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TIMOTHY G MATTSON Timothy G Mattson earned a PhD in chemistry from the University of California at Santa Cruz for his work on quantum molecular scattering theory This was followed by a postdoc at Caltech where he ported his molecular scattering software to the Caltech/JPL hypercubes Since then, he has held a number of commercial and academic positions with computational science on high performance computers as the common thread He has been involved with a number of noteworthy projects in parallel computing, including the ASCI Red project (the first TeraFLOP MPP), the creation of OpenMP, and OSCAR (a popular package for cluster computing) Currently he is responsible for Intel's strategy for the life sciences market and is Intel's chief spokesman to the life sciences community BEVERLY A SANDERS Beverly A Sanders received a PhD in applied mathematics fr om Harvard University She has held faculty positions at the University of Maryland, the Swiss Federal Institute of Technology (ETH Zurich), and Caltech, and is currently with the Department of Computer and Information Science and Engineering at the University of Florida A main theme of her teaching and research has been the development and application of techniques, including design patterns, formal methods, and programming language concepts, to help programmers construct high quality, correct programs, particularly programs involving concurrency BERNA L MASSINGILL Berna L Massingill earned a PhD in computer science from Caltech This was followed by a postdoc at the University of Florida, where she and the other authors began their work on design patterns for parallel computing She currently holds a faculty position in the Department of Computer Science at Trinity University (San Antonio, Texas) She also spent more than ten years as a working programmer, first in mainframe systems programming and later as a developer for a software company Her research interests include parallel and distributed computing, design patterns, and formal methods, and a goal of her teaching and research has been applying ideas from these fields to help programmers construct high quality, correct programs.

Finally, we add each individual part to our Multipart object, and assign this object as the content of our message

Then the SimpleDB class can set parameters with the following code:

// Add msg body and attachment to multipart message partaddBodyPart(msgBody); partaddBodyPart(attachment); // Set our multipart message as the msg contents messagesetContent (part);

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Consider the molecular dynamics problem described in Sec 313 Pseudocode for this example is shown again in Fig 33 Before performing the task decomposition, we need to better understand some details of the problem First, the neighbor_list () computation is time consuming The gist of the computation is a loop over each atom, inside of which every other atom is checked to determine whether it falls within the indicated cutoff volume Fortunately, the time steps are very small, and the atoms don't move very much in any given time step Hence, this time consuming computation is only carried out every 10 to 100 steps

requestsetParam("DomainName", "users");

Running SendAttachment The syntax for SendAttachment is as follows:

Figure 33 Pseudocode for the molecular dynamics example Int const N // number of atoms Array Array Array Array of of of of Real Real Real List :: :: :: :: atoms (3,N) //3D coordinates velocities (3,N) //velocity vector forces (3,N) //force in each dimension neighbors(N) //atoms in cutoff volume

The lightbulb server defines a single method, main, which allows it to be run as an application The application encloses almost all of the code in a try { } catch block, since networking errors that occur at runtime must be caught The most likely error to occur is for a RemoteException to be thrown, if the service could not be started or if the server is unable to register with the rmiregistry

That approach will work, but when you start to think about it, you realize that seven of nine will need to set this domain name parameterThe inconvenience of having to repeat the hard-coded constant DomainName seven times suggests refactoring it into a class constant However, it seems much more appropriate to make the Request class responsible

loop over time steps vibrational_forces (N, atoms, forces) rotational_forces (N, atoms, forces) neighbor_list (N, atoms, neighbors)

public static void main(String args[]) { Systemoutprintln ("Loading RMI service"); try { } catch (RemoteException re) { Systemerrprintln ("Remote Error - " + re); } catch (Exception e) { Systemerrprintln ("Error - " + e); } }

ExpectedValue (optional) The value to check for a conditional writeThis value must exist in SimpleDB in order for the conditional write to succeedThis parameter is only valid when an ExpectedName is also includedThe maximum length of this parameter is 1,024 bytes ExpectedExists (optional) The flag to check for existence in a conditional writeWhen set to true, write only succeeds when the ExpectedName existsWhen false, write only succeeds when the ExpectedName does not existThis parameter is only valid when an ExpectedName is also includedThe maximum length of this parameter is 1,024 bytes AttributeValue (optional) The attribute value to be deleted Passed as a list in combination with an AttributeNameThis is only used when some values, but not all, of a multi-valued attribute are to be deleted

non_bonded_forces (N, atoms, neighbors, forces) update_atom_positions_and_velocities( N, atoms, velocities, forces) physical_properties ( Lots of stuff ) end loop

The next step is to create an instance of the RMI lightbulb service defined by the RMILightBulbImpl class The constructor for this class takes no parameters and is simple to

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