Implementing parallel hmm-pfam on the EARTH multithreaded architecture
Hmmpfam is a widely used computation-intensive bioinformatics software for sequence classification. This poster describes a new parallel implementation of hmmpfam on EARTH, which is an event-driven fine-grain multithreaded programming execution model. The comparison results of the original PVM implementation and our implementation shows notable improvements on absolute speedup and scalability. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes.

title: Exploring Financial Applications on Many-Core-on-a-Chip Architecture: A First Experiment
abstract: Computational requirements for solving models of financial derivatives, for example, the option pricing problems, are huge and demand efficient algorithms and high performance computing capabilities. This demand has been rekindled by the recent developments in the mobile technology making wireless trading a possibility. In this paper, we focus on the development of a Monte-Carlo algorithm on a modern multi-core chip architecture, Cyclops-64 (C64) under development at IBM as the experimental platform for our study in pricing options. The timing results on C64 show that various sets of simulations could be done in a real-time fashion while yielding high performance/price improvement over traditional microprocessors for finance applications.

title: Toward a Software Infrastructure for the Cyclops-64 Cellular Architecture
abstract: This paper presents the initial design of the Cyclops-64 (C64) system software infrastructure and tools under development as a joint effort between IBM T.J. Watson Research Center, ETI Inc. and the University of Delaware. The C64 system is the latest version of the Cyclops cellular architecture that consists of a large number of compute nodes each employs a multiprocessor-on-a-chip architecture with 160 hardware thread units. The first version of the C64 system software has been developed and is now under evaluation. The current version of the C64 software infrastructure includes a C64 toolchain (compiler, linker, functionally accurate simulator, runtime thread library, etc.) and other tools for system control (system initialization, diagnostics and recovery, job scheduler, program launching, etc.) This paper focuses on the following aspects of the C64 system software: (1) the C64 software toolchain; (2) the C64 Thread Virtual Machine (C64 TVM) with emphasis on TiNy ThreadsTM, the implementation of the C64 TVM; (3) the system software for host control. In addition, we illustrate, through two case studies, what an application developer can expect from the C64 architecture as well as some advantages of this architecture, in particular, how it provides a cost-effective solution. A C64 chip’s performance varies across different applications from 5 to 35 times faster than common off-the-self microprocessors.

title: Optimization of Dense Matrix Multiplication on IBM Cyclops-64: Challenges and Experiences
abstract: This paper presents a study of performance optimization of dense matrix multiplication on IBM Cyclops-64(C64) chip architecture. Although much has been published on how to optimize dense matrix applications on shared memory architecture with multi-level caches, little has been reported on the applicability of the existing methods to the new generation of multi-core architectures like C64. For such architectures a more economical use of on-chip storage resources appears to discourage the use of caches, while providing tremendous on-chip memory bandwidth per storage area. 
 
This paper presents an in-depth case study of a collection of well known optimization methods and tries to re-engineer them to address the new challenges and opportunities provided by this emerging class of multi-core chip architectures. Our study demonstrates that efficiently exploiting the memory hierarchy is the key to achieving good performance. The main contributions of this paper include: (a) identifying a set of key optimizations for C64-like architectures, and (b) exploring a practical order of the optimizations, which yields good performance for applications like matrix multiplication.

title: Sequential Consistency Revisit: The Sufficient Condition and Method to Reason the Consistency Model of a Multiprocessor-on-a-Chip Architecture
abstract: In his seminal paper in 1979  on memory consistency, Lamport proposed two requirements for a multiprocessor system to be sequentially consistent. The second condition stated that memory “requests from all processors issued to an individual memory module are serviced from a single FIFO queue. Issuing a memory request consists of entering the request on this queue”. Recently, the authors have the opportunity to revisit Lamport’s conditions in the context of a design study of the IBM Cyclops multiprocessoron-a-chip architecture (known as BG/C) from the system software angle. We find that when a multiprocessor system employs a network to communicate with its shared memory modules – such as in the BG/C architecture we need to carefully elaborate Lamport’s requirements to cover the network. Thus we have refined the Lamport’s second requirement along this line and demonstrated that the revised conditions are sufficient for ensuring the sequentially consistent behaviors for a class of BG/C-like architectures.

title: Fast handover in clustered wireless ATM
abstract: ATM networks can be extended to wireless networks by attaching wireless base stations to ATM networks, which allows mobile users to roam with little restriction. Due to the physical limitation, handovers become unavoidable when mobiles move from one area to another. As ATM networks are connection-oriented, connections have to be rerouted if a mobile device is moving out of its current cell. To have seamless communication, the handover process must be performed with small delay, minimal cell loss and no change in cell sequence. The authors propose an architecture to link ATM network to wireless networks. The proposed architecture is built on a hierarchical structure that groups cells into clusters. Different handover protocols are used, depending on whether a handover is in the same cluster or between clusters. In addition, the protocols take appropriate actions based on the type of communication. The performance of this protocol is superior to existing solutions in terms of speed and resource consumption.

title: Queue structures for shared-memory multiprocessor systems
abstract: Three basic structures have been proposed to organize the task queues for shared-memory multiprocessor systems: centralized, distributed, and hierarchical structures. The hierarchical structure intends to combine the advantage of the other two structures and eliminate their disadvantages. Unfortunately, we find it still has serious load imbalancing, in particular when the workload is heavy and irregular. We propose the use of a forest structure in place of a hierarchical one. Simulation shows the proposed structure can provide better load balancing and less contention than the hierarchical one.

title: A Hopfield neural network based task mapping method
abstract: With a prior knowledge of a program, static mapping aims to identify an optimal clustering strategy that can produce the best performance. In this paper we present a static method that uses Hopfield neural network to cluster the tasks of a parallel program for a given system. This method takes into account both load balancing and communication minimization. The method has been tested on a distributed shared memory system against other three clustering methods. Four programs, SOR, N-body, Gaussian Elimination and VQ, are used in the test. The result shows that our method is superior to the other three.

title: Cluster queue structure for shared-memory multiprocessor systems
abstract: Three basic organizations have been proposed to construct the task queues for a shared memory multiprocessor system: centralized, distributed, and hierarchical structures. The centralized structure is not suitable for massively parallel systems since the centralized queue is a bottleneck. The distributed structure, on the other hand, will end up with load imbalancing due to the random execution time of tasks. The hierarchical structure tends to combine the advantages of the previous two structures and reduces the impact of bottleneck and load imbalancing. However, we found out that the load imbalancing still exists in the hierarchical structure. It also affects system performance, in particular, when the workload becomes heavier. We further identified the cause of this problem. We propose the use of a forest structure to provide load balancing and contention minimization.

title: Implementation of process migration in Amoeba
abstract: The design of a process migration mechanism for the Amoeba distributed operating system is described. The primary motivation for this implementation is to carry out experimental and realistic studies of load balancing algorithms for a distributed operating system. Our aim has been the implementation of a mechanism which is general, efficient and fully transparent and which is reliable in the presence of network and processor failures.<<ETX>>