A Malleable-Job System for Timeshared Parallel Machines
Malleable jobs are parallel programs that can change the number of processors on which they are executing at run time in response to an external command. One of the advantages of such jobs is that a job scheduler for malleable jobs can provide improved system utilization and average response time over a scheduler for traditional jobs. In this paper, we present a programming system for creating malleable jobs that is more general than other current malleable systems. In particular, it is not limited to the master-worker paradigm or the Fortran SPMD programming model, but can also support general purpose parallel programs including those written in MPI and Charm++, and has built-in migration and load-balancing, among other features.

title: NAMD: Biomolecular Simulation on Thousands of Processors
abstract: 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: 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: Recognition of human actions using moment based features and artificial neural networks
abstract: This paper presents performance of view-based approach in automated recognition of predefined hand and gross body actions using artificial neural network. This approach represents motion by a static grey scale image template computed by collapsing the temporal components into the cumulative image-difference of frames. The seven invariant Hu moments are used as the feature vectors. The performance of the system is tested in real time using feed forward multilayer perceptron (MLP) based on back propagation.

title: A combinatorial approach for studying LOCC transformations of multipartite states
abstract: We develop graph theoretic methods for analysing maximally entangled pure states distributed between a number of different parties. We introduce a technique called {\it bicolored merging}, based on the monotonicity feature of entanglement measures, for determining combinatorial conditions that must be satisfied for any two distinct multiparticle states to be comparable under local operations and classical communication (LOCC). We present several results based on the possibility or impossibility of comparability of pure multipartite states. We show that there are exponentially many such entangled multipartite states among $n$ agents. Further, we discuss a new graph theoretic metric on a class of multi-partite states, and its implications.

title: Compilation, architectural support, and evaluation of SIMD graphics pipeline programs on a general-purpose CPU
abstract: Graphics and media processing is quickly emerging to become one of the key computing workloads. Programmable graphics processors give designers extra flexibility by running a small program for each fragment in the graphics pipeline. We investigate low-cost mechanisms to obtain good performance for modern graphics programs on a general purpose CPU. We present a compiler that compiles SIMD graphics program and generates efficient code on a general purpose CPU. The generated code can process between 25-0.3 million vertices per second on a 2.2 GHz Intel Pentium/spl reg/ 4 processor for a group of typical graphics programs. We also evaluate the impact of three changes in the architecture and compiler. Adding support for new specialized instructions improves the performance of the programs by 27.4% on average. A novel compiler optimization called mask analysis improves the performance of the programs by 19.5% on average. Increasing the number of architectural SIMD registers from 8 to 16 registers significantly reduces the number of memory accesses due to register spills.

title: Carbon: architectural support for fine-grained parallelism on chip multiprocessors
abstract: Chip multiprocessors (CMPs) are now commonplace, and the number of cores on a CMP is likely to grow steadily. However, in order to harness the additional compute resources of a CMP, applications must expose their thread-level parallelism to the hardware. One common approach to doing this is to decompose a program into parallel "tasks" and allow an underlying software layer to schedule these tasks to different threads. Software task scheduling can provide good parallel performance as long as tasks are large compared to the software overheads.
 We examine a set of applications from an important emerging domain: Recognition, Mining, and Synthesis (RMS). Many RMS applications are compute-intensive and have abundant thread-level parallelism, and are therefore good targets for running on a CMP. However, a significant number have small tasks for which software task schedulers achieve only limited parallel speedups.
 We propose Carbon, a hardware technique to accelerate dynamic task scheduling on scalable CMPs. Carbon has relatively simple hardware, most of which can be placed far from the cores. We compare Carbon to some highly tuned software task schedulers for a set of RMS benchmarks with small tasks. Carbon delivers significant performance improvements over the best software scheduler: on average for 64 cores, 68% faster on a set of loop-parallel benchmarks, and 109% faster on aset of task-parallel benchmarks.