7537228
Achieving strong scaling with NAMD on Blue Gene/L
NAMD is a scalable molecular dynamics application, which has demonstrated its performance on several parallel computer architectures. Strong scaling is necessary for molecular dynamics as problem size is fixed, and a large number of iterations need to be executed to understand interesting biological phenomenon. The Blue Gene/L machine is a massive source of compute power. It consists of tens of thousands of embedded Power PC 440 processors. In this paper, we present several techniques to scale NAMD to 8192 processors of Blue Gene/L. These include topology specific optimizations, new messaging protocols, load-balancing, and overlap of computation and communication. We were able to achieve 1.2 TF of peak performance for cutoff simulations and 0.99 TF with PME.
9639915
Support for adaptivity in ARMCI using migratable objects
Many new paradigms of parallel programming have emerged that compete with and complement the standard and well-established MPI model. Most notable, and successful, among these are models that support some form of global address space. At the same time, approaches based on migratable objects (also called virtualized processes) have shown that resource management concerns can be separated effectively from the overall parallel programming effort. For example, Charm++ supports dynamic load balancing via an intelligent adaptive run-time system. It is also becoming clear that a multi-paradigm approach that allows modules written in one or more paradigms to coexist and co-operate will be necessary to tame the parallel programming challenge. ARMCI is a remote memory copy library that serves as a foundation of many global address space languages and libraries. This paper presents our preliminary work on integrating and supporting ARMCI with the adaptive run-time system of Charm++ as a part of our overall effort in the multi-paradigm approach
2648412
Performance evaluation of adaptive MPI
Processor virtualization via migratable objects is a powerful technique that enables the runtime system to carry out intelligent adaptive optimizations like dynamic resource management. Charm++ is an early language/system that supports migratable objects. This paper describes Adaptive MPI (or AMPI), an MPI implementation and extension, that supports processor virtualization. AMPI implements virtual MPI processes (VPs), several of which may be mapped to a single physical processor. AMPI includes a powerful runtime support system that takes advantage of the degree of freedom afforded by allowing it to assign VPs onto processors. With this runtime system, AMPI supports such features as automatic adaptive overlapping of communication and computation, automatic load balancing, flexibility of running on arbitrary number of processors, and checkpoint/restart support. It also inherits communication optimization from Charm++ framework. This paper describes AMPI, illustrates its performance benefits through a series of benchmarks, and shows that AMPI is a portable and mature MPI implementation that offers various performance benefits to dynamic applications.
60476874
High-level synthesis using computation-unit integrated memories
High-level synthesis (HLS) of memory-intensive applications has featured several innovations in terms of enhancements made to the basic memory organization and data layout. However, increasing performance and energy demands faced by application-specific integrated circuits (ASIC) are forcing designers to alter the fundamental architectural template of the HLS output, namely, a controller-datapath associated with a memory subsystem (monolithic, banked, etc.). We propose an architectural template for the HLS output that consists of a controller-datapath circuit associated with a memory subsystem into which computation units have been integrated. The enhanced memory subsystem is called computation-unit integrated memory (CIM). A CIM offers higher memory bandwidth (relative to what is offered through the system bus) to computation units present locally within it and reduces the overall communication between the memory subsystem and the controller-datapath, thus providing a template highly suitable for deriving efficient implementations of memory-intensive applications. This work addresses the challenge of providing an automatic synthesis framework for a CIM-based architecture. Our framework can analyze the various trade-offs involved in selecting suitable operations in a behavior for execution using a CIM and generate a high-performance, low-overhead implementation. Experiments with several behaviors indicate that an average performance improvement of 1.88/spl times/ (a maximum of 2.63/spl times/) is possible with very low area overheads. The energy-delay product improves by an average of 2.1/spl times/ (maximum of 3.4/spl times/).
904578
Simulation-based test algorithm generation for random access memories
Although there are well known test algorithms that have been used by the industry for years for testing semiconductor random-access memories (RAMs), systematic evaluation of their effectiveness and efficiency has been a difficult job. In the past, it was mainly done manually by proving a certain algorithm can detect a certain type of fault. As memory technology keeps innovating, the growing complexity of the memories and number of fault types that need to be covered will require more effective and efficient test algorithms to be discovered in much shorter time. A systematic approach for developing and evaluating memory test algorithms is thus desired. We propose such an approach here: test algorithm generation by simulation (TAGS), which generates and optimizes test algorithms, given a test time budget. Experimental results show that the algorithms generated by TAGS are more efficient than the traditional test algorithms. Using TAGS, a series of test algorithms with a detailed list of faults covered by each algorithm can be generated, providing easy trade-off between test time and fault coverage.
17604511
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein-protein interaction networks. The goal of this study was to create a virtual protein-protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein-protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners.
1236122
Range-free localization and its impact on large scale sensor networks
With the proliferation of location dependent applications in sensor networks, location awareness becomes an essential capability of sensor nodes. Because coarse accuracy is sufficient for most sensor network applications, solutions in range-free localization are being pursued as a cost-effective alternative to more expensive range-based approaches. In this paper, we present APIT, a novel localization algorithm that is range-free. We show that our APIT scheme performs best when an irregular radio pattern and random node placement are considered, and low communication overhead is desired. We compare our work, via extensive simulation, with three state-of-the-art range-free localization schemes to identify the preferable system configurations of each. In addition, we provide insight into the impact of localization accuracy on various location dependent applications and suggestions on improving their performance in the presence of such inaccuracy.
53223861
Design and test of a scalable security processor