Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm

An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.

Parallel algorithm for solving integer linear programs

Linear programs, or LPs, are often used in optimization problems, such as improving manufacturing efficiency of maximizing the yield from limited resources. The most common method for solving LPs is the Simplex Method, which will yield a solution, if one exists, but over the real numbers. From a purely numerical standpoint, it will be an optimal solution, but quite often we desire an optimal integer solution. A linear program in which the variables are also constrained to be integers is called an integer linear program or ILP. It is the focus of this report to present a parallel algorithm for solving ILPs. We discuss a serial algorithm using a breadth-first branch-and-bound search to check the feasible solution space, and then extend it into a parallel algorithm using a client-server model. In the parallel mode, the search may not be truly breadth-first, depending on the solution time for each node in the solution tree. Our search takes advantage of pruning, often resulting in super-linear improvements in solution time. Finally, we present results from sample ILPs, describe a few modifications to enhance the algorithm and improve solution time, and offer suggestions for future work.

Reflection, refraction, and rejection : copper smelting heritage and the execution of environmental policy

This dissertation examines the global technological and environmental history of copper smelting and the conflict that developed between historic preservation and environmental remediation at major copper smelting sites in the United States after their productive periods ended. Part I of the dissertation is a synthetic overview of the history of copper smelting and its environmental impact. After reviewing the basic metallurgy of copper ores, the dissertation contains successive chapters on the history of copper smelting to 1640, culminating in the so-called German, or Continental, processing system; on the emergence of the rival Welsh system during the British industrial revolution; and on the growth of American dominance in copper production the late 19th and early 20th centuries. The latter chapter focuses, in particular, on three of the most important early American copper districts: Michigan’s Keweenaw Peninsula, Tennessee’s Copper Basin, and Butte-Anaconda, Montana. As these three districts went into decline and ultimately out of production, they left a rich industrial heritage and significant waste and pollution problems generated by increasingly more sophisticated technologies capable of commercially processing steadily growing volumes of decreasingly rich ores. Part II of the dissertation looks at the conflict between historic preservation and environmental remediation that emerged locally and nationally in copper districts as they went into decline and eventually ceased production. Locally, former copper mining communities often split between those who wished to commemorate a region’s past importance and develop heritage tourism, and local developers who wished to clear up and clean out old industrial sites for other purposes. Nationally, Congress passed laws in the 1960s and 1970s mandating the preservation of historical resources (National Historic Preservation Act) and laws mandating the cleanup of contaminated landscapes (CERCLA, or Superfund), objectives sometimes in conflict – especially in the case of copper smelting sites. The dissertation devotes individual chapters to the conflicts that developed between environmental remediation, particularly involving the Environmental Protection Agency and the heritage movement in the Tennessee, Montana, and Michigan copper districts. A concluding chapter provides a broad model to illustrate the relationship between industrial decline, federal environmental remediation activities, and the growth of heritage consciousness in former copper mining and smelting areas, analyzes why the outcome varied in the three areas, and suggests methods for dealing with heritage-remediation issues to minimize conflict and maximize heritage preservation.

Development of a high performance parallel computing platform and its use in the study of nanostructures : clusters, sheets and tubes .

Small clusters of gallium oxide, technologically important high temperature ceramic, together with interaction of nucleic acid bases with graphene and small-diameter carbon nanotube are focus of first principles calculations in this work. A high performance parallel computing platform is also developed to perform these calculations at Michigan Tech. First principles calculations are based on density functional theory employing either local density or gradient-corrected approximation together with plane wave and gaussian basis sets. The bulk Ga2O3 is known to be a very good candidate for fabricating electronic devices that operate at high temperatures. To explore the properties of Ga2O3 at nonoscale, we have performed a systematic theoretical study on the small polyatomic gallium oxide clusters. The calculated results find that all lowest energy isomers of GamOn clusters are dominated by the Ga-O bonds over the metal-metal or the oxygen-oxygen bonds. Analysis of atomic charges suggest the clusters to be highly ionic similar to the case of bulk Ga2O3. In the study of sequential oxidation of these slusters starting from Ga2O, it is found that the most stable isomers display up to four different backbones of constituent atoms. Furthermore, the predicted configuration of the ground state of Ga2O is recently confirmed by the experimental result of Neumark's group. Guided by the results of calculations the study of gallium oxide clusters, performance related challenge of computational simulations, of producing high performance computers/platforms, has been addressed. Several engineering aspects were thoroughly studied during the design, development and implementation of the high performance parallel computing platform, rama, at Michigan Tech. In an attempt to stay true to the principles of Beowulf revolutioni, the rama cluster was extensively customized to make it easy to understand, and use - for administrators as well as end-users. Following the results of benchmark calculations and to keep up with the complexity of systems under study, rama has been expanded to a total of sixty four processors. Interest in the non-covalent intereaction of DNA with carbon nanotubes has steadily increased during past several years. This hybrid system, at the junction of the biological regime and the nanomaterials world, possesses features which make it very attractive for a wide range of applicatioins. Using the in-house computational power available, we have studied details of the interaction between nucleic acid bases with graphene sheet as well as high-curvature small-diameter carbon nanotube. The calculated trend in the binding energies strongly suggests that the polarizability of the base molecules determines the interaction strength of the nucleic acid bases with graphene. When comparing the results obtained here for physisorption on the small diameter nanotube considered with those from the study on graphene, it is observed that the interaction strength of nucleic acid bases is smaller for the tube. Thus, these results show that the effect of introducing curvature is to reduce the binding energy. The binding energies for the two extreme cases of negligible curvature (i.e. flat graphene sheet) and of very high curvature (i.e. small diameter nanotube) may be considered as upper and lower bounds. This finding represents an important step towards a better understanding of experimentally observed sequence-dependent interaction of DNA with Carbon nanotubes.

GENERATING PLANS IN CONCURRENT, PROBABILISTIC, OVER-SUBSCRIBED DOMAINS

Planning in realistic domains typically involves reasoning under uncertainty, operating under time and resource constraints, and finding the optimal subset of goals to work on. Creating optimal plans that consider all of these features is a computationally complex, challenging problem. This dissertation develops an AO* search based planner named CPOAO* (Concurrent, Probabilistic, Over-subscription AO*) which incorporates durative actions, time and resource constraints, concurrent execution, over-subscribed goals, and probabilistic actions. To handle concurrent actions, action combinations rather than individual actions are taken as plan steps. Plan optimization is explored by adding two novel aspects to plans. First, parallel steps that serve the same goal are used to increase the plan’s probability of success. Traditionally, only parallel steps that serve different goals are used to reduce plan execution time. Second, actions that are executing but are no longer useful can be terminated to save resources and time. Conventional planners assume that all actions that were started will be carried out to completion. To reduce the size of the search space, several domain independent heuristic functions and pruning techniques were developed. The key ideas are to exploit dominance relations for candidate action sets and to develop relaxed planning graphs to estimate the expected rewards of states. This thesis contributes (1) an AO* based planner to generate parallel plans, (2) domain independent heuristics to increase planner efficiency, and (3) the ability to execute redundant actions and to terminate useless actions to increase plan efficiency.

PARTITIONING THE BLOCKS OF A STEINER TRIPLE SYSTEM INTO PARTIAL PARALLEL CLASSES

Does there exist a Steiner Triple System on v points, whose blocks can be partitioned into partial parallel classes of size m, where m ≤ [v⁄3], m | b and b is the number of blocks of the STS(v)? We give the answer for 9 ≤ v ≤ 43. We also show that whenever 2|b, v ≡ 3 (mod 6) we can find an STS(v) whose blocks can be partitioned into partial parallel classes of size 2, and whenever 4|b , v ≡ 3 (mod 6), there exists an STS(v) whose blocks can be partitioned into partial parallel classes of size 4.