbug/ cache: http://../../archive/Debugging_with_the_Eclipse_Platform.htm.
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Kuo-Bin Li.
ClustalW-MPI: ClustalW Analysis Using Distributed and
Parallel Computing.
Bioinformatics, 19(12):1585-1586, 2003.
http://bioinformatics.oupjournals.org/cgi/content/abstract/19/12/1585?ijkey=12ACOyqyrKpFz&keytype=ref cache: ../../archive/1585.pdf.
ClustalW is a tool for aligning multiple protein or
nucleotide sequences. ClustalW-MPI is a distributed and parallel
implementation of ClustalW.
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Minglu Li, Xian-He Sun, Qianni Deng, and Jun Ni, editors.
Grid and Cooperative Computing: Second International Workshop,
GCC 2003, Shanghai, China, December 7-10, 2003, Revised Papers, Part 1,
volume 3032 of Lecture Notes in Computer Science.
Springer-Verlag, 2004.
ISBN: 3-540-21988-9.
http://www.springerlink.com.ezproxy.lib.monash.edu.au/openurl.asp?genre=issue&issn=0302-9743&volume=3032 cache: https://bubble.csse.monash.edu.au/archive/lncs3032/.
Papers presented at the 2nd International Workshop
on Grid and Cooperative Computing, GCC 2003, held in Shanghai, P.R. China.
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Minglu Li, Xian-He Sun, Qianni Deng, and Jun Ni, editors.
Grid and Cooperative Computing: Second International Workshop,
GCC 2003, Shanghai, China, December 7-10, 2003, Revised Papers, Part 2,
volume 3033 of Lecture Notes in Computer Science.
Springer-Verlag, 2004.
ISBN: 3-540-21993-5.
http://www.springerlink.com.ezproxy.lib.monash.edu.au/openurl.asp?genre=issue&issn=0302-9743&volume=3033 cache: https://bubble.csse.monash.edu.au/archive/lncs3033/.
Papers presented at the 2nd International Workshop
on Grid and Cooperative Computing, GCC 2003, held in Shanghai, P.R. China.
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Hans-Wolfgang Loidl and Philip W. Trinder.
A Gentle Introduction to GPH.
Department of Computing and Electrical Engineering, Heriot-Watt
University, July 2001.
http://www.macs.hw.ac.uk/~dsg/gph/docs/Gentle-GPH/gph-gentle-intro.html.
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Daniel Lyons.
Linux Rules Supercomputers.
Forbes.com, March 2005.
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Linux is used by approximately 60top500 list.
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J. Maassen and R. van Nieuwpoort.
Fast Parallel Java.
Master's thesis, Vrije Universiteit, Amsterdam, August 1998.
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Jason Maassen, Rob van Nieuwpoort, Ronald Veldema, Henri E. Bal, and Aske
Plaat.
An Efficient Implementation of Java's Remote Method
Invocation.
In Proc. Seventh ACM SIGPLAN Symposium on Principles and
Practice of Parallel Programming (PPoPP'99), pages 173-182, Atlanta, GA,
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Igor Mandrichenko.
GridFTP Protocol Improvements.
Technical Report GFD-E.021, Integrated Systems Development
Department, Computing Division, Fermi National Accelerator Laboratory, July
2003.
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List of suggested improvements to GridFTP, based
upon the experience of various groups who have implemented GridFTP.
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Dana Mastrovito.
MPIDL Overview.
Princeton Plasma Physics Laboratory, January 2003.
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Vijay Menon and Anne E. Trefethen.
MultiMATLAB: Integrating MATLAB with High-Performance
Parallel Computing.
In Proceedings of the 1997 ACM/IEEE conference on
Supercomputing, pages 1-18, San Jose, California, 1997.
ISBN: 0-89791-985-8
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MultiMATLAB is a system for binding together
multiple Matlab processes via MEX compiled code and a native MPI library.
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P. Miller.
Parallel, Distributed Scripting with Python.
Technical Report UCRL-JC-148522, Lawrence Livermore National
Laboratory, 2002.
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Robin Milner, Mads Tofte, and Robert Harper.
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Cleve Moler.
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J. E. Moreira, S. P. Midkiff, M. Gupta, P. V. Artigas, M. Snir, and R. D.
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Pat Morin.
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The CGM model extended to heterogeneous systems-
HCGM.
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Steven Morin, Israel Koren, and C. Mani Krishna.
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JMPI is a native Java MPI implementation, that uses
RMI for low-level communication (ether Sun's RMI or KaRMI, a third-party RMI
implementation). As such, it is significantly slower than a native MPI
binding.
- 124
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Philippe Mougin and Stéphane Ducasse.
OOPAL: Integrating Array Programming in Object-Oriented
Programming.
In Proceedings of the 18th ACM SIGPLAN, 2003.
ISBN:1-58113-712-5
http://www.iam.unibe.ch/~scg/Archive/Papers/Moug03aOOPALOOPSLA.pdf cache: ../../archive/Moug03aOOPALOOPSLA.pdf.
OOPAL is a model for adding array-programming
features to object-oriented languages.
- 125
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Cherri M. Pancake and Donna Bergmark.
Do Parallel Languages Respond to the Needs of Scientific
Programmers?
Computer, 23(12):13-23, December 1990.
http://ieeexplore.ieee.org.ezproxy.lib.monash.edu.au/xpl/tocresult.jsp?isNumber=2260&puNumber=2 http://portal.acm.org/citation.cfm?id=98874.
- 126
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Michael Philippsen.
Is Java ready for computational science?
In 2nd European Parallel and Distributed Systems Conference,
pages 1-6, July 1998.
http://www.ubka.uni-karlsruhe.de/vvv/1998/informatik/27/27.ps.gz cache: ../../archive/javaCS.ps.gz.
Discussion of the pros and cons of using Java for
computational science. Cons include the restriction of infix arithmetic to
primitives, the absence of complex numbers from the standard mathematical
library (java.lang.math), the lack of type-safe generic classes (available in
Java 1.5).
- 127
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David Leo Presotto.
Inferno Security.
In Proceedings of COMPCON 97, pages 251-253. Bell Labs -
Lucent Technologies, February 1997.
http://ieeexplore.ieee.org/xpl/tocresult.jsp?isNumber=12649&page=2 cache: ../../archive/00584721.pdf.
Description of the (optional) security mechanisms
available for Inferno that provide secure communication between machines.
This allows for mutual authentication of parties and encryption and/or
authentication of messages amongst them.
- 128
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David J. Pritchard and Jeff Reeve, editors.
Euro-Par '98 Parallel Processing, 4th International Euro-Par
Conference, Southampton, UK, September 1-4, 1998, Proceedings, volume 1470
of Lecture Notes in Computer Science.
Springer Verlag, September 1998.
ISBN: 3-540-64952-2.
- 129
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José Rolim, editor.
Parallel and Distributed Processing, 15 IPDPS 2000
Workshops, Cancun, Mexico, May 1-5, 2000, Proceedings, volume 1800
of Lecture Notes in Computer Science, New York, May 2000.
Springer-Verlag.
ISBN: 3-540-67442-X
http://www.informatik.uni-trier.de/~ley/db/conf/ipps/ipdpsW2000.html.
- 130
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Thomas Sandholm and Jarek Gawor.
Globus Toolkit 3 Core - A Grid Service Container
Framework.
White Paper, July 2003.
http://www-unix.globus.org/toolkit/3.0/ogsa/docs/gt3_core.pdf cache: ../../archive/gt3_core.pdf.
The Globus Toolkit 3 (GT3) Core consists of runtime
and development support for Grid services.
- 131
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Heinz W. Schmidt.
Data-Parallel Object-Oriented Programming.
In Proceedings of the 5th Australian Supercomputer Conference,
pages 263-272, Melbourne, December 1992.
Exploration of some of the issues around combining
data-parallel and object-oriented programming, focussing on dpSather, a
data-parallel extension of the object-oriented language sather
(http://www.gnu.org/software/sather/).
Also appeared as CSIRO
Division of Information Technology technical report TR-HJ-92-17.
- 132
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J. T. Schwartz, R. B. K. Dewar, E. Dubinsky, and E. Schonberg.
Programming with Sets: An Introduction to SETL.
Springer-Verlag, New York, 1986.
- 133
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Aamir Shafi, Bryan Carpenter, and Mark Baker.
MPJ Express.
poster, September 2005.
http://dsg.port.ac.uk/projects/mpj/docs/res/mpj-ahm-poster.pdf cache: ../../archive/mpj-ahm-poster.pdf.
MPJ Express is an implementation of the mpiJava 1.2
API on top of the MPJ device model.
- 134
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Ravi Sharma.
Distributed application development with Inferno.
In Design Automation Conference, proceedings, pages 146-150.
Bell Laboratories - Lucent Technologies, June 1999.
http://www.sigda.org/Archives/ProceedingArchives/Dac/Dac99/papers/1999/dac99/pdffiles/09_1.pdf cache: ../../archive/00781300.pdf.
This paper discusses the Namespace technology, a
simple but still flexible programming model that allows for network
transparency. The Namespace is a hierarchy of resources available to a
program. These resources are represented/named/accessed as files.
- 135
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Jack Shirazi.
Java Performance Tuning.
O'Reilly, 2 edition, January 2003.
ISBN: 0-596-00377-3
http://proquest.safaribooksonline.com.ezproxy.lib.monash.edu.au/0596003773 http://www.oreilly.com/catalog/javapt2/, associated website:
http://www.javaperformancetuning.com/.
Chapter 3 discusses improvements made in the
various JDK's over time.
- 136
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Jürgen K. Singer.
Is Fortran portability a myth?
In Michael Metcalf, editor, ACM SIGPLAN Fortran Forum,
volume 18, pages 2-4. ACM Press, New York, NY, USA, April 1999.
http://portal.acm.org.ezproxy.lib.monash.edu.au/citation.cfm?id=310410&coll=portal&dl=ACM&CFID=27396630&CFTOKEN=99779241.
- 137
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David B. Skillicorn.
Architecture-Independent Parallel Computation.
IEEE Computer, 23(12):38-50, December 1990.
cache: ../../archive/00062092.pdf.
- 138
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David B. Skillicorn, Jonathan M. D. Hill, and W. F. McColl.
Questions and answers about BSP.
Technical Report PRG-TR-15-96, Programming Research Group, Oxford
University Computing Laboratory, 1996.
http://www.qucis.queensu.ca/~skill/QandA.ps cache: ../../archive/skillicorn96question.ps.gz.
- 139
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Sven Skyum.
Introduction to Parallel Algorithms.
Number LS-95-2 in BRICS Lecture Series. Denmark, June 1995.
ISSB 1395-2048
http://www.brics.dk/LS/95/2/BRICS-LS-95-2/BRICS-LS-95-2.html.
- 140
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David Slogsnat, Patrick R. Haspel, Holger Froening, and Ulrich Bruening.
The ATOLL System Area Network (SAN).
Newsletter of the IEEE Computer Society's Task Force on Cluster
Computing, 5(2), September/October 2003.
http://www.clustercomputing.org/index.jsp?page=/content/tfcc-5-2-slogsnat.shtml cache: ../../archive/atoll.html.
The ATOLL System Area Network is a the integration
of a switch, network ports and interfaces on a single chip, optimized for
MPI. Benchmarks using NetPIPE show this architecture performs comparably to
the Myrinet PCIX architecture, and the article hints at a better
price/performance ratio.
- 141
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L.A. Smith, J.M. Bull, and J. Obdrzálek.
A parallel java grande benchmark suite.
In Conference on High Performance Networking and Computing
Proceedings of the 2001 ACM/IEEE conference on Supercomputing. ACM Press,
2001.
ISBN:1-58113-293-X.
- 142
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Lawrence Snyder.
A Programmer's Guide to ZPL.
Scientific and Engineering Computation series. MIT Press, March 1999.
ISBN: 0-262-69217-1
http://mitpress.mit.edu/catalog/item/default.asp?tid=4104&ttype=2.
Early(?)
version: http://www.ing.uc.edu.ve/~drey/zpl_guide.pdf cache: ../../archive/zpl_guide.pdf
- 143
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Rok Sosic and David Abramson.
Guard: A Relative Debugger.
Software - Practice and Experience, 27(2):185-206, February
1997.
http://www.csse.monash.edu.au/~davida/papers/guard.pdf.
- 144
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Daniel H. Steinberg.
Write Twice, Run Anywhere.
WWW, September 2002.
http://www.macdevcenter.com/pub/a/mac/2002/09/06/osx_java.html cache: http://../../archive/write_twice/osx_java1.html.
- 145
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T. Suganuma, T. Ogasawara, M. Takeuchi, T. Yasue, M. Kawahito, K. Ishizaki,
H. Komatsu, and T. Nakatani.
Overview of the IBM Java Just-in-Time Compiler.
IBM Systems Journal, 39(1):175-193, 2000.
http://www.research.ibm.com/journal/sj/391/suganuma.pdf cache: ../../archive/suganuma.pdf.
- 146
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Sun Microsystems, Inc.
jdb - The Java Debugger, 2001.
http://java.sun.com/j2se/1.3/docs/tooldocs/solaris/jdb.html cache: http://../../archive/jdb.html.
- 147
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Alexander S. Szalay and Jim Gray.
Scientific Data Federation: The World-Wide Telescope,
chapter 7, pages 95-108.
In Foster and Kesselman [70], November 2003.
ISBN: 1-55860-933-4
http://books.elsevier.com/uk/mk/uk/subindex.asp?isbn=1558609334.
The scale of the datasets astronomers are
interested in (currently terabytes, though soon the figure will best be
measured in petabytes) make it difficult for researchers to download a full
copy of the archive for local processing. The "Virtual Observatory" aka the
"World-Wide Telescope" is an effort to provide software services that unify
astronomical archives (literature, images, raw data, derived data, simulation
data) throughout the world.
Astronomy software is largely written in
Fortran, C, C++ with some Java code appearing more recently. Code is rarely
reused, causing larger and larger software costs. An example given is the
Sloan Digital Sky Survey, of which approximately 30% of the project's budget
was applied to software. It is estimated that at least half of this software
could likely have been implemented in generic, reusable code. The Virtual
Observatory project aims to build subsystems that makes this possible.
- 148
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Guillermo L. Taboada, Juan Touri no, and Ramón Doallo.
Performance analysis of java message-passing libraries on fast
ethernet, myrinet and sci clusters.
In Proceedings of the IEEE International Conference on Cluster
Computing (CLUSTER '03), pages 118-126, December 2003.
http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1253307 cache: ../../archive/01253307.pdf.
- 149
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Tech-X Corporation.
FastDL User Reference, January 2004.
http://www.techxhome.com/pdf/FastDL_UserReference.pdf cache: ../../archive/FastDL_UserReference.pdf.
- 150
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unknown author.
Open Grid Service Infrastructure Primer, March 2004.
Last modified 11/3/2004,
https://forge.gridforum.org/projects/ogsi-wg/document/draft-ggf-ogsi-gridserviceprimer/en/1 cache: ../../archive/draft-ggf-ogsi-gridserviceprimer.doc.
Gentle introduction to OGSI. Design goals include
extensibility/refinement, introspection (an ability for systems to describe
their own capabilities and interfaces), statefullness(?), "soft-state"(?),
behaviour which gives artefacts (identities/information/resource allocations)
explicit lifetimes.
- 151
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Leslie G. Valiant.
A Bridging Model for Parallel Computation.
Communications of the ACM, 33(8):103-111, August 1990.
http://portal.acm.org/citation.cfm?id=79181 cache: ../../archive/p103-valiant.pdf.
The BSP model is proposed as a bridge between
high-level parallel languages and low-level hardware, which can be exploited
for high performance programming.
- 152
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Rob V. van Nieuwpoort.
Efficient Java-Centric Grid-Computing.
PhD thesis, ije Universiteit Amsterdam, the Netherlands, September
2003.
http://www.cs.vu.nl/~rob/papers/thesis.ps.gz cache: ../../archive/java-centric-grid-computing-thesis.ps.gz.
- 153
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Rob V. van Nieuwpoort, Jason Maassen, Rutget Hofman, Thilo Kielmann, and
Henri E. Bal.
Ibis: an Efficient Java-based Grid Programming Environment.
Joint ACM Java Grande - ISCOPE 2002 Conference, November 2002.
http://www.gridlab.org/Resources/Papers/jgi02.pdf cache: ../../archive/jgi02.pdf.
Ibis aims to increase the efficiency of Java
message passing, to approach the efficiency of MPI, without compromising the
portability of code.
- 154
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C. van Reeuwijk, F. Kuijlman, and H.J. Sips.
Spar: a Set of Extensions to Java for Scientific Computation,
pages 277-299.
Volume 15 of Fox [74], 2003.
http://www.pds.ewi.tudelft.nl/~reeuwijk/publications/downloads/cpe-jgrande2001.pdf cache: ../../archive/cpe-jgrande2001.pdf.
Extensions to Java (known as "Spar"- collectively
"Spar/Java") are demonstrated by example, with comparisons to Java, C, C++
and HPF.
The features added are:
- true
multidimensional arrays
- parallelization constructs, "each" and
"foreach"
- specialized array representations
- complex numbers
as a primitive type
For the sake of simplicity, the Spar/Java
compiler does not support all features of Java (threads and dynamic class
loading are unsupported, inner classes and interfaces are only partially
supported). These restrictions are not inherant to the design of the
language. The compiler does not generate JVM bytecode, but instead to an
intermediate language "vnus", which can then be compiled into C++ code. The
resulting code is SPMD, with explicit message passing (MPI, PVM, Panda were
supported at the time of this paper).
Link: Timber (Spar/Java
compiler)- http://pds.twi.tudelft.nl/timber/index.html
- 155
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Guido van Rossum and editor Fred L. Drake, Jr.
Python Library Reference.
PythonLabs, release 2.3.4 edition, May 2004.
http://www.python.org/doc/current/lib/lib.html.
- 156
-
Guido van Rossum and editor Fred L. Drake, Jr.
Python/C API Reference Manual.
PythonLabs, release 2.3.4 edition, May 2004.
http://docs.python.org/api/api.html.
- 157
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Gary V. Vaughan, Ben Elliston, Tom Tromey, and Ian Lance Taylor.
GNU Autoconf, Automake, and Libtool.
New Riders publishing, October 2000.
ISBN: 1578701902 http://sources.redhat.com/autobook/.
- 158
-
Gary V. Vaughan, Ben Elliston, Tom Tromey, and Ian Lance Taylor.
Writing Portable C with GNU Autotools, chapter 15,
pages 177-194.
In [157], October 2000.
http://sources.redhat.com/autobook/autobook/autobook_110.html.
- 159
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R. Veldema and Henri E. Bal.
Optimizing Java specific overheads, Java at the speed of C?
In Proc. HPCN 2001, 2001.
http://www.cs.vu.nl/~rob/papers/hpcn01.pdf cache: ../../archive/hpcn01.pdf.
- 160
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Markus Voelter.
Aspect-Oriented Programming in Java.
Java Report, January 2000.
http://www.voelter.de/data/articles/aop/aop.html cache: ../../archive/aop.html.
Introduction to the concepts of Aspect-Oriented
Programming (AOP) and the AspectJ language (AOP concepts added to Java).
- 161
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Werner Vogels.
HPC.NET - are CLI-based Virtual Machines Suitable for
High Performance Computing.
[4].
http://www.sc-conference.org/sc2003/paperpdfs/pap251.pdf cache: ../../archive/pap251.pdf.
The Java Grande Forum has been proposing that Java
is a viable platform for use in high performance computing. This paper
investigates the relative performance of the Common Language Infrastructure
(CLI), which is the basis for Microsoft's .NET framework. If the performance
of CLI-based VM's approaches or exceeds that of the Java VM, then CLI should
be as viable as Java in HPC, while offering significant software engineering
advantages over Java.
Porting code from Java to C# is relatively
simple, using automated translation tools or even manual translation. The
areas of code that require the most work are those which are
platform-specific services, or Java libraries which currently have no
standard equivalent in CLI libraries.
Microsoft's (commercial) CLR
appears approximately as good as the fastest Java VM, with the opensource
Mono lagging behind a little. It is noted that Mono's performance has been
increasing with each release.
- 162
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Gregor von Laszewski, Ian Foster, Jarek Gawor, and Peter Lane.
A Java Commodity Grid Kit.
Concurrency and Computation: Practice and Experience,
13(8-9):643-662, July-August 2001.
http://www3.interscience.wiley.com/cgi-bin/jissue/84503215 cache: ../../archive/vonlaszewski01java.pdf.
Part of the Cog Kit Project:
http://www.cogkit.org/, which aims to give computational scientists
easier access to grid services by lowering the amount of prerequisite
knowledge required. These "kits" are available for Java
(http://www-unix.globus.org/cog/java/), Python
(http://www-unix.globus.org/cog/python/), Matlab
(http://www-unix.globus.org/cog/matlab/) and (web?) "Portals"
(http://www.ogce.org/).
- 163
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Niklaus Wirth.
Programming in Modula-2.
Springer-Verlag, 4 edition, 1988.
ISBN: 0387501509.
- 164
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Joachim Worringen, Andreas Gäer, and Frank Reker.
Exploiting transparent remote memory access for non-contiguous and
one-sided-communication.
In IPDPS 2002, Workshop for Communication Architecture in
Clusters (CAC '02), Fort Lauderdale, Florida, April 2002. IEEE Computer
Society.
http://www.ipdps.org/ipdps2002/ ISBN: 0769515738,
cache: ../../archive/paper_cac02_revised_ohne_tb.pdf.
This paper presents benchmarks of two new features
in SCI-MPICH (a variant of MPICH optimized for the SCI interconnect)- use of
non-contiguous MPI datatypes, and one-sided communication. Results appear
promising, though with much room for improvement.
- 165
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Gu Yan.
JBSP: A BSP Programming Library In Java.
Master's thesis, Nanyang Technological University, August 1999.
http://www.cs.jhu.edu/~yangu/publications/thesis.ps cache: ../../archive/jbsp-thesis.ps.gz.
An implementation of a BSP library for Java, on top
of a combination of message passing and RMI.
- 166
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Kathy Yelick, Luigi Semenzato, Geoff Pike, Carleton Miyamoto, Ben Libit, Arvind
Krishnamurthy, Paul Hilfinger, Susan Graham, David Gay, Phil Colella, and
Alex Aiken.
Titanium: A High-Performance Java Dialect.
In Concurrency- Practice and Experience, Java Special Issue,
volume 10, 1998.
- 167
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Tong Zhang, Chuanfu Zhang, Yunsheng Liu, and Yabing Zha.
A Design of Distributed Simulation Based on GT3 Core.
In Li et al. [110], pages 590-596.
http://www.springerlink.com/link.asp?id=gfv94n620m5m5et2 cache: https://bubble.csse.monash.edu.au/archive/lncs3033/p590-596.pdf.
A simple distributed two dimensional combat
simulation is designed and described as an example of the use of GT3.
2006-09-21