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Second, the physical_properties() function computes energies, correlation coefficients, and a host of interesting physical properties These computations, however, are simple and do not significantly affect the program's overall runtime, so we will ignore them in this discussion Because the bulk of the computation time will be in non_bonded_forces(), we must pick a problem decomposition that makes that computation run efficiently in parallel The problem is made easier by the fact that each of the functions inside the time loop has a similar structure: In the sequential version, each function includes a loop over atoms to compute contributions to the force vector Thus, a natural task definition is the update required by each atom, which corresponds to a loop iteration in the sequential version After performing the task decomposition, therefore, we obtain the following tasks

invoke Once the service has been created, the application obtains a remote reference to the newly created lightbulb service and displays its contents so that it is possible to see exactly where the service is located Each service binds to a local TCP port through which it is located, and the reference is composed of the hostname and port of the service

All the attributes you pass for deletion will be deleted as a unit However, the update will not be immediately visible from calls to GetAttributes or Select The time it takes for updates to become visible is subject to eventual consistency Don t do a delete and then immediately do a get to make sure it worked without also passing the ConsistentRead flag If the delete has not been fully processed yet, you will get back old values

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// Load the service RMILightBulbImpl bulbService = new RMILightBulbImpl(); // Examine the service, to see where it is stored RemoteRef location = bulbServicegetRef(); Systemoutprintln (locationremoteToString());

Tasks that find the vibrational forces on an atom Tasks that find the rotational forces on an atom Tasks that find the nonbonded forces on an atom Tasks that update the position and velocity of an atom A task to update the neighbor list for all the atoms (which we will leave sequential)

No operation-specific data values come back from a successful DeleteAttributes call If the call returns normally, the delete was processed and the full contents of the request will be processed If the operation returns an error code, nothing will be deleted:

The final step is to register the service with the rmiregistry, so that other clients can access it This registry could be located on any computer on the local network, or on the Internet, or it could be found on the current host By default, the server will attempt a registration on the local machine, but if the hostname of a registry is specified on the command line, this setting will be overridden

With our collection of tasks in hand, we can consider the accompanying data decomposition The key data structures are the neighbor list, the atomic coordinates, the atomic velocities, and the force vector Every iteration that updates the force vector needs the coordinates of a neighborhood of atoms The computation of nonbonded forces, however, potentially needs the coordinates of all the atoms, because the molecule being simulated might fold back on itself in unpredictable ways We will use this information to carry out the data decomposition (in the Data Decomposition pattern) and the data sharing analysis (in the Data Sharing pattern)

// Check to see String registry if (argslength { registry = } if a registry was specified = "localhost"; >=1) args[0];

NoSuchDomain The error code returned if the DomainName parameter does not correspond to a domain created with your account at that endpoint InvalidParameterValue The error code returned if you pass an ItemName, AttributeName, or AttributeValue longer than 1,024 bytes in length MissingParameter The error code returned if you fail to pass a DomainName or an ItemNameThe API of your client will protect you from getting this error AttributeDoesNotExist Returned when the ExpectedExists parameter was set to true and the ExpectedName or ExpectedValue did not exist ConditionalCheckFailed Returned when the ExpectedName parameter unexpectedly exists or when ExpectedValue was different than the actual value MultiValuedAttribute Returned when the conditional check was applied to a multi-valued attribute Conditional checks can only be applied to singlevalued attributes

Task based decompositions are extremely common in parallel computing For example, the distance geometry code DGEOM [Mat96] uses a task based decomposition, as does the parallel WESDYN molecular dynamics program [MR95]

// Registration format //registry_hostname:port /service // Note the :port field is optional String registration = "rmi://" + registry + "/RMILightBulb"; // Register with service so that clients can find us Namingrebind( registration, bulbService );

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