16722634
Scaling applications to massively parallel machines using Projections performance analysis tool
Some of the most challenging applications to parallelize scalably are the ones that present a relatively small amount of computation per iteration. Multiple interacting performance challenges must be identified and solved to attain high parallel efficiency in such cases. We present case studies involving NAMD, a parallel classic molecular dynamics application for large biomolecular systems, and CPAIMD, Car-Parrinello ab initio molecular dynamics application, and efforts to scale them to large number of processors. Both applications are implemented in Charm++, and the performance analysis was carried out using Projections, the performance visualization/analysis tool associated with Charm++. We showcase a series of optimizations facilitated by Projections. The resultant performance of NAMD led to a Gordon Bell award at SC 2002 with unprecedented speedup on 3000 processors with teraflops level peak performance. We also explore the techniques for applying the performance visualization/analysis tool on future generation extreme-scale parallel machines and discuss the scalability issues with Projections.
13464889
Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study
Some of the most challenging applications to parallelize scalably are the ones that present a relatively small amount of computation per iteration. Multiple interacting performance challenges must be identified and solved to attain high parallel efficiency in such cases. We present a case study involving NAMD, a parallel molecular dynamics application, and efforts to scale it to run on 3000 processors with Tera-FLOPS level performance. NAMD is implemented in Charm++, and the performance analysis was carried out using "projections", the performance visualization/analysis tool associated with Charm++. We will showcase a series of optimizations facilitated by projections. The resultant performance of NAMD led to a Gordon Bell award at SC2002.
5358328
Teletraffic Performance of Mobile Radio Networks with Hierarchical Cells and Overflow
Wireless mobile networks, comprising a hierarchical layer of cells, use the cell layering to provide alternate routing for calls. This paper proposes a model for multilayered wireless mobile communications networks that provides a unified treatment of overflow to account for intra- and interlayer overflow. This takes account of the inherent overlap between cells in the same layer and between layers, and hence the prospect of controlling the overflow to achieve a tradeoff between new call and handover performance. The mobility of users within the layers is included in the model, and this allows handover performance to be estimated. Network performance is evaluated in terms of caller-perceived performance by calculating the probability of call failure using a Markov chain model of call progress. An example is presented that provides a comparison of the network performance for a range of overflow policies. The main contribution of this paper is the development of an analytic method that treats overflow in a unified manner. This allows the approximate performance of overflow strategies that balance the need to maintain calls in progress with the desire to accept more new calls to be evaluated for large networks.
9259468
Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data
MOTIVATION
High-density DNA microarray measures the activities of several thousand genes simultaneously and the gene expression profiles have been used for the cancer classification recently. This new approach promises to give better therapeutic measurements to cancer patients by diagnosing cancer types with improved accuracy. The Support Vector Machine (SVM) is one of the classification methods successfully applied to the cancer diagnosis problems. However, its optimal extension to more than two classes was not obvious, which might impose limitations in its application to multiple tumor types. We briefly introduce the Multicategory SVM, which is a recently proposed extension of the binary SVM, and apply it to multiclass cancer diagnosis problems.


RESULTS
Its applicability is demonstrated on the leukemia data (Golub et al., 1999) and the small round blue cell tumors of childhood data (Khan et al., 2001). Comparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods.


SUPPLEMENTARY INFORMATION
http://www.stat.ohio-state.edu/~yklee/msvm.htm
9335901
Performance upgrade for large object bases using disk arrays
The authors propose the use of multiple disks to increase the bandwidth of disk I/O so as to alleviate the I/O bottleneck problem existed in OODB applications. However, a major difficulty in using multiple disks for the support of OODBs is that an object may reference or be referenced by other objects through associations. This requires that the search of objects be sequential through the association links, which is sometimes referred to as the navigational search of objects in an object base. This restriction limits the concurrency in object retrieval and invalidates the use of multiple disks. Techniques such as clustering/indexing of objects do not help to resolve this problem. By using a two-phase query processing strategy previously proposed by them, objects of interest can be accessed in parallel from multiple disk. The aim of the paper is to design a probability-based evaluation model to estimate the performance of using multiple disks and to compare it with a single disk system. The result shows that the scheme is viable and a significant improvement is achieved while multiple disks are used.
1931080
Between Chaos and Routine: Boundary Negotiating Artifacts in Collaboration
Empirical studies of material artifacts in practice continue to be a rich source of theoretical concepts for CSCW. This paper explores the foundational concept of boundary objects and presents the results of a year-long ethnographic study of collaborative work. This research questions the assumption that artifacts exist necessarily within a web of standardized processes and that disorderly processes should be treated as "special cases". I suggest that artifacts can serve to establish and destabilize protocols themselves and that artifacts can be used to push boundaries rather than merely sailing across them.
19284732
Smart sinks: real-world opportunities for context-aware interaction
Can implicit interaction with a computer easily drive useful interface improvements in physical world settings? This paper presents a case study presenting multiple such context-aware interaction improvements in a sink. We have identified opportunities where automated interfaces at the sink have positive consequences for safety, hygiene and ecology. The danger of scalding oneself with hot water is confronted by transforming the water into a graphical user interface and using image understanding to dispense the proper temperature of water. Audio-visual feedback at the sink can motivate users to conserve water. Used in combination with an RFID reader, the sink can serve as an effective means of verifying hand-washing compliance for clean environments. Finally, automatic actuation of the sink's height based on the user and task can prevent burns and ergonomic injuries. This project demonstrates that the integration of digital interaction in a hostile environment can facilitate and improve our daily rituals.