NAMD: Biomolecular Simulation on Thousands of Processors
NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.

title: A framework for collective personalized communication
abstract: The paper explores collective personalized communication. For example, in all-to-all personalized communication (AAPC), each processor sends a distinct message to every other processor. However, for many applications, the collective communication pattern is many-to-many, where each processor sends a distinct message to a subset of processors. We first present strategies that reduce per-message cost to optimize AAPC. We then present performance results of these strategies in both all-to-all and many-to-many scenarios. These strategies are implemented in a flexible, asynchronous library with a non-blocking interface, and a message-driven runtime system. This allows the collective communication to run concurrently with the application, if desired. As a result the computational overhead of the communication is substantially reduced, at least on machines such as PSC Lemieux, which sport a co-processor capable of remote DMA. We demonstrate the advantages of our framework with performance results on several benchmarks and applications.

title: Physical simulation for animation and visual effects: parallelization and characterization for chip multiprocessors
abstract: We explore the emerging application area of physics-based simulation for computer animation and visual special effects. In particular, we examine its parallelization potential and characterize its behavior on a chip multiprocessor (CMP). Applications in this domain model and simulate natural phenomena, and often direct visual components of motion pictures. We study a set of three workloads that exemplify the span and complexity of physical simulation applications used in a production environment: fluid dynamics, facial animation, and cloth simulation. They are computationally demanding, requiring from a few seconds to several minutes to simulate a single frame; therefore, they can benefit greatly from the acceleration possible with large scale CMPs.
 Starting with serial versions of these applications, we parallelize code accounting for at least 96% of the serial execution time, targeting a large number of threads.We then study the most expensive modules using a simulated 64-core CMP.
 For the code representing key modules, we achieve parallel scaling of 45x, 50x, and 30x for fluid, face, and cloth simulations, respectively. The modules have a spectrum of parallel task granularity and locking behavior, and all but one are dominated by loop-level parallelism. Many modules operate on streams of data. In some cases, modules iterate over their data, leading to significant temporal locality. This streaming behavior leads to very high on-die and main memory bandwidth requirements. Finally, most modules have little inter-thread communication since they are data-parallel, but a few require heavy communication between data-parallel operations.

title: Hybrid transactional memory
abstract: High performance parallel programs are currently difficult to write and debug. One major source of difficulty is protecting concurrent accesses to shared data with an appropriate synchronization mechanism. Locks are the most common mechanism but they have a number of disadvantages, including possibly unnecessary serialization, and possible deadlock. Transactional memory is an alternative mechanism that makes parallel programming easier. With transactional memory, a transaction provides atomic and serializable operations on an arbitrary set of memory locations. When a transaction commits, all operations within the transaction become visible to other threads. When it aborts, all operations in the transaction are rolled back.Transactional memory can be implemented in either hardware or software. A straightforward hardware approach can have high performance, but imposes strict limits on the amount of data updated in each transaction. A software approach removes these limits, but incurs high overhead. We propose a novel hybrid hardware-software transactional memory scheme that approaches the performance of a hardware scheme when resources are not exhausted and gracefully falls back to a software scheme otherwise.

title: A novel progressive thick slab paradigm for volumetric medical image compression and navigation
abstract: In this paper, we propose a novel thick slab paradigm which provides an efficient scheme to navigate through large three dimensional (3-D) medical data sets within the framework of wavelet based lossless volumetric compression. We also propose a 3-D wavelet-like multi-resolution decomposition to perform 3-D image compression, which provides better compression ratio and 3 times faster decoding than JPEG-2000 for large data sets of computed tomography modality, along with a clinical workflow for navigation application. The proposed method suits radiology applications better than JPEG-2000 as it improves the productivity of radiologists by reducing their waiting time while the data is being transferred from a remote database over the network, along with reduction in diagnosis time, by providing an efficient navigation scheme with high compression performance.

title: MEGA2: molecular evolutionary genetics analysis software
abstract: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.


AVAILABILITY
http://www.megasoftware.net.

title: A hierarchical field framework for unified context-based classification
abstract: We present a two-layer hierarchical formulation to exploit different levels of contextual information in images for robust classification. Each layer is modeled as a conditional field that allows one to capture arbitrary observation-dependent label interactions. The proposed framework has two main advantages. First, it encodes both the short-range interactions (e.g., pixelwise label smoothing) as well as the long-range interactions (e.g., relative configurations of objects or regions) in a tractable manner. Second, the formulation is general enough to be applied to different domains ranging from pixelwise image labeling to contextual object detection. The parameters of the model are learned using a sequential maximum-likelihood approximation. The benefits of the proposed framework are demonstrated on four different datasets and comparison results are presented