Abstract: A method for managing flow of particles into an array of pairwise-point-interaction-module includes receiving a first set of particles into a first queue. The first set is a proper subset of a second set of particles that comprises all particles that are to be passed into an array of pairwise-point-interaction-modules during a current time period. Prior to having received all particles from the second set, particles from the first set are allowed to pass from the first queue into the array.

Abstract: A method comprising causing a simulation machine for molecular dynamic simulation to determine that a topological distance that separates two particles is less than a threshold. The simulation machine includes nodes connected by a network. The nodes collectively representing a volume with each node corresponding to a portion of the simulation space. A topological relationship between the nodes corresponds to spatial relationship thereof in the simulation space. The simulation volume is occupied by particles that interact with each other. The two particles are among these particles. The simulation volume includes node boxes, each of which is handled by one of the nodes. Each of the nodes is implemented as an application specific integrated circuit that includes a combination of first and second hardware elements. The first hardware elements are especially designed to perform pairwise interactions. The second hardware elements operate to provide potentially interacting particles to the first hardware elements.

Abstract: A method for managing flow of particles into an array of pairwise-point-interaction-module includes receiving a first set of particles into a first queue. The first set is a proper subset of a second set of particles that comprises all particles that are to be passed into an array of pairwise-point-interaction-modules during a current time period. Prior to having received all particles from the second set, particles from the first set are allowed to pass from the first queue into the array.

Abstract: A method comprising causing a computer to determine that a topological distance between two particles is less than a threshold.

Abstract: A data communication apparatus includes a router, first and second packet producers, and a penalizer. The router is directly connected to the first and second producers. The penalizer assesses penalties against each producer whenever that producer is serviced. The penalty value depends at least in part on an expected extent to which the first producer requires service. The penalizer then accumulates penalties against each producer.

Abstract: An apparatus for high-performance parallel computation, includes plural computation nodes, each having dispatch units, memories in communication with the dispatch units, and processors, each of which is in communication with the memories and the dispatch units. Each dispatch unit is configured to recognize, as ready for execution, one or more computational tasks that have become ready for execution as a result of counted remote writes into the memories. Each of the dispatch units is configured to receive a dispatch request from a processor and to determine whether there exist one or more computational tasks that are both ready and available for execution by the processor.

Abstract: A data communication apparatus includes a router, first and second packet producers, and a penalizer. The router is directly connected to the first and second producers. The penalizer assesses penalties against each producer whenever that producer is serviced. The penalty value depends at least in part on an expected extent to which the first producer requires service. The penalizer then accumulates penalties against each producer.

Abstract: An apparatus for high-performance parallel computation, includes plural computation nodes, each having dispatch units, memories in communication with the dispatch units, and processors, each of which is in communication with the memories and the dispatch units. Each dispatch unit is configured to recognize, as ready for execution, one or more computational tasks that have become ready for execution as a result of counted remote writes into the memories. Each of the dispatch units is configured to receive a dispatch request from a processor and to determine whether there exist one or more computational tasks that are both ready and available for execution by the processor.