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Landing CG on EARTH: A Case Study of Fine-Grained Multithreading on an Evolutionary Path

K.B. Theobald, G. Agrawal, R. Kumar, G. Heber, Guang R. Gao, P. Stodghill, K. Pingali
2000 ACM/IEEE SC 2000 Conference (SC'00)  
Three major observations from our experiments on the EARTH multithreaded testbed are: (1) The scalability of our CG implementation is impressive, e.g., absolute speedup is 90 on 120 processors for the  ...  This paper presents an effective mechanism for the reduction-broadcast phase, which is integrated with the sparse MVM, resulting in a scalable implementation of the complete CG application.  ...  with Jet Propulsion Laboratory (JPL) and the California Institute of Technology (Cal-Tech) for the Hybrid Technology Multithreaded Architecture Project at the University of Delaware.  ... 
doi:10.1109/sc.2000.10011 dblp:conf/sc/TheobaldAKHGSP00 fatcat:bhxp75zh6nchlfs3hssbdnnj5y

Experiences with non-numeric applications on multithreaded architectures

Angela Sodan, Guang R. Gao, Olivier Maquelin, Jens-Uwe Schultz, Xin-Min Tian
1997 Proceedings of the sixth ACM SIGPLAN symposium on Principles and practice of parallel programming - PPOPP '97  
In this paper, we show the benefits provided by EARTH for applications of this sort by presenting experimental results from several AI applications run on the MANNA machine, which is a distributed-memory  ...  EARTH-MANNA is shown to extend the range of programs that can be parallelized and run effectively on distributed-memory machines.  ...  Acknowledgments Our thanks go to Gerd Kock, Klaus Miiller, and Nikola Serbedzija of GMD FIRST for interesting discussions on neural networks.  ... 
doi:10.1145/263764.263782 dblp:conf/ppopp/SodanGMST97 fatcat:6oj3tyr5ojeprml6azb3d3pz5y

Hierarchical multithreading: programming model and system software

G.R. Gao, T. Sterling, R. Stevens, M. Hereld, Weirong Zhu
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
Finally, we plan to implement our method in an experimental testbed for a HEC architecture and perform a qualitative and quantitative evaluation on selected applications.  ...  We are developing a hierarchical threaded virtual machine (HTVM) that defines a dynamic, multithreaded execution model and programming model, providing an architecture abstraction for HEC system software  ...  We acknowledge Hongbo Rong, who has been instrumental in the development and documentation of some key ideas in this paper.  ... 
doi:10.1109/ipdps.2006.1639574 dblp:conf/ipps/GaoSSHZ06 fatcat:lkcf3jbp7jcr3mikequlczalhu

Author's index

2000 ACM/IEEE SC 2000 Conference (SC'00)  
and Landing CG on EARTH: A Case Study of Fine-Grained Multithreading on an John B.  ...  and Landing CG on EARTH: A Case Study of Fine-Grained Multithreading on an Evolutionary Path Stout, Quentin F.  ... 
doi:10.1109/sc.2000.10057 fatcat:siz2mgpg3jhwbeos4ew7z3jmmq

Modern Computational Techniques for the HMMER Sequence Analysis

Xiandong Meng, Yanqing Ji
2013 ISRN Bioinformatics  
The characteristics of the sequence analysis, such as data and compute-intensive natures, make it very attractive to optimize and parallelize by using both traditional software approach and innovated hardware  ...  This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of  ...  Conflict of Interests The authors confirm that they have no financial relationships related to the commercial identities involved in this study or referred to in the paper.  ... 
doi:10.1155/2013/252183 pmid:25937944 pmcid:PMC4393056 fatcat:kdo43qa23je4zflfpkvkhoxkfu

A cluster-based solution for high performance hmmpfam using EARTH execution model

Zhu, Niu, Lu, Shen, Gao
2003 Proceedings IEEE International Conference on Cluster Computing CLUSTR-03  
The contribution of this paper is the first largely scalable and robust cluster-based solution of parallel hmmpfam based on EARTH (Efficient Architecture for Running Threads), which is an event-driven  ...  Compared with the original PVM implementation, our implementation shows notable improvements on absolute speed-up and better scalability.  ...  We would like to thank the Bioinformatics and Microbial Genomics Team at the Biochemical Sciences and Engineering Division within DuPont CR&D for the useful discussions during the course of this work.  ... 
doi:10.1109/clustr.2003.1253296 dblp:conf/cluster/ZhuNLSG03 fatcat:udnsiw6apnbthlf4ckvepgf2n4

A cluster-based solution for high performance hmmpfam using EARTH execution model

Weirong Zhu, Yanwei Niu, Jizhu Lu, Chuan Shen, Guang R. Gao
2004 International Journal of High Performance Computing and Networking  
The contribution of this paper is the first largely scalable and robust cluster-based solution of parallel hmmpfam based on EARTH (Efficient Architecture for Running Threads), which is an event-driven  ...  Compared with the original PVM implementation, our implementation shows notable improvements on absolute speed-up and better scalability.  ...  We would like to thank the Bioinformatics and Microbial Genomics Team at the Biochemical Sciences and Engineering Division within DuPont CR&D for the useful discussions during the course of this work.  ... 
doi:10.1504/ijhpcn.2004.008893 fatcat:htv3a6ccrvggnmjqbrj7bkn4za

Multithreaded Xios Version Adapted To Many‐Core Architectures, And Supporting Grib2 Format (D2.4)

Yushan Wang, Yann Meurdesoif
2018 Zenodo  
With this motivation, we developed a portable multithreaded interface for XIOS based on the concept of MPI endpoints.  ...  The multithreaded version of XIOS was developed and then integrated and tested in the LMDZ model. The performance report of the multithreaded XIOS is detailed in this deliverable.  ...  For example, if we want to perform a put operation from endpoint 2 to the server, knowing that endpoint 2 is the thread 0 of process 1, the 0 th window (win A) of the server side should be used.  ... 
doi:10.5281/zenodo.1453853 fatcat:ekxnvqpxazep5m3nwfm3wdelru

Advances in the dataflow computational model

Walid A Najjar, Edward A Lee, Guang R Gao
1999 Parallel Computing  
This paper is a review of the current state-of-the-art in the applications of the data¯ow model of computation.  ...  Because it relies on a graph representation of programs, the strengths of the data¯ow model are very much the complements of those of the stored-program one.  ...  The last author thanks members of his Computer Architecture and Parallel Systems Laboratory (CAPSL) group, Department of Electrical and Computer Engineering, University of Delaware, for their valuable  ... 
doi:10.1016/s0167-8191(99)00070-8 fatcat:72oq72crzvho3cptrgvknxteea

Non-strict Evaluation of the FFT Algorithm in Distributed Memory Systems [chapter]

Alfredo Cristóbal-Salas, Andrei Tchernykh, Jean-Luc Gaudiot
2003 Lecture Notes in Computer Science  
This paper focuses on the partial evaluation of local and remote memory accesses of distributed applications, not only to remove much of the excess overhead of message passing implementations, but also  ...  We show that by incorporating non-strict information processing to FFT MPI, a significant reduction of the number of messages can be archievd, and the overall system performance can be improved. 195 execution  ...  Our DISSC is a further development of the ISSC system designed for non-blocking multithreaded architectures and tested for the EARTH [14] .  ... 
doi:10.1007/978-3-540-39924-7_28 fatcat:6okfvufhbvccpdsg53ul4tfyqq

Active Proxy-G: Optimizing the Query Execution Process in the Grid

H. Andrade, T. Kurc, A. Sussman, J. Saltz
2002 ACM/IEEE SC 2002 Conference (SC'02)  
We present an experimental evaluation to illustrate the effects of various design tradeoffs. We also show the benefits that two real applications gain from using the middleware.  ...  the cache, and submit the subqueries for final processing at application servers that store the raw datasets.  ...  Their excellent comments helped us significantly in improving the presentation and content of the paper, specifically towards suggesting ideas on how our prototype can be integrated with the available  ... 
doi:10.1109/sc.2002.10031 dblp:conf/sc/AndradeKSS02 fatcat:ridc2pvg4bdzlfghuni6374v4e

COMP Superscalar, an interoperable programming framework

Rosa M. Badia, Javier Conejero, Carlos Diaz, Jorge Ejarque, Daniele Lezzi, Francesc Lordan, Cristian Ramon-Cortes, Raul Sirvent
2015 SoftwareX  
A runtime system is in charge of exploiting the inherent concurrency of the code, automatically detecting and enforcing the data dependencies between tasks and spawning these tasks to the available resources  ...  COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts.  ...  Acknowledgments This work has been supported by the following institutions:  ... 
doi:10.1016/j.softx.2015.10.004 fatcat:wdihysbvvzgythxojl4uu7fbg4

Task-parallel Analysis of Molecular Dynamics Trajectories [article]

Ioannis Paraskevakos and Andre Luckow and Mahzad Khoshlessan and George Chantzialexiou and Thomas E. Cheatham and Oliver Beckstein and Geoffrey C. Fox and Shantenu Jha
2018 arXiv   pre-print
Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities.  ...  We provide a conceptual basis for comparing and understanding different frameworks that enable users to select the optimal system for each application.  ...  This work is funded by NSF 1443054 and 1440677.  ... 
arXiv:1801.07630v3 fatcat:m7tb4qef2vagdod4xfwswdyr4a

High Performance Computing in Satellite SAR Interferometry: A Critical Perspective

Pasquale Imperatore, Antonio Pepe, Eugenio Sansosti
2021 Remote Sensing  
In this paper, a perspective on the state-of-the-art of high performance computing (HPC) methodologies applied to spaceborne SAR interferometry (InSAR) is presented, and the different parallel algorithms  ...  Synthetic aperture radar (SAR) interferometry has rapidly evolved in the last decade and can be considered today as a mature technology, which incorporates computationally intensive and data-intensive  ...  Large-scale remote sensing data processing typically demands massive and sophisticated computations on a large amount of data, thus comprising computational-intensive and data-intensive applications.  ... 
doi:10.3390/rs13234756 fatcat:flsy4h75gzdvzgjpfx4xwivem4

Sens-ation: a service-oriented platform for developing sensor-based infrastructures

Tom Gross, Tareg Egla, Nicolai Marquardt
2006 International Journal of Internet Protocol Technology  
On a whole, Sens-ation facilitates the development allowing developers to concentrate on the semantics of their infrastructures, and to develop innovative concepts and implementations of context-aware  ...  The service-oriented paradigm of Sens-ation enables standardised communication within individual infrastructures, between infrastructures and their sensors, but also among distributed infrastructures.  ...  for contributing to the concepts and implementing the Sens-ation platform.  ... 
doi:10.1504/ijipt.2006.009741 fatcat:i6gddmw4lnhkzjqazjsgt5fz5i
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