GLB: Lifeline-based Global Load Balancing library in X10

We present GLB, a programming model and an associated implementation that can handle a wide range of irregular paral- lel programming problems running over large-scale distributed systems. GLB is applicable both to problems that are easily load-balanced via static scheduling and to problems that are hard to statically load balance. GLB hides the intricate syn- chronizations (e.g., inter-node communication, initialization and startup, load balancing, termination and result collection) from the users. GLB internally uses a version of the lifeline graph based work-stealing algorithm proposed by Saraswat et al. Users of GLB are simply required to write several pieces of sequential code that comply with the GLB interface. GLB then schedules and orchestrates the parallel execution of the code correctly and efficiently at scale. We have applied GLB to two representative benchmarks: Betweenness Centrality (BC) and Unbalanced Tree Search (UTS). Among them, BC can be statically load-balanced whereas UTS cannot. In either case, GLB scales well-- achieving nearly linear speedup on different computer architectures (Power, Blue Gene/Q, and K) -- up to 16K cores

Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond

In this and a set of companion whitepapers, the USQCD Collaboration lays out a program of science and computing for lattice gauge theory. These whitepapers describe how calculation using lattice QCD (and other gauge theories) can aid the interpretation of ongoing and upcoming experiments in particle and nuclear physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers

Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

cphVB: A System for Automated Runtime Optimization and Parallelization of Vectorized Applications

Modern processor architectures, in addition to having still more cores, also require still more consideration to memory-layout in order to run at full capacity. The usefulness of most languages is deprecating as their abstractions, structures or objects are hard to map onto modern processor architectures efficiently. The work in this paper introduces a new abstract machine framework, cphVB, that enables vector oriented high-level programming languages to map onto a broad range of architectures efficiently. The idea is to close the gap between high-level languages and hardware optimized low-level implementations. By translating high-level vector operations into an intermediate vector bytecode, cphVB enables specialized vector engines to efficiently execute the vector operations. The primary success parameters are to maintain a complete abstraction from low-level details and to provide efficient code execution across different, modern, processors. We evaluate the presented design through a setup that targets multi-core CPU architectures. We evaluate the performance of the implementation using Python implementations of well-known algorithms: a jacobi solver, a kNN search, a shallow water simulation and a synthetic stencil simulation. All demonstrate good performance