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

Argobots: A Lightweight Low-Level Threading and Tasking Framework

In the past few decades, a number of user-level threading and tasking models have been proposed in the literature to address the shortcomings of OS-level threads, primarily with respect to cost and flexibility. Current state-of-the-art user-level threading and tasking models, however, either are too specific to applications or architectures or are not as powerful or flexible. In this paper, we present Argobots, a lightweight, low-level threading and tasking framework that is designed as a portable and performant substrate for high-level programming models or runtime systems. Argobots offers a carefully designed execution model that balances generality of functionality with providing a rich set of controls to allow specialization by end users or high-level programming models. We describe the design, implementation, and performance characterization of Argobots and present integrations with three high-level models: OpenMP, MPI, and colocated I/O services. Evaluations show that (1) Argobots, while providing richer capabilities, is competitive with existing simpler generic threading runtimes; (2) our OpenMP runtime offers more efficient interoperability capabilities than production OpenMP runtimes do; (3) when MPI interoperates with Argobots instead of Pthreads, it enjoys reduced synchronization costs and better latency-hiding capabilities; and (4) I/O services with Argobots reduce interference with colocated applications while achieving performance competitive with that of a Pthreads approach

The reduce-or process model for parallel execution of logic programs

AbstractA method for parallel execution of logic programs is presented. It uses REDUCE-OR trees instead of AND-OR or SLD trees. The REDUCE-OR trees represent logic-program computations in a manner suitable for parallel interpretation. The REDUCE-OR process model is derived from the tree representation by providing a process interpretation of tree development, and devising efficient bookkeeping mechanisms and algorithms. The process model is complete—it produces any particular solution eventually—and extracts full OR parallelism. This is in contrast to most other schemes that extract AND parallelism. It does this by solving the problem of interaction between AND and OR parallelism effectively. An important optimization that effectively controls the apparent overhead in the process model is given. Techniques that trade parallelism for reducing overhead are also described

Application Oriented And Computer Science Centered Hpcc Research

At this time, there is a perception of a backlash against the HPCC program, and even the idea of massively parallel computing itself. In preparation to defining an agenda for HPCC, this paper first analyzes the reasons for this backlash. Although beset with unrealistic expectations, parallel processing will be a beneficial technology with a broad impact, beyond applications in science. However, this will require significant advances and work in computer science in addition to parallel hardware and end-applications which are emphasized currently. The paper presents a possible agenda that could lead to a successful HPCC program in the future. 1 Introduction It is clear that amid the excitement about the emerging high performance computing technology, a backlash of sorts is developing. This backlash is against the HPCC program as well as the idea of massively parallel computing itself. Ken Kennedy, a leading researcher in parallel computing, wrote an article recently, titled "High Perfor..

A fault tolerance protocol with fast fault recovery

Fault tolerance is an important issue for large machines with tens or hundreds of thousands of processors. Checkpoint-based methods, currently used on most machines, rollback all processors to previous checkpoints after a crash. This wastes a significant amount of computation as all processors have to redo all the computation from that checkpoint onwards. In addition, recovery time is bound by the time between the last checkpoint and the crash. Protocols based on message logging avoid the problem of rolling back all processors to their earlier state. However, the recovery time of existing message logging protocols is no smaller than the time between the last checkpoint and crash. We present a fault tolerance protocol, in this paper, that provides fast restarts by using the ideas of message logging and object-based processor virtualization. We evaluate our implementation of the protocol in the Charm++/Adaptive MPI runtime system. We show that our protocol provides fast restarts and, for many applications, has low fault-free overhead.