3176337
EMC-Y: parallel processing element optimizing communication and computation
EMC-Y is a new processing element for highly parallel computers designed to achieve high performance parallel computation by fusing a dataflow mechanism and a von Neumann execution pipeline. We have already developed EMC-R, which is the processing element used in the EM-4 prototype. EMC-Y improves on EMC-R's packet communication performance, allowing it to tolerate a more network traffic. This paper presents the architecture of EMC-Y, concentrating on the principles of packet communication. EMC-Y uses an output packet buffer and optimal packet routing to improve the performance of packet sending and transferring. EMC-Y changes the memory access priority for input packet buffer operation to improve the performance of receiving packets. Since the EMC-Y processor not only improves the performance of packet input and output but also balances them, it can tolerate a large amount of traffic and can improve the execution performance. We evaluate the improvements of EMC-Y architecture using a clock level simulator. The results show that EMC-Y improves performance by 50% to 70% in several programs over EMC-R at the same clock speed.
37770987
A Blocking Algorithm for Parallel 1-D FFT on Clusters of PCs
In this paper, we propose a blocking algorithm for a parallel one-dimensional fast Fourier transform (FFT) on clusters of PCs. Our proposed parallel FFT algorithm is based on the six-step FFT algorithm. The six-step FFT algorithm can be altered into a block nine-step FFT algorithm to reduce the number of cache misses. The block nine-step FFT algorithm improves performance by utilizing the cache memory effectively. We use the block nine-step FFT algorithm to design the parallel one-dimensional FFT algorithm. In our proposed parallel FFT algorithm, since we use cyclic distribution, all-to-all communication is required only once. Moreover, the input data and output data are both can be given in natural order. We successfully achieved performance of over 1.3 GFLOPS on an 8-node dual Pentium III 1 GHz PC SMP cluster.
16720525
Resource manager for Globus-based wide-area cluster computing
In this paper, we present a new type of Globus resource allocation manager (GRAM) called RMF (Resource Manager beyond the Firewall) for wide-area cluster computing. RMF manages computing resources such as cluster systems and enables utilization of them beyond the firewall in global computing environments. RMF consists of two basic modules, a remote job queuing system (Q system) and a resource allocator. The Q system is a remote job queuing system, which schedules jobs submitted from global computing sites. The resource allocator manages resources and allocates them for requested jobs. For communications beyond the firewall between job processes, we designed the Nexus Proxy, which relays TCP communication links beyond the firewall. RMF and the Nexus Proxy provide a global computing environment in which users can easily utilize such parallel systems as cluster systems and supercomputers beyond the firewall.
41634108
Utilizing the Metaserver Architecture in the Ninf Global Computing System
Rapid increase in speed and availability of global-network is opening up the possibilities of globally-distributed supercomputing, including our Ninf system. Ninf is designed to utilize existing numerical libraries and resources on the Web. It also has global scheduling server called the Ninf Metaserver, which is responsible for scheduling and load-distribution of parallel tasks. The metaserver keeps track of computational servers, and gathers information needed for scheduling. Using the information, it balances loads over computational servers. We performed preliminary benchmarks using the metaserver. There, we observed that scheduling cost can be ignored and dynamic scheduling by the server gained better score than static-cyclic distribution. We also report on our collaborative efforts in bridging Ninf with NetSolve, a similar system being developed at Univ. of Tennessee/ORNL.
206034930
Performance Evaluation of a Workstation Cluster, TMC CM-5, and Intel Paragon/XP Using a Parallel Homology Analysis Program
Abstract In the homology analysis, required memory size and computing time proportionally increase with the square of the number of amino acids in protein. In order to expand the limit of size and to carry out analysis effectively, we parallelized for homology analysis program adopting the wavefront method with tiling. The performance of a workstation cluster, CM5, and Paragon was compared by using our program. For performance evaluation of these machines, we have made a model of our parallel homology analysis computation. Using the model, we can understand the characteristics of these machines with respect to our program. Execution time estimated by the execution model is in good agreement with the observation. The averaged error of the estimation to the observation on a workstation cluster, CM5, and Paragon are 0.1%, 5%, and 2%. Almost linear speed-up has been observed from 1PU to 20PUs on them. The ratio of the performance of Paragon, CM5, and the workstation cluster is 1:0.38:0.22. This ratio is constant to the variety of the size of problem and the number of processors.
15841052
The second trans-Pacific Grid Datafarm testbed and experiments for SC2003
The Grid Datafarm architecture is designed for global petascale data-intensive computing. It provides a global parallel file system (Gfarm file system) with online petascale storage, scalable I/O bandwidth, and scalable parallel processing by federating thousands of local file systems in a grid of clusters securely using Grid security infrastructure. One of features is that it manages file replicas in filesystem metadata for fault tolerance and load balancing. Here, we present an overview of our planned experiment performed as the SC2003 Bandwidth Challenge at the Supercomputing 2003 site in Phoenix, Arizona, USA. In the experiment, five clusters in Japan and three clusters in US comprise a Gfarm file system, on which world-wide largescale data analysis is performed. In the Gfarm file system, a file is dispersed in several cluster nodes, each of which is replicated independently and in parallel by multiple third-party transfers between multiple cluster nodes. For the Challenge, terabyte-scale experimental data is replicated between US and Japan via APAN/TransPAC and SuperSINET (about 10,000 km or 6,000 miles). At the workshop we present the full detail of the experiment.
27411446
A Purely Functional Language with Encapsulated Assignment
We introduce a new functional programming language with assignment. The language, which we call Λ, is a conservative extension of the λβ-calculus, and as such it it a higher order functional language in which we can manipulate functions as first class objects. Λ has a lazy evaluation semantics and Λ programs can be evaluated in parallel. Λ also supports imperative programming in terms of assignments. All the assingments in Λ are encapsulated within suitable scope of the let constructs. The language is therefore side-effect free and referentially transparent. We show by an example that we can smoothly reason about Λ programs.
28509315
Development of a method to construct three-dimensional finite element models of thoracic aortic aneurysms from MRI images
Most patients die when thoracic aortic aneurysms rupture. In order to avoid the ruptures, the aneurysms are replaced with aortic prostheses when their maximum diameter exceeds 5 cm. Because this criterion is based on the experiences, some aneurysms rupture even if the diameters are smaller than this criterion. To treat the aneurysm properly, it is necessary to find out the new criterion. The rupture is thought to have a close relationship with the stress in the wall. Hence, there is much research about the stress, but this research uses the straight tube model. The model shape does not seem appropriate to a thoracic aorta shape. Hence, we developed the method to construct three-dimensional finite element models of thoracic aortic aneurysms from MRI images.
46610662
CAL: A Computer Assisted Learning System for Computation and Logic
In this paper, we describe a computer system CAL which assists students' understanding of a lecture course in logic and computation. We introduce a new foundational theory of expressions, which is inspired by the theory of expressions due to Martin-Lof [6], and use the expressions determined by the theory to implement various syntactic objects in CAL. We also introduce the concept of derivation game, and show that various logical and computational systems given in the lecture course can be defined uniformly by derivation games.
32331384
Intuitionistic and Classical Natural Deduction Systems with the Catch and the Throw Rules
8686702
Theory of Judgments and Derivations
We propose a computational and logical framework NF (Natural Framework) which is suitable for presenting mathematics formally. Our framework is an extendable framework since it is open-ended both computationally and logically in the sense of Martin-Lof's theory or types. NF is developed in three steps. Firstly, we introduce a theory of expressions and schemata which is used to provide a universe for representing mathematical objects, in particular, judgments and derivations as well as other usual mathematical objects. Secondly, we develop a theory of judgments within the syntactic universe of expressions. Finally, we introduce the notions of derivation and derivation game and will show that we can develop mathematics as derivation games by regarding mathematics as an open-ended process of defining new concepts and deriving new judgments. Our theory is inspired by Martin-Lof's theory of expressions and Edinburgh LF, but conceptually much simpler. Our theory is also influenced by Gentzen's natural deduction systems.