Evaluation of OpenMP for the Cyclops multithreaded architecture

Multithreaded architectures have the potential of tolerating large memory and functional unit latencies and increase resource utilization. The Blue Gene/Cyclops architecture, being developed at the IBM T. J. Watson Research Center, is one such systems that offers massive intra-chip parallelism. Although the BG/C architecture was initially designed to execute specific applications, we believe that it can be effectively used on a broad range of parallel numerical applications. Programming such applications for this unconventional design requires a significant porting effort when using the basic built-in mechanisms for thread management and synchronization. In this paper, we describe the implementation of an OpenMP environment for parallelizing applications, currently under development at the CEPBA-IBM Research Institute, targeting BG/C. The environment is evaluated with a set of simple numerical kernels and a subset of the NAS OpenMP benchmarks. We identify issues that were not initially considered in the design of the BG/C architecture to support a programming model such as OpenMP. We also evaluate features currently offered by the BG/C architecture that should be considered in the implementation of an efficient OpenMP layer for massive intra-chip parallel architectures.Peer ReviewedPostprint (author's final draft

Optimizing NANOS OpenMP for the IBM Cyclops multithreaded architecture

In this paper, we present two approaches to improve the execution of OpenMP applications on the IBM Cyclops multithreaded architecture. Both solutions are independent and they are focused to obtain better performance through a better management of the cache locality. The first solution is based on software modifications to the OpenMP runtime library to balance stack accesses across all data caches. The second solution is a small hardware modification to change the data cache mapping behavior, with the same goal. Both solutions help parallel applications to improve scalability and obtain better performance in this kind of architectures. In fact, they could also be applied to future multi-core processors. We have executed (using simulation) some of the NAS benchmarks to prove these proposals. They show how, with small changes in both the software and the hardware, we achieve very good scalability in parallel applications. Our results also show that standard execution environments oriented to multiprocessor architectures can be easily adapted to exploit multithreaded processors.Peer ReviewedPostprint (author's final draft

Reliable Software for Unreliable Hardware - A Cross-Layer Approach

A novel cross-layer reliability analysis, modeling, and optimization approach is proposed in this thesis that leverages multiple layers in the system design abstraction (i.e. hardware, compiler, system software, and application program) to exploit the available reliability enhancing potential at each system layer and to exchange this information across multiple system layers

The fast multipole method at exascale

This thesis presents a top to bottom analysis on designing and implementing fast algorithms for current and future systems. We present new analysis, algorithmic techniques, and implementations of the Fast Multipole Method (FMM) for solving N- body problems. We target the FMM because it is broadly applicable to a variety of scientific particle simulations used to study electromagnetic, fluid, and gravitational phenomena, among others. Importantly, the FMM has asymptotically optimal time complexity with guaranteed approximation accuracy. As such, it is among the most attractive solutions for scalable particle simulation on future extreme scale systems. We specifically address two key challenges. The first challenge is how to engineer fast code for today’s platforms. We present the first in-depth study of multicore op- timizations and tuning for FMM, along with a systematic approach for transforming a conventionally-parallelized FMM into a highly-tuned one. We introduce novel opti- mizations that significantly improve the within-node scalability of the FMM, thereby enabling high-performance in the face of multicore and manycore systems. The second challenge is how to understand scalability on future systems. We present a new algorithmic complexity analysis of the FMM that considers both intra- and inter- node communication costs. Using these models, we present results for choosing the optimal algorithmic tuning parameter. This analysis also yields the surprising prediction that although the FMM is largely compute-bound today, and therefore highly scalable on current systems, the trajectory of processor architecture designs, if there are no significant changes could cause it to become communication-bound as early as the year 2015. This prediction suggests the utility of our analysis approach, which directly relates algorithmic and architectural characteristics, for enabling a new kind of highlevel algorithm-architecture co-design. To demonstrate the scientific significance of FMM, we present two applications namely, direct simulation of blood which is a multi-scale multi-physics problem and large-scale biomolecular electrostatics. MoBo (Moving Boundaries) is the infrastruc- ture for the direct numerical simulation of blood. It comprises of two key algorithmic components of which FMM is one. We were able to simulate blood flow using Stoke- sian dynamics on 200,000 cores of Jaguar, a peta-flop system and achieve a sustained performance of 0.7 Petaflop/s. The second application we propose as future work in this thesis is biomolecular electrostatics where we solve for the electrical potential using the boundary-integral formulation discretized with boundary element methods (BEM). The computational kernel in solving the large linear system is dense matrix vector multiply which we propose can be calculated using our scalable FMM. We propose to begin with the two dielectric problem where the electrostatic field is cal- culated using two continuum dielectric medium, the solvent and the molecule. This is only a first step to solving biologically challenging problems which have more than two dielectric medium, ion-exclusion layers, and solvent filled cavities. Finally, given the difficulty in producing high-performance scalable code, productivity is a key concern. Recently, numerical algorithms are being redesigned to take advantage of the architectural features of emerging multicore processors. These new classes of algorithms express fine-grained asynchronous parallelism and hence reduce the cost of synchronization. We performed the first extensive performance study of a recently proposed parallel programming model, called Concurrent Collections (CnC). In CnC, the programmer expresses her computation in terms of application-specific operations, partially-ordered by semantic scheduling constraints. The CnC model is well-suited to expressing asynchronous-parallel algorithms, so we evaluate CnC using two dense linear algebra algorithms in this style for execution on state-of-the-art mul- ticore systems. Our implementations in CnC was able to match and in some cases even exceed competing vendor-tuned and domain specific library codes. We combine these two distinct research efforts by expressing FMM in CnC, our approach tries to marry performance with productivity that will be critical on future systems. Looking forward, we would like to extend this to distributed memory machines, specifically implement FMM in the new distributed CnC, distCnC to express fine-grained paral- lelism which would require significant effort in alternative models.Ph.D