A Hierarchical Cache Coherent Protocol

As the number of processors in distributed-memory multiprocessors grows, efficiently supporting a shared-memory programming model becomes difficult. We have designed the Protocol for Hierarchical Directories (PHD) to allow shared-memory support for systems containing massive numbers of processors. PHD eliminates bandwidth problems by using a scalable network, decreases hot-spots by not relying on a single point to distribute blocks, and uses a scalable amount of space for its directories. PHD provides a shared-memory model by synthesizing a global shared memory from the local memories of processors. PHD supports sequentially consistent read, write, and test- and-set operations. This thesis also introduces a method of describing locality for hierarchical protocols and employs this method in the derivation of an abstract model of the protocol behavior. An embedded model, based on the work of Johnson[ISCA19], describes the protocol behavior when mapped to a k-ary n-cube. The thesis uses these two models to study the average height in the hierarchy that operations reach, the longest path messages travel, the number of messages that operations generate, the inter-transaction issue time, and the protocol overhead for different locality parameters, degrees of multithreading, and machine sizes. We determine that multithreading is only useful for approximately two to four threads; any additional interleaving does not decrease the overall latency. For small machines and high locality applications, this limitation is due mainly to the length of the running threads. For large machines with medium to low locality, this limitation is due mainly to the protocol overhead being too large. Our study using the embedded model shows that in situations where the run length between references to shared memory is at least an order of magnitude longer than the time to process a single state transition in the protocol, applications exhibit good performance. If separate controllers for processing protocol requests are included, the protocol scales to 32k processor machines as long as the application exhibits hierarchical locality: at least 22% of the global references must be able to be satisfied locally; at most 35% of the global references are allowed to reach the top level of the hierarchy.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.