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Parallel Fock Matrix Construction with distributed shared memory Model for the FMO-MO Method

JOURNAL OF COMPUTATIONAL CHEMISTRY 2010年第13期31卷 2381-2388页

作者： Umeda, Hiroaki Inadomi, Yuichi Watanabe, Toshio Yagi, Toru Ishimoto, Takayoshi Ikegami, Tsutomu Tadano, Hiroto Sakurai, Tetsuya Nagashima, Umpei Univ Tsukuba Ctr Computat Sci Tsukuba Ibaraki Japan Natl Inst Nat Sci Inst Mol Sci Aichi Japan Natl Inst Adv Ind Sci & Technol Res Inst Computat Sci Tsukuba Ibaraki Japan Inst Syst Informat Technol & Nanotechnol Sawara Ku Fukuoka Japan Tokyo Inst Technol Global Sci Informat & Comp Ctr Tokyo 152 Japan Edogawa Univ Fac Media Commun Chiba Japan Kyushu Univ INAMORI Frontier Res Center Nishi Ku Fukuoka 812 Japan Natl Inst Adv Ind Sci & Technol Informat Technol Res Inst Tsukuba Ibaraki Japan Univ Tsukuba Dept Comp Sci Tsukuba Ibaraki Japan

A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-3IG level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2381-2388, 2010

关键词： parallel Fock matrix construction FMO-MO method distributed shared memory large MO calculation Sakurai Sugiura method

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MIRAGE+ - A KERNEL IMPLEMENTATION OF distributed shared-memory ON A NETWORK OF PERSONAL COMPUTERS

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SOFTWARE-PRACTICE & EXPERIENCE 1994年第10期24卷 887-909页

作者： FLEISCH, BD HYDE, RL JUUL, N UNIV COPENHAGEN DEPT COMP SCIDK-2100 COPENHAGENDENMARK

We describe the evolution of a distributed shared memory (DSM) system, Mirage, and the difficulties encountered when moving the system from a Unix-based kernel on the VAX to a Unix-based kernel on personal computers. Mirage provides a network transparent form of shared memory for a loosely coupled environment. The system hides network boundaries for processes that are accessing shared memory and is upward compatible with the Unix System V Interface Definition. This paper addresses the architectural dependencies in the design of the system and evaluates performance of the implementation. The new version, Mirage+, performs well compared to Mirage even though eight times the amount of data is sent on each page fault because of the larger page size used in the implementation. We show that performance of systems with a large page size to network packet size can be dramatically improved on conventional hardware by applying three well-known techniques: packet blasting, compression, and running at interrupt level. The measured time for a page fault in Mirage+ has been reduced 37 per cent by sending a page using packet blasting instead of using a handshake for each portion of the page. When compression was added to Mirage+, the time to fault a page across the network was further improved by 47 per cent when the page was compressed into one network packet. Our measured performance compares favorably with the amount of time it takes to fault a page from disk. Lastly, running at interrupt level may improve performance 16 per cent when faulting pages without compression.

关键词： distributed shared memory OPERATING SYSTEMS distributed SYSTEMS COMMUNICATION COMPRESSION PERFORMANCE

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Checkpointing distributed shared memory

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JOURNAL OF SUPERCOMPUTING 1997年第2期11卷 137-158页

作者： Silva, LM Silva, JG Departamento Engenharia Informatica Universidade de Coimbra Coimbra Portugal

distributed shared memory (DSM) is a very promising programming model for exploiting the parallelism of distributed memory systems, because it provides a higher level of abstraction than simple message passing. Although the nodes of standard distributed systems exhibit high crash rates only very few DSM environments have some kind of support for fault-tolerance. In this article, we present a checkpointing mechanism for a DSM system that is efficient and portable. It offers some portability because it is built on top of MPI and uses only the services offered by MPI and a POSIX compliant local file system. As far as we know, this is the first real implementation of such a scheme for DSM. Along with the description of the algorithm we present experimental results obtained in a cluster of workstations. We hope that our research shows that efficient, transparent and portable checkpointing is viable for DSM systems.

关键词： distributed shared memory checkpointing fault-tolerance portability

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A dynamic coherence protocol for distributed shared memory enforcing high data availability at low costs

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 1996年第9期7卷 915-930页

作者： Theel, OE Fleisch, BD UNIV CALIF RIVERSIDE DEPT COMP SCIRIVERSIDECA 92521

DSM coherence protocols should scale well for large networks. Fault-tolerance in terms of highly available data access and uninterrupted DSM service is needed in large-scale environments that have a greater number of potentially malfunctioning components. We present a new class of dynamic coherence protocols for DSM systems in error-prone networks whose instances offer highly available access to DSM data at low operation costs. The approach is based on the highly scalable Boundary-Restricted (BR) coherence protocol class. The new protocol class, called the Dynamic Boundary-Restricted (DBR) coherence protocol class, maintains read/write frequencies of DSM requests at run-time. This information is used to dynamically adjust the minimum number of cached copies of a single DSM page in order to guarantee a given degree of data availability. The description of the new protocol class is accompanied by an analysis covering a large variety of workloads. This analysis presents the overall savings achieved by using a DBR coherence protocol in comparison to a static BR protocol.

关键词： distributed systems fault-tolerance availability distributed shared memory dynamic coherence protocols adaptability stochastic modeling

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Characterizing distributed shared memory performance: A case study of the convex SPP1000

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 1998年第2期9卷 206-216页

作者： Abandah, GA Davidson, ES Univ Michigan Dept Elect Engn & Comp Sci Adv Comp Architecture Lab Ann Arbor MI 48109 USA

In a distributed shared memory (DSM) multiprocessor, the processors cooperate in solving a parallel application by accessing the shared memory. The latency of a memory access depends on several factors, including the distance to the nearest valid data copy, data sharing conditions, and traffic of other processors. To provide a better understanding of DSM performance and to support application tuning and compiler development for DSM systems, this paper extends microbenchmarking techniques to characterize the important aspects of a DSM system. We present an experiment-based methodology for characterizing the memory, communication, scheduling, and synchronization performance, and apply it to the Convex SPP1000. We present carefully designed microbenchmarks to characterize the performance of the local and remote memory, producer-consumer communication involving two or more processors, and the effects on performance when multiple processors contend for utilization of the distributed memory and the interconnection network.

关键词： performance evaluation memory performance communication performance microbenchmarking distributed shared memory convex SPP1000

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Proteus: an efficient runtime reconfigurable distributed shared memory system

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JOURNAL OF SYSTEMS AND SOFTWARE 2001年第3期56卷 247-260页

作者： Ueng, JC Shieh, CK Liang, TY Chang, JB Natl Cheng Kung Univ Dept Elect Engn Tainan 701 Taiwan

This paper describes Proteus, a distributed shared memory (DSM) system which supports runtime node reconfiguration. Proteus allows users to change the node set during the execution of a DSM program. The capability of node addition allows users to further shorten the execution time of their DSM programs by dynamically adding newly available nodes to the system. Furthermore, competition for resources between system users and computer owners can be avoided by dynamically deleting nodes from the system. To make the system adapt to the node configuration efficiently, Proteus employs several techniques, including adaptive workload redistribution, affinity page movement, and forced update. Proteus supports both sequential consistency and release consistency. It provides an object-oriented parallel programming environment. This paper describes the design and implementation of node reconfiguration in Proteus, and presents the performance of the system. Experimental results indicate that Proteus can further improve the performance of the tested programs by taking advantage of node reconfiguration. Our results further demonstrate that the techniques employed in Proteus minimize communication and overhead. (C) 2001 Elsevier Science Inc. All rights reserved.

关键词： distributed shared memory workload redistribution page movement synchronization

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Multi-threaded design for a software distributed shared memory system

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IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS 1999年第12期E82D卷 1512-1523页

作者： Ueng, JC Shieh, CK Mac, SC Lai, AC Liang, TY Natl Cheng Kung Univ Dept Elect Engn Tainan 70101 Taiwan Inst Informat Ind Technol Res Div Taipei Taiwan Purdue Univ Dept Elect & Comp Engn W Lafayette IN 47907 USA

This paper describes the design and implementation of a multi-threaded distributed shared memory (DSM) system, called Cohesion, which provides high programming flexibility and latency masking, and supports load balancing. Cohesion offers a parallel programming environment which is very similar to that on a multiprocessors system. Threads could be created recursively in this environment, and users are not required to handle the locations of the threads. Instead of supporting a shared variable model, Cohesion provides a global shared address space among all nodes in the system. The space is further divided into three regions, i.e., release, conventional, and object-based memory, each is applied with different consistency protocol. In this paper, the design issues in an ordinary thread system, such as thread management, load balancing, and synchronization, have been reconsidered with the memory management provided by the DSM system. Several real applications have been used to evaluate the performance of the system. The results show that multi-threading usually has better performance than single-threading because the network latency can be masked by overlapping communication and computation. However, the gain depends on program behavior and the number of threads executed on each node in the system.

关键词： distributed shared memory multi-threading latency masking programming flexibility thread management synchronization

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A Methodological Construction of an Efficient Sequentially Consistent distributed shared memory

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COMPUTER JOURNAL 2010年第9期53卷 1523-1534页

作者： Cholvi, Vicent Fernandez, Antonio Jimenez, Ernesto Manzano, Pilar Raynal, Michel Univ Jaume 1 Castellon de La Plana Spain Univ Rey Juan Carlos LADyR GSyC Mostoles 28933 Spain Univ Politecn Madrid Madrid 28031 Spain Univ Rennes IRISA F-35042 Rennes France

The paper proposes a simple protocol that ensures sequential consistency. The protocol assumes that the shared memory abstraction is supported by the local memories of nodes that can communicate only by exchanging messages through reliable channels. Unlike other sequential consistency protocols, the one proposed here does not rely on a strong synchronization mechanism, such as an atomic broadcast primitive or a central node managing a copy of every shared object. From a methodological point of view, the protocol is built incrementally starting from the very definition of sequential consistency. It has the noteworthy property that a process that issues a write operation never has to wait for other processes. Depending on the current local state, most read operations issued also have the same property.

关键词： distributed systems distributed shared memory sequential consistency

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A real-time operating system supporting distributed shared memory for embedded control systems

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CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS 2019年第1-Sup期22卷 989-998页

作者： Tamura, Yuji Truong Thi Doan Chiba, Takahiro Yoo, Myungryun Yokoyama, Takanori Tokyo City Univ Setagaya Ku 1-28-1 Tamazutsumi Tokyo 1588557 Japan LINE Corp Tokyo Japan Syst Engn Consultants Co LTD Tokyo Japan

The paper presents a real-time operating system (RTOS) that provides a distributed shared memory (DSM) service for distributed embedded control systems. Model-based design is widely adopted in embedded control software design and the source code of software modules can be generated from a controller model. The generated software modules exchange their input and output values through shared variables. We develop a RTOS with a DSM service to provide a location-transparent environment, in which distributed software modules can exchange input and output values through the DSM. The RTOS is an extension to OSEK OS. We use a real-time network called FlexRay, which is based on a time division multiple access (TDMA) protocol. The consistency of the DSM is maintained according to the order of data transfer through FlexRay, not using inter-node synchronization. The worst case response time of the DSM is predictable if the FlexRay communication is well configured.

关键词： Operating systems Real-time systems Embedded systems distributed shared memory distributed control systems

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Improving the performance of software distributed shared memory with speculation

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 2005年第9期16卷 885-896页

作者： Kistler, M Alvisi, L IBM Corp Austin Res Lab Austin TX 78758 USA Univ Texas Dept Comp Sci Austin TX 78712 USA

We study the performance benefits of speculation in a release consistent software distributed shared memory system. We propose a new protocol, Speculative Home-based Release Consistency (SHRC), that speculatively updates data at remote nodes to reduce the latency of remote memory accesses. Our protocol employs a predictor that uses patterns in past accesses to shared memory to predict future accesses. We have implemented our protocol in a release consistent software distributed shared memory system that runs on commodity hardware. We evaluate our protocol implementation using eight software distributed shared memory benchmarks and show that it can result in significant performance improvements.

关键词： distributed shared memory protocol design and analysis speculation

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