4,692 research outputs found
Accelerating exhaustive pairwise metagenomic comparisons
In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec
When parallel speedups hit the memory wall
After Amdahl's trailblazing work, many other authors proposed analytical
speedup models but none have considered the limiting effect of the memory wall.
These models exploited aspects such as problem-size variation, memory size,
communication overhead, and synchronization overhead, but data-access delays
are assumed to be constant. Nevertheless, such delays can vary, for example,
according to the number of cores used and the ratio between processor and
memory frequencies. Given the large number of possible configurations of
operating frequency and number of cores that current architectures can offer,
suitable speedup models to describe such variations among these configurations
are quite desirable for off-line or on-line scheduling decisions. This work
proposes new parallel speedup models that account for variations of the average
data-access delay to describe the limiting effect of the memory wall on
parallel speedups. Analytical results indicate that the proposed modeling can
capture the desired behavior while experimental hardware results validate the
former. Additionally, we show that when accounting for parameters that reflect
the intrinsic characteristics of the applications, such as degree of
parallelism and susceptibility to the memory wall, our proposal has significant
advantages over machine-learning-based modeling. Moreover, besides being
black-box modeling, our experiments show that conventional machine-learning
modeling needs about one order of magnitude more measurements to reach the same
level of accuracy achieved in our modeling.Comment: 24 page
Parallelizing RRT on distributed-memory architectures
This paper addresses the problem of improving the performance of the Rapidly-exploring Random Tree (RRT) algorithm by parallelizing it. For scalability reasons we do so on a distributed-memory architecture, using the message-passing paradigm. We present three parallel versions of RRT along with the technicalities involved in their implementation. We also evaluate the algorithms and study how they behave on different motion planning problems
Iso-energy-efficiency: An approach to power-constrained parallel computation
Future large scale high performance supercomputer systems require high energy efficiency to achieve exaflops computational power and beyond. Despite the need to understand energy efficiency in high-performance systems, there are few techniques to evaluate energy efficiency at scale. In this paper, we propose a system-level iso-energy-efficiency model to analyze, evaluate and predict energy-performance of data intensive parallel applications with various execution patterns running on large scale power-aware clusters. Our analytical model can help users explore the effects of machine and application dependent characteristics on system energy efficiency and isolate efficient ways to scale system parameters (e.g. processor count, CPU power/frequency, workload size and network bandwidth) to balance energy use and performance. We derive our iso-energy-efficiency model and apply it to the NAS Parallel Benchmarks on two power-aware clusters. Our results indicate that the model accurately predicts total system energy consumption within 5% error on average for parallel applications with various execution and communication patterns. We demonstrate effective use of the model for various application contexts and in scalability decision-making
PowerPack: Energy Profiling and Analysis of High-Performance Systems and Applications
Energy efficiency is a major concern in modern high-performance computing system design. In the past few years, there has been mounting evidence that power usage limits system scale and computing density, and thus, ultimately system performance. However, despite the impact of power and energy on the computer systems community, few studies provide insight to where and how power is consumed on high-performance systems and applications. In previous work, we designed a framework called PowerPack that was the first tool to isolate the power consumption of devices including disks, memory, NICs, and processors in a high-performance cluster and correlate these measurements to application functions. In this work, we extend our framework to support systems with multicore, multiprocessor-based nodes, and then provide in-depth analyses of the energy consumption of parallel applications on clusters of these systems. These analyses include the impacts of chip multiprocessing on power and energy efficiency, and its interaction with application executions. In addition, we use PowerPack to study the power dynamics and energy efficiencies of dynamic voltage and frequency scaling (DVFS) techniques on clusters. Our experiments reveal conclusively how intelligent DVFS scheduling can enhance system energy efficiency while maintaining performance
Petuum: A New Platform for Distributed Machine Learning on Big Data
What is a systematic way to efficiently apply a wide spectrum of advanced ML
programs to industrial scale problems, using Big Models (up to 100s of billions
of parameters) on Big Data (up to terabytes or petabytes)? Modern
parallelization strategies employ fine-grained operations and scheduling beyond
the classic bulk-synchronous processing paradigm popularized by MapReduce, or
even specialized graph-based execution that relies on graph representations of
ML programs. The variety of approaches tends to pull systems and algorithms
design in different directions, and it remains difficult to find a universal
platform applicable to a wide range of ML programs at scale. We propose a
general-purpose framework that systematically addresses data- and
model-parallel challenges in large-scale ML, by observing that many ML programs
are fundamentally optimization-centric and admit error-tolerant,
iterative-convergent algorithmic solutions. This presents unique opportunities
for an integrative system design, such as bounded-error network synchronization
and dynamic scheduling based on ML program structure. We demonstrate the
efficacy of these system designs versus well-known implementations of modern ML
algorithms, allowing ML programs to run in much less time and at considerably
larger model sizes, even on modestly-sized compute clusters.Comment: 15 pages, 10 figures, final version in KDD 2015 under the same titl
Parallelizing RRT on large-scale distributed-memory architectures
This paper addresses the problem of parallelizing the Rapidly-exploring Random Tree (RRT) algorithm on large-scale distributed-memory architectures, using the Message Passing Interface. We compare three parallel versions of RRT based on classical parallelization schemes. We evaluate them on different motion planning problems and analyze the various factors influencing their performance
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