14726525
Grid environment for computational astrophysics driven by GRAPE-6 with HMCS-G and OmniRPC
In computational astrophysics, the effect of gravity is essential even with very heavy computation of O(N/sup 2/) for N particles. Several special purpose machines have been implemented as gravity engine to handle this problem extremely fast, however there are few sites in the world to operate such systems. We have developed a grid environment to access such a system based on grid-RPC, named HMCS-G. Using HMCS-G, a multi-physical computational astrophysics simulation can be performed with the combination of a PC-cluster and the gravity engine GRAPE-6. In typical size of problems for galaxy formation, however, the computation power of PC-cluster is much weaker than that of GRAPE-6, and we need multiple sets of PC-clusters to share the power of GRAPE-6 on grid environment. We have developed such a system using OmniRPC, a grid-enabled RPC system. In this system, OmniRPC are used both to distribute jobs for parameter search on multiple PC-clusters and to access GRAPE-6 server from these clusters. We performed an actual problem to search several formations of galaxy on this system, and confirmed such a solution is useful for wide variety of computational astrophysics research.
32545241
Ninf: A Network Based Information Library for Global World-Wide Computing Infrastructure
Ninf is an ongoing global network-wide computing infrastructure project which allows users to access computational resources including hardware, software and scientific data distributed across a wide area network. Ninf is intended not only to exploit high performance in network parallel computing, but also to provide high quality numerical computation services and accesses to scientific database published by other researchers. Computational resources are shared as Ninf remote libraries executable at a remote Ninf server. Users can build an application by calling the libraries with the Ninf Remote Procedure Call, which is designed to provide a programming interface similar to conventional function calls in existing languages, and is tailored for scientific computation. In order to facilitate location transparency and network-wide parallelism, Ninf metaserver maintains global resource information regarding computational server and databases, allocating and scheduling coarse-grained computation for global load balancing. Ninf also interfaces with the WWW browsers for easy accessibility.
195869612
The EM-X parallel computer: architecture and basic performance
Latency tolerance is essential in achieving high performance on parallel computers for remote function calls and fine-grained remote memory accesses. EM-X supports interprocessor communication on an execution pipeline with small and simple packets. It can create a packet in one cycle, and receive a packet from the network in the on-chip buffer without interruption. EM-X invokes threads on packet arrival, minimizing the overhead of thread switching. It can tolerate communication latency by using efficient multi-threading and optimizing packet flow of fine grain communication. EM-X also supports the synchronization of two operands, direct remote memory read/write operations and flexible packet scheduling with priority. The paper describes distinctive features of the EM-X architecture and reports the performance of small synthetic programs and larger more realistic programs.
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.
12665758
Direct Execution of Linux Binary on Windows for Grid RPC Workers
Local area or campus-type networks consist of PCs using different operating systems such as Windows and Linux. These PCs are expected to have enormous potential computing power for grid computing. The majority of PCs in this type of environment run on Windows, while grid applications and middleware are often developed on Linux. The challenge is to absorb the heterogeneity of operating systems. Grid RPC is a promising programming model for the development of grid applications. We have designed and implemented an agent called BEE, which enables direct execution of Linux binary programs on Windows for a grid RPC worker. We have integrated the BEE agent into an OmniRPC system in order to make use of Windows PCs as computing resources in a hybrid grid environment combining Windows PCs into grid computing resources. The BEE agent allows Linux binaries of the program of the OmniRPC worker to be exported and run under Windows without any modification of its Linux binaries. The results of our experiments show that the performance of a worker program using BEE is almost the same as that of Windows native binary and Cygwin and is better that that of using VMware. We have demonstrated a hybrid grid environment combining Window PCs in a conventional grid of Linux nodes.
6990232
OmniRPC: A Grid RPC Facility for Cluster and Global Computing in OpenMP
Omni remote procedure call facility, OmniRPC, is a thread-safe grid RPC facility for cluster and global computing environments. The remote libraries are implemented as executable programs in each remote computer, and OmniRPC automatically allocates remote library calls dynamically on appropriate remote computers to facilitate location transparency. We propose to use OpenMP as an easy-to-use and simple programming environment for the multi-threaded client of OmniRPC. We use the POSIX thread implementation of the Omni OpenMP compiler which allows multi-threaded execution of OpenMP programs by POSIX threads even in a single processor. Multiple outstanding requests of OmniRPC calls in OpenMP work-sharing construct are dispatched to different remote computers to exploit network-wide parallelism.
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.
27739305
Explicit Environments
We introduce λƐ, a simply typed calculus with environments as first class values. As well as the usual constructs of λ and application, we have e[[a]] which evaluates term a in an environment e. Our environments are a set of variable-value pairs, but environments can also be computed by function application and evaluation in some other environments. The notion of environments here is a generalization of explicit substitutions and records. We show that the calculus has desirable properties such as subject reduction, confluence, conservativity over the simply typed λβ-calculus and strong normalizability.
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.
1580777
Classical Brouwer-Heyting-Kolmogorov Interpretation
The Brouwer-Heyting-Kolmogorov interpretation explains the meaning of logical operations as operators that construct proofs from proofs of the operands. The BHK interpretation is usually understood as giving intuitionistic interpretation for the logical operators, but, as pointed out by Troelstra and van Dalen [12], it is possible to understand the BHK interpretation classically. We elaborate this idea and develop a classical theory of proofs as abstract mathematical entities where the truth of a proposition becomes equivalent to the existence of proofs of the proposition.
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.