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592 appendix cOn the right side of the visual program:• Double-click Import and enter the path and the .general file name /home/mpaez/SlitBarrier.general.• Double-click AutoColor and select 0.0 for min (use expand) and 0.8 for max.• Double-click the right-hand Scale and enter [1 1 2]. The scale for the barrieris smaller than the one for the wave packet so that the barrier does not hidetoo much of the wave packet.In this scheme we use the Image icon to manipulate the image to obtain the bestview. This needs to be done just once.−101COPYRIGHT 2008, PRINCET O N UNIVE R S I T Y P R E S SEVALUATION COPY ONLY. NOT FOR USE IN COURSES.ALLpup_06.04 — 2008/2/15 — Page 592
Appendix D: An MPI TutorialIn this appendix we present a tutorial on the use of MPI on a small Beowulf clustercomposed of Unix or Linux computers. 1 This follows our philosophy of “learning whiledoing.” Our presentation is meant to help the user from the ground up, somethingthat might not be needed if you were working at a central computing center with areasonable level of support. Although your problem is still to take the program youhave written to generate the bifurcation plot for bug populations and run differentranges of µ values simultaneously on several CPUs, in a more immediate senseyour task is to get the experience of running MPI, to understand some of the MPIcommands within the programs, and then to run a timing experiment. In §D.9 at theend of the appendix we give a listing and a brief description of the MPI commands anddata types. General information about MPI is given in [MPI], detailed informationabout the syntax of MPI commands appears in [MPI2], and other useful materialcan be found in [MPImis]. The standard reference on the C language is [K&R 88],although we prefer [OR]. MPI is very much the standard software protocol for parallelcomputing and is at a higher level than its predecessor PVM [PVM] (which has itsown tutorial on the CD).While in the past we have run Java programs with a version of MPI, thedifference in communication protocols used by MPI and Java have led to poor performanceor to additional complications needed to improve performance [Fox 03].In addition, you usually would not bother parallelizing a program unless it requiresvery large amounts of computing time, and those types of programs are usuallywritten in Fortran or C (both for historical reasons and because Java is slower). So itmakes sense for us to use Fortran or C for our MPI examples. We will use C becauseit is similar to Java.D.1 Running on a BeowulfA Beowulf cluster is a collection of independent computers each with its own memoryand operating system that are connected to each other by a fast communicationnetwork over which messages are exchanged among processors. MPI is a library ofcommands that make communication between programs running on the differentcomputers possible. The messages are sent as data contained in arrays. Becausedifferent processors do not directly access the memory on some other computer,when a variable is changed on one computer, it is not changed automatically in1 This material was developed with the help of Kristopher Wieland, Kevin Kyle, Dona Hertel,and Phil Carter. Some of the other materials derive from class notes from the Ohio SuperComputer Center, which were written in part by Steve Gordon.−101COPYRIGHT 2008, PRINCET O N UNIVE R S I T Y P R E S SEVALUATION COPY ONLY. NOT FOR USE IN COURSES.ALLpup_06.04 — 2008/2/15 — Page 593
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Page 595 and 596: Appendix A: Glossaryabsolute value
Page 597 and 598: glossary 557control character — A
Page 599 and 600: glossary 559log in (on) — To sign
Page 601 and 602: glossary 561supercomputer — The c
Page 603 and 604: installing ptplot & java developer
Page 609 and 610: industrial-strength data visualizat
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Page 635 and 636: an mpi tutorial 595• Open a shell
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Page 643 and 644: an mpi tutorial 603✞> cd $HOME Do
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Page 647 and 648: an mpi tutorial 607Argument Namemsg
Page 649 and 650: an mpi tutorial 609D.3.4 Broadcast
Page 651 and 652: an mpi tutorial 611D.4 Parallel Tun
Page 653 and 654: an mpi tutorial 613✝}MPI_Recv ( &
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Page 661 and 662: an mpi tutorial 621D.9 List of MPI
Page 663 and 664: Appendix E: Calling LAPACK from CCa
Page 665 and 666: calling LAPACK from C 625E.2 Compil
Page 667 and 668: software on the CD 627JavaCodes Con
Page 669 and 670: software on the CD 629JavaCodes Con
Page 671 and 672: software on the CD 631Applets Direc
Page 673 and 674: software on the CD 633Fortran77code
Page 675 and 676: Appendix G: Compression via DWTwith
Page 677 and 678: compression via DWT with thresholdi
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Page 681 and 682: BIBLIOGRAPHY[Abar 93] Abarbanel, H.
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ibliography 643[Erco] Ercolessi, F.
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ibliography 645[L&F 93] Landau, R.
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ibliography 647[P&W 91] Pinson, L.
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ibliography 649[VdeV 94] van de Vel
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IndexAbstract data structures,70Abs
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index 653drand, 114Driving force, 2
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index 655Libraries, see Subroutines
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index 657structured, 10for virtual
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