A sweep algorithm for massively parallel simulation of circuit-switched networks

A new massively parallel algorithm is presented for simulating large asymmetric circuit-switched networks, controlled by a randomized-routing policy that includes trunk-reservation. A single instruction multiple data (SIMD) implementation is described, and corresponding experiments on a 16384 processor MasPar parallel computer are reported. A multiple instruction multiple data (MIMD) implementation is also described, and corresponding experiments on an Intel IPSC/860 parallel computer, using 16 processors, are reported. By exploiting parallelism, our algorithm increases the possible execution rate of such complex simulations by as much as an order of magnitude

MPRAnalyze: statistical framework for massively parallel reporter assays.

Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods

Fast parallel solution of fixed point equations for the performance evaluation of circuit-switched networks

Massively parallel algorithms are presented for solving systems of fixed point equations, modeling state-dependent routing in large asymmetric circuit-switched networks. Our focus is on the Aggregated Least Busy Alternative (ALBA) routing policy of Mitra, Gibbens and Huang. On a 16384 processor MasPar parallel computer, about a minute is required to compute estimates of the call blocking probabilities for every node-pair, for realistic networks of over 100 nodes. A few hours are required on a high speed workstation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31594/1/0000523.pd

Stealth databases : ensuring user-controlled queries in untrusted cloud environments

Sensitive data is increasingly being hosted online in ubiquitous cloud storage services. Recent advances in multi-cloud service integration through provider multiplexing and data dispersion have alleviated most of the associated risks for hosting files which are retrieved by users for further processing. However, for structured data managed in databases, many issues remain, including the need to perform operations directly on the remote data to avoid costly transfers. In this paper, we motivate the need for distributed stealth databases which combine properties from structure-preserving dispersed file storage for capacity-saving increased availability with emerging work on structure-preserving encryption for on-demand increased confidentiality with controllable performance degradation. We contribute an analysis of operators executing in map-reduce or map-carry-reduce phases and derive performance statistics. Our prototype, StealthDB, demonstrates that for typical amounts of personal structured data, stealth databases are a convincing concept for taming untrusted and unsafe cloud environments

Asymmetric Load Balancing on a Heterogeneous Cluster of PCs

In recent years, high performance computing with commodity clusters of personal computers has become an active area of research. Many organizations build them because they need the computational speedup provided by parallel processing but cannot afford to purchase a supercomputer. With commercial supercomputers and homogenous clusters of PCs, applications that can be statically load balanced are done so by assigning equal tasks to each processor. With heterogeneous clusters, the system designers have the option of quickly adding newer hardware that is more powerful than the existing hardware. When this is done, the assignment of equal tasks to each processor results in suboptimal performance. This research addresses techniques by which the size of the tasks assigned to processors is a suitable match to the processors themselves, in which the more powerful processors can do more work, and the less powerful processors perform less work. We find that when the range of processing power is narrow, some benefit can be achieved with asymmetric load balancing. When the range of processing power is broad, dramatic improvements in performance are realized our experiments have shown up to 92% improvement when asymmetrically load balancing a modified version of the NAS Parallel Benchmarks\u27 LU application

Scalable Parallel Computers for Real-Time Signal Processing

We assess the state-of-the-art technology in massively parallel processors (MPPs) and their variations in different architectural platforms. Architectural and programming issues are identified in using MPPs for time-critical applications such as adaptive radar signal processing. We review the enabling technologies. These include high-performance CPU chips and system interconnects, distributed memory architectures, and various latency hiding mechanisms. We characterize the concept of scalability in three areas: resources, applications, and technology. Scalable performance attributes are analytically defined. Then we compare MPPs with symmetric multiprocessors (SMPs) and clusters of workstations (COWs). The purpose is to reveal their capabilities, limits, and effectiveness in signal processing. We evaluate the IBM SP2 at MHPCC, the Intel Paragon at SDSC, the Gray T3D at Gray Eagan Center, and the Gray T3E and ASCI TeraFLOP system proposed by Intel. On the software and programming side, we evaluate existing parallel programming environments, including the models, languages, compilers, software tools, and operating systems. Some guidelines for program parallelization are provided. We examine data-parallel, shared-variable, message-passing, and implicit programming models. Communication functions and their performance overhead are discussed. Available software tools and communication libraries are also introducedpublished_or_final_versio

OpenFPM: A scalable environment for particle and particle-mesh codes on parallel computers

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established tool of discovery, together with theory and experiment. Meanwhile, the performance of computing hardware grows with increasing heterogeneous hardware, enabling simulations of ever more complex models. However, efficiently implementing scalable codes on heterogeneous, distributed hardware systems becomes the bottleneck. This bottleneck can be alleviated by intermediate software layers that provide higher-level abstractions closer to the problem domain, hence allowing the computational scientist to focus on the simulation. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of particles-only and hybrid particle-mesh simulations of both discrete and continuous models, as well as non-simulation codes. This infrastructure is complemented with frequently used numerical routines, as well as interfaces to third-party libraries. This thesis will present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed-Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), Vortex Methods, stencil codes, high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing software frameworks