Efficient hypercube communications

Hypercube algorithms may be developed for a variety of communication-intensive tasks such as sending a message from one node to another, broadcasting a message from one node to all others, broadcasting a message from each node to all others, all-to-all personalized communication, one-to-all personalized communication, and exchanging messages between nodes via fixed permutations. All these communication patterns are special cases of many-to-many personalized communication. The problem of many-to-many personalized communication is investigated here. Two routing algorithms for many-to-many personalized communication are presented here. The algorithms proposed yield very high performance with respect to the number of time steps and packet transmissions. The first algorithm yields high performance through attempts to equibalance the number of messages at intermediate nodes. This technique tries to avoid creating a bottleneck at any node and thus reduces the total communication time. The second algorithm yields high performance through one-step time-lookahead equibalancing. It chooses from the candidate intermediate nodes the one which will probably have the minimum number of messages in the next cycle

Optimal cube-connected cube multiprocessors

Many CFD (computational fluid dynamics) and other scientific applications can be partitioned into subproblems. However, in general the partitioned subproblems are very large. They demand high performance computing power themselves, and the solutions of the subproblems have to be combined at each time step. The cube-connect cube (CCCube) architecture is studied. The CCCube architecture is an extended hypercube structure with each node represented as a cube. It requires fewer physical links between nodes than the hypercube, and provides the same communication support as the hypercube does on many applications. The reduced physical links can be used to enhance the bandwidth of the remaining links and, therefore, enhance the overall performance. The concept and the method to obtain optimal CCCubes, which are the CCCubes with a minimum number of links under a given total number of nodes, are proposed. The superiority of optimal CCCubes over standard hypercubes was also shown in terms of the link usage in the embedding of a binomial tree. A useful computation structure based on a semi-binomial tree for divide-and-conquer type of parallel algorithms was identified. It was shown that this structure can be implemented in optimal CCCubes without performance degradation compared with regular hypercubes. The result presented should provide a useful approach to design of scientific parallel computers

Designing Networks with Good Equilibria under Uncertainty

We consider the problem of designing network cost-sharing protocols with good equilibria under uncertainty. The underlying game is a multicast game in a rooted undirected graph with nonnegative edge costs. A set of k terminal vertices or players need to establish connectivity with the root. The social optimum is the Minimum Steiner Tree. We are interested in situations where the designer has incomplete information about the input. We propose two different models, the adversarial and the stochastic. In both models, the designer has prior knowledge of the underlying metric but the requested subset of the players is not known and is activated either in an adversarial manner (adversarial model) or is drawn from a known probability distribution (stochastic model). In the adversarial model, the designer's goal is to choose a single, universal protocol that has low Price of Anarchy (PoA) for all possible requested subsets of players. The main question we address is: to what extent can prior knowledge of the underlying metric help in the design? We first demonstrate that there exist graphs (outerplanar) where knowledge of the underlying metric can dramatically improve the performance of good network design. Then, in our main technical result, we show that there exist graph metrics, for which knowing the underlying metric does not help and any universal protocol has PoA of $\Omega(\log k)$, which is tight. We attack this problem by developing new techniques that employ powerful tools from extremal combinatorics, and more specifically Ramsey Theory in high dimensional hypercubes. Then we switch to the stochastic model, where each player is independently activated. We show that there exists a randomized ordered protocol that achieves constant PoA. By using standard derandomization techniques, we produce a deterministic ordered protocol with constant PoA.Comment: This version has additional results about stochastic inpu

Data broadcasting and reduction, prefix computation, and sorting on reduced hypercube (RH) parallel computers

The binary hypercube parallel computer has been very popular due to its rich interconnection structure and small average internode distance which allow the efficient embedding of frequently used topologies. Communication patterns of many parallel algorithms also match the hypercube topology. The hypercube has high VLSI complexity. however. due to the logarithmic increase in the number of connections to each node with the increase in the number of dimensions of the hypercube. The reduced hypercube (RH) interconnection network. which is obtained by a uniform reduction in the number of links for each hypercube node. yields lower-complexity interconnection networks when compared to hypercubes with the same number of nodes. It has been shown elsewhere that the RH interconnection network achieves performance comparable to that of the hypercube. at lower hardware cost. The reduced VLSI complexity of the RH also permits the construction of larger systems. thus. making the RH suitable for massively parallel processing. This thesis proposes algorithms for data broadcasting and reduction. prefix computation, and sorting on the RH parallel computer. All these operations are fundamental to many parallel algorithms. A worst case analysis of each algorithm is given and compared with equivalent- algorithms for the regular hypercube. It is shown that the proposed algorithms for the RH yield performance comparable to that for the regular hypercube

Processor allocation strategies for modified hypercubes

Parallel processing has been widely accepted to be the future in high speed computing. Among the various parallel architectures proposed/implemented, the hypercube has shown a lot of promise because of its poweful properties, like regular topology, fault tolerance, low diameter, simple routing, and ability to efficiently emulate other architectures. The major drawback of the hypercube network is that it can not be expanded in practice because the number of communication ports for each processor grows as the logarithm of the total number of processors in the system. Therefore, once a hypercube supercomputer of a certain dimensionality has been built, any future expansions can be accomplished only by replacing the VLSI chips. This is an undesirable feature and a lot of work has been under progress to eliminate this stymie, thus providing a platform for easier expansion. Modified hypercubes (MHs) have been proposed as the building blocks of hypercube-based systems supporting incremental growth techniques without introducing extra resources for individual hypercubes. However, processor allocation on MHs proves to be a challenge due to a slight deviation in their topology from that of the standard hypercube network. This thesis addresses the issue of processor allocation on MHs and proposes various strategies which are based, partially or entirely, on table look-up approaches. A study of the various task allocation strategies for standard hypercubes is conducted and their suitability for MHs is evaluated. It is shown that the proposed strategies have a perfect subcube recognition ability and a superior performance. Existing processor allocation strategies for pure hypercube networks are demonstrated to be ineffective for MHs, in the light of their inability to recognize all available subcubes. A comparative analysis that involves the buddy strategy and the new strategies is carried out using simulation results

Fault-tolerance embedding of rings and arrays in star and pancake graphs

The star and pancake graphs are useful interconnection networks for connecting processors in a parallel and distributed computing environment. The star network has been widely studied and is shown to possess attactive features like sublogarithmic diameter, node and edge symmetry and high resilience. The star/pancake interconnection graphs, {dollar}S\sb{n}/P\sb{n}{dollar} of dimension n have n! nodes connected by {dollar}{(n-1).n!\over2}{dollar} edges. Due to their large number of nodes and interconnections, they are prone to failure of one or more nodes/edges; In this thesis, we present methods to embed Hamiltonian paths (H-path) and Hamiltonian cycles (H-cycle) in a star graph {dollar}S\sb{n}{dollar} and pancake graph {dollar}P\sb{n}{dollar} in a faulty environment. Such embeddings are important for solving computational problems, formulated for array and ring topologies, on star and pancake graphs. The models considered include single-processor failure, double-processor failure, and multiple-processor failures. All the models are applied to an H-cycle which is formed by visiting all the ({dollar}{n!\over4!})\ S\sb4/P\sb4{dollar}s in an {dollar}S\sb{n}/P\sb{n}{dollar} in a particular order. Each {dollar}S\sb4/P\sb4{dollar} has an entry node where the cycle/path enters that particular {dollar}S\sb4/P\sb4{dollar} and an exit node where the path leaves it. Distributed algorithms for embedding hamiltonian cycle in the presence of multiple faults, are also presented for both {dollar}S\sb{n}{dollar} and {dollar}P\sb{n}{dollar}

Optical control plane: theory and algorithms

In this thesis we propose a novel way to achieve global network information dissemination in which some wavelengths are reserved exclusively for global control information exchange. We study the routing and wavelength assignment problem for the special communication pattern of non-blocking all-to-all broadcast in WDM optical networks. We provide efficient solutions to reduce the number of wavelengths needed for non-blocking all-to-all broadcast, in the absence of wavelength converters, for network information dissemination. We adopt an approach in which we consider all nodes to be tap-and-continue capable thus studying lighttrees rather than lightpaths. To the best of our knowledge, this thesis is the first to consider “tap-and-continue” capable nodes in the context of conflict-free all-to-all broadcast. The problem of all to-all broadcast using individual lightpaths has been proven to be an NP-complete problem [6]. We provide optimal RWA solutions for conflict-free all-to-all broadcast for some particular cases of regular topologies, namely the ring, the torus and the hypercube. We make an important contribution on hypercube decomposition into edge-disjoint structures. We also present near-optimal polynomial-time solutions for the general case of arbitrary topologies. Furthermore, we apply for the first time the “cactus” representation of all minimum edge-cuts of graphs with arbitrary topologies to the problem of all-to-all broadcast in optical networks. Using this representation recursively we obtain near-optimal results for the number of wavelengths needed by the non-blocking all-to-all broadcast. The second part of this thesis focuses on the more practical case of multi-hop RWA for non- blocking all-to-all broadcast in the presence of Optical-Electrical-Optical conversion. We propose two simple but efficient multi-hop RWA models. In addition to reducing the number of wavelengths we also concentrate on reducing the number of optical receivers, another important optical resource. We analyze these models on the ring and the hypercube, as special cases of regular topologies. Lastly, we develop a good upper-bound on the number of wavelengths in the case of non-blocking multi-hop all-to-all broadcast on networks with arbitrary topologies and offer a heuristic algorithm to achieve it. We propose a novel network partitioning method based on “virtual perfect matching” for use in the RWA heuristic algorithm

Functional Traits Affecting Photosynthesis, Growth, and Mortality of Trees Inferred from a Field Study and Simulation Experiments

abstract: Functional traits research has improved our understanding of how plants respond to their environments, identifying key trade-offs among traits. These studies primarily rely on correlative methods to infer trade-offs and often overlook traits that are difficult to measure (e.g., root traits, tissue senescence rates), limiting their predictive ability under novel conditions. I aimed to address these limitations and develop a better understanding of the trait space occupied by trees by integrating data and process models, spanning leaves to whole-trees, via modern statistical and computational methods. My first research chapter (Chapter 2) simultaneously fits a photosynthesis model to measurements of fluorescence and photosynthetic response curves, improving estimates of mesophyll conductance (gm) and other photosynthetic traits. I assessed how gm varies across environmental gradients and relates to other photosynthetic traits for 4 woody species in Arizona. I found that gm was lower at high aridity sites, varied little within a site, and is an important trait for obtaining accurate estimates of photosynthesis and related traits under dry conditions. Chapter 3 evaluates the importance of functional traits for whole-tree performance by fitting an individual-based model of tree growth and mortality to millions of measurements of tree heights and diameters to assess the theoretical trait space (TTS) of “healthy” North American trees. The TTS contained complicated, multi-variate structure indicative of potential trade-offs leading to successful growth. In Chapter 4, I applied an environmental filter (light stress) to the TTS, leading to simulated stand-level mortality rates up to 50%. Tree-level mortality was explained by 6 of the 32 traits explored, with the most important being radiation-use efficiency. The multidimentional space comprising these 6 traits differed in volume and location between trees that survived and died, indicating that selective mortality alters the TTS.Dissertation/ThesisDoctoral Dissertation Biology 201