15,624 research outputs found
An Overview of Multi-Processor Approximate Message Passing
Approximate message passing (AMP) is an algorithmic framework for solving
linear inverse problems from noisy measurements, with exciting applications
such as reconstructing images, audio, hyper spectral images, and various other
signals, including those acquired in compressive signal acquisiton systems. The
growing prevalence of big data systems has increased interest in large-scale
problems, which may involve huge measurement matrices that are unsuitable for
conventional computing systems. To address the challenge of large-scale
processing, multiprocessor (MP) versions of AMP have been developed. We provide
an overview of two such MP-AMP variants. In row-MP-AMP, each computing node
stores a subset of the rows of the matrix and processes corresponding
measurements. In column- MP-AMP, each node stores a subset of columns, and is
solely responsible for reconstructing a portion of the signal. We will discuss
pros and cons of both approaches, summarize recent research results for each,
and explain when each one may be a viable approach. Aspects that are
highlighted include some recent results on state evolution for both MP-AMP
algorithms, and the use of data compression to reduce communication in the MP
network
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
Improving the scalability of parallel N-body applications with an event driven constraint based execution model
The scalability and efficiency of graph applications are significantly
constrained by conventional systems and their supporting programming models.
Technology trends like multicore, manycore, and heterogeneous system
architectures are introducing further challenges and possibilities for emerging
application domains such as graph applications. This paper explores the space
of effective parallel execution of ephemeral graphs that are dynamically
generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The
workloads are expressed using the semantics of an Exascale computing execution
model called ParalleX. For comparison, results using conventional execution
model semantics are also presented. We find improved load balancing during
runtime and automatic parallelism discovery improving efficiency using the
advanced semantics for Exascale computing.Comment: 11 figure
A distributed agent architecture for real-time knowledge-based systems: Real-time expert systems project, phase 1
We propose a distributed agent architecture (DAA) that can support a variety of paradigms based on both traditional real-time computing and artificial intelligence. DAA consists of distributed agents that are classified into two categories: reactive and cognitive. Reactive agents can be implemented directly in Ada to meet hard real-time requirements and be deployed on on-board embedded processors. A traditional real-time computing methodology under consideration is the rate monotonic theory that can guarantee schedulability based on analytical methods. AI techniques under consideration for reactive agents are approximate or anytime reasoning that can be implemented using Bayesian belief networks as in Guardian. Cognitive agents are traditional expert systems that can be implemented in ART-Ada to meet soft real-time requirements. During the initial design of cognitive agents, it is critical to consider the migration path that would allow initial deployment on ground-based workstations with eventual deployment on on-board processors. ART-Ada technology enables this migration while Lisp-based technologies make it difficult if not impossible. In addition to reactive and cognitive agents, a meta-level agent would be needed to coordinate multiple agents and to provide meta-level control
High Performance Computing of Gene Regulatory Networks using a Message-Passing Model
Gene regulatory network reconstruction is a fundamental problem in
computational biology. We recently developed an algorithm, called PANDA
(Passing Attributes Between Networks for Data Assimilation), that integrates
multiple sources of 'omics data and estimates regulatory network models. This
approach was initially implemented in the C++ programming language and has
since been applied to a number of biological systems. In our current research
we are beginning to expand the algorithm to incorporate larger and most diverse
data-sets, to reconstruct networks that contain increasing numbers of elements,
and to build not only single network models, but sets of networks. In order to
accomplish these "Big Data" applications, it has become critical that we
increase the computational efficiency of the PANDA implementation. In this
paper we show how to recast PANDA's similarity equations as matrix operations.
This allows us to implement a highly readable version of the algorithm using
the MATLAB/Octave programming language. We find that the resulting M-code much
shorter (103 compared to 1128 lines) and more easily modifiable for potential
future applications. The new implementation also runs significantly faster,
with increasing efficiency as the network models increase in size. Tests
comparing the C-code and M-code versions of PANDA demonstrate that this
speed-up is on the order of 20-80 times faster for networks of similar
dimensions to those we find in current biological applications
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