Simulating the universe on an intercontinental grid of supercomputers

Understanding the universe is hampered by the elusiveness of its most common constituent, cold dark matter. Almost impossible to observe, dark matter can be studied effectively by means of simulation and there is probably no other research field where simulation has led to so much progress in the last decade. Cosmological N-body simulations are an essential tool for evolving density perturbations in the nonlinear regime. Simulating the formation of large-scale structures in the universe, however, is still a challenge due to the enormous dynamic range in spatial and temporal coordinates, and due to the enormous computer resources required. The dynamic range is generally dealt with by the hybridization of numerical techniques. We deal with the computational requirements by connecting two supercomputers via an optical network and make them operate as a single machine. This is challenging, if only for the fact that the supercomputers of our choice are separated by half the planet, as one is located in Amsterdam and the other is in Tokyo. The co-scheduling of the two computers and the 'gridification' of the code enables us to achieve a 90% efficiency for this distributed intercontinental supercomputer.Comment: Accepted for publication in IEEE Compute

IMPROVING SMART GRID SECURITY USING MERKLE TREES

Abstract—Presently nations worldwide are starting to convert their aging electrical power infrastructures into modern, dynamic power grids. Smart Grid offers much in the way of efficiencies and robustness to the electrical power grid, however its heavy reliance on communication networks will leave it more vulnerable to attack than present day grids. This paper looks at the threat to public key cryptography systems from a fully realized quantum computer and how this could impact the Smart Grid. We argue for the use of Merkle Trees in place of public key cryptography for authentication of devices in wireless mesh networks that are used in Smart Grid applications

VoroCrust: Voronoi Meshing Without Clipping

Polyhedral meshes are increasingly becoming an attractive option with particular advantages over traditional meshes for certain applications. What has been missing is a robust polyhedral meshing algorithm that can handle broad classes of domains exhibiting arbitrarily curved boundaries and sharp features. In addition, the power of primal-dual mesh pairs, exemplified by Voronoi-Delaunay meshes, has been recognized as an important ingredient in numerous formulations. The VoroCrust algorithm is the first provably-correct algorithm for conforming polyhedral Voronoi meshing for non-convex and non-manifold domains with guarantees on the quality of both surface and volume elements. A robust refinement process estimates a suitable sizing field that enables the careful placement of Voronoi seeds across the surface circumventing the need for clipping and avoiding its many drawbacks. The algorithm has the flexibility of filling the interior by either structured or random samples, while preserving all sharp features in the output mesh. We demonstrate the capabilities of the algorithm on a variety of models and compare against state-of-the-art polyhedral meshing methods based on clipped Voronoi cells establishing the clear advantage of VoroCrust output.Comment: 18 pages (including appendix), 18 figures. Version without compressed images available on https://www.dropbox.com/s/qc6sot1gaujundy/VoroCrust.pdf. Supplemental materials available on https://www.dropbox.com/s/6p72h1e2ivw6kj3/VoroCrust_supplemental_materials.pd

Distributed match-making

In many distributed computing environments, processes are concurrently executed by nodes in a store- and-forward communication network. Distributed control issues as diverse as name server, mutual exclusion, and replicated data management involve making matches between such processes. We propose a formal problem called distributed match-making as the generic paradigm. Algorithms for distributed match-making are developed and the complexity is investigated in terms of messages and in terms of storage needed. Lower bounds on the complexity of distributed match-making are established. Optimal algorithms, or nearly optimal algorithms, are given for particular network topologies

The Tree-Particle-Mesh N-body Gravity Solver

The Tree-Particle-Mesh (TPM) N-body algorithm couples the tree algorithm for directly computing forces on particles in an hierarchical grouping scheme with the extremely efficient mesh based PM structured approach. The combined TPM algorithm takes advantage of the fact that gravitational forces are linear functions of the density field. Thus one can use domain decomposition to break down the density field into many separate high density regions containing a significant fraction of the mass but residing in a very small fraction of the total volume. In each of these high density regions the gravitational potential is computed via the tree algorithm supplemented by tidal forces from the external density distribution. For the bulk of the volume, forces are computed via the PM algorithm; timesteps in this PM component are large compared to individually determined timesteps in the tree regions. Since each tree region can be treated independently, the algorithm lends itself to very efficient parallelization using message passing. We have tested the new TPM algorithm (a refinement of that originated by Xu 1995) by comparison with results from Ferrell & Bertschinger's P^3M code and find that, except in small clusters, the TPM results are at least as accurate as those obtained with the well-established P^3M algorithm, while taking significantly less computing time. Production runs of 10^9 particles indicate that the new code has great scientific potential when used with distributed computing resources.Comment: 24 pages including 9 figures, uses aaspp4.sty; revised to match published versio

On the design and implementation of broadcast and global combine operations using the postal model

There are a number of models that were proposed in recent years for message passing parallel systems. Examples are the postal model and its generalization the LogP model. In the postal model a parameter λ is used to model the communication latency of the message-passing system. Each node during each round can send a fixed-size message and, simultaneously, receive a message of the same size. Furthermore, a message sent out during round r will incur a latency of hand will arrive at the receiving node at round r + λ - 1. Our goal in this paper is to bridge the gap between the theoretical modeling and the practical implementation. In particular, we investigate a number of practical issues related to the design and implementation of two collective communication operations, namely, the broadcast operation and the global combine operation. Those practical issues include, for example, 1) techniques for measurement of the value of λ on a given machine, 2) creating efficient broadcast algorithms that get the latency hand the number of nodes n as parameters and 3) creating efficient global combine algorithms for parallel machines with λ which is not an integer. We propose solutions that address those practical issues and present results of an experimental study of the new algorithms on the Intel Delta machine. Our main conclusion is that the postal model can help in performance prediction and tuning, for example, a properly tuned broadcast improves the known implementation by more than 20%

Design of testbed and emulation tools

The research summarized was concerned with the design of testbed and emulation tools suitable to assist in projecting, with reasonable accuracy, the expected performance of highly concurrent computing systems on large, complete applications. Such testbed and emulation tools are intended for the eventual use of those exploring new concurrent system architectures and organizations, either as users or as designers of such systems. While a range of alternatives was considered, a software based set of hierarchical tools was chosen to provide maximum flexibility, to ease in moving to new computers as technology improves and to take advantage of the inherent reliability and availability of commercially available computing systems