7,424 research outputs found
Formal and Informal Methods for Multi-Core Design Space Exploration
We propose a tool-supported methodology for design-space exploration for
embedded systems. It provides means to define high-level models of applications
and multi-processor architectures and evaluate the performance of different
deployment (mapping, scheduling) strategies while taking uncertainty into
account. We argue that this extension of the scope of formal verification is
important for the viability of the domain.Comment: In Proceedings QAPL 2014, arXiv:1406.156
Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations
Spatial stochastic molecular simulations in biology are limited by the
intense computation required to track molecules in space either in a discrete
time or discrete space framework, meaning that the serial limit has already
been reached in sub-cellular models. This calls for parallel simulations that
can take advantage of the power of modern supercomputers; however exact methods
are known to be inherently serial. We introduce an operator splitting
implementation for irregular grids with a novel method to improve accuracy, and
demonstrate potential for scalable parallel simulations in an initial MPI
version. We foresee that this groundwork will enable larger scale, whole-cell
stochastic simulations in the near future.Comment: 33 pages, 10 figure
Some simple but challenging Markov processes
In this note, we present few examples of Piecewise Deterministic Markov
Processes and their long time behavior. They share two important features: they
are related to concrete models (in biology, networks, chemistry,. . .) and they
are mathematically rich. Their math-ematical study relies on coupling method,
spectral decomposition, PDE technics, functional inequalities. We also relate
these simple examples to recent and open problems
Limits on Fundamental Limits to Computation
An indispensable part of our lives, computing has also become essential to
industries and governments. Steady improvements in computer hardware have been
supported by periodic doubling of transistor densities in integrated circuits
over the last fifty years. Such Moore scaling now requires increasingly heroic
efforts, stimulating research in alternative hardware and stirring controversy.
To help evaluate emerging technologies and enrich our understanding of
integrated-circuit scaling, we review fundamental limits to computation: in
manufacturing, energy, physical space, design and verification effort, and
algorithms. To outline what is achievable in principle and in practice, we
recall how some limits were circumvented, compare loose and tight limits. We
also point out that engineering difficulties encountered by emerging
technologies may indicate yet-unknown limits.Comment: 15 pages, 4 figures, 1 tabl
PCODE: an efficient and reliable collective communication protocol for unreliable broadcast domain
Existing programming environments for clusters are typically built on top of a point-to-point communication layer (send and receive) over local area networks (LANs) and, as a result, suffer from poor performance in the collective communication part. For example, a broadcast that is implemented using a TCP/IP protocol (which is a point-to-point protocol) over a LAN is obviously inefficient as it is not utilizing the fact that the LAN is a broadcast medium. We have observed that the main difference between a distributed computing paradigm and a message passing parallel computing paradigm is that, in a distributed environment the activity of every processor is independent while in a parallel environment the collection of the user-communication layers in the processors can be modeled as a single global program. We have formalized the requirements by defining the notion of a correct global program. This notion provides a precise specification of the interface between the transport layer and the user-communication layer. We have developed PCODE, a new communication protocol that is driven by a global program and proved its correctness.
We have implemented the PCODE protocol on a collection of IBM RS/6000 workstations and on a collection of Silicon Graphics Indigo workstations, both communicating via UDP broadcast. The experimental results we obtained indicate that the performance advantage of PCODE over the current point-to-point approach (TCP) can be as high as an order of magnitude on a cluster of 16 workstations
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