Design and Evaluation of the Hamal Parallel Computer

Parallel shared-memory machines with hundreds or thousands of processor-memory nodes have been built; in the future we will see machines with millions or even billions of nodes. Associated with such large systems is a new set of design challenges. Many problems must be addressed by an architecture in order for it to be successful; of these, we focus on three in particular. First, a scalable memory system is required. Second, the network messaging protocol must be fault-tolerant. Third, the overheads of thread creation, thread management and synchronization must be extremely low. This thesis presents the complete system design for Hamal, a shared-memory architecture which addresses these concerns and is directly scalable to one million nodes. Virtual memory and distributed objects are implemented in a manner that requires neither inter-node synchronization nor the storage of globally coherent translations at each node. We develop a lightweight fault-tolerant messaging protocol that guarantees message delivery and idempotence across a discarding network. A number of hardware mechanisms provide efficient support for massive multithreading and fine-grained synchronization. Experiments are conducted in simulation, using a trace-driven network simulator to investigate the messaging protocol and a cycle-accurate simulator to evaluate the Hamal architecture. We determine implementation parameters for the messaging protocol which optimize performance. A discarding network is easier to design and can be clocked at a higher rate, and we find that with this protocol its performance can approach that of a non-discarding network. Our simulations of Hamal demonstrate the effectiveness of its thread management and synchronization primitives. In particular, we find register-based synchronization to be an extremely efficient mechanism which can be used to implement a software barrier with a latency of only 523 cycles on a 512 node machine.

Keyword Join: Realizing Keyword Search in P2P-based Database Systems

In this paper, we present a P2P-based database sharing system that provides information sharing capabilities through keyword-based search techniques. Our system requires neither a global schema nor schema mappings between different databases, and our keyword-based search algorithms are robust in the presence of frequent changes in the content and membership of peers. To facilitate data integration, we introduce keyword join operator to combine partial answers containing different keywords into complete answers. We also present an efficient algorithm that optimize the keyword join operations for partial answer integration. Our experimental study on both real and synthetic datasets demonstrates the effectiveness of our algorithms, and the efficiency of the proposed query processing strategies.

Protein Microarray: "Theory" to "Real Practice"

Fueled by ever-growing genomic information and rapid developments of proteomics–the large scale analysis of proteins and mapping its functional role has become one of the most important disciplines for characterizing complex cell function. For building functional linkages between the biomolecules, and for providing insight into the mechanisms of biological processes, last decade witnessed the exploration of combinatorial and chip technology for the detection of bimolecules in a high throughput and spatially addressable fashion. Among the various techniques developed, the protein chip technology has been rapid. Recently we demonstrated a new platform called “Spacially addressable protein array” (SAPA) to profile the ligand receptor interactions. To optimize the platform, the present study investigated various parameters such as the surface chemistry and role of additives for achieving high density and high-throughput detection with minimal nonspecific protein adsorption. In summary the present poster will address some of the critical challenges in protein micro array technology and the process of fine tuning to achieve the optimum system for solving real biological problems.