MPSalsa a finite element computer program for reacting flow problems. Part 2 - user`s guide

This manual describes the use of MPSalsa, an unstructured finite element (FE) code for solving chemically reacting flow problems on massively parallel computers. MPSalsa has been written to enable the rigorous modeling of the complex geometry and physics found in engineering systems that exhibit coupled fluid flow, heat transfer, mass transfer, and detailed reactions. In addition, considerable effort has been made to ensure that the code makes efficient use of the computational resources of massively parallel (MP), distributed memory architectures in a way that is nearly transparent to the user. The result is the ability to simultaneously model both three-dimensional geometries and flow as well as detailed reaction chemistry in a timely manner on MT computers, an ability we believe to be unique. MPSalsa has been designed to allow the experienced researcher considerable flexibility in modeling a system. Any combination of the momentum equations, energy balance, and an arbitrary number of species mass balances can be solved. The physical and transport properties can be specified as constants, as functions, or taken from the Chemkin library and associated database. Any of the standard set of boundary conditions and source terms can be adapted by writing user functions, for which templates and examples exist

MPSalsa a finite element computer program for reacting flow problems. Part 2 - user`s guide

This manual describes the use of MPSalsa, an unstructured finite element (FE) code for solving chemically reacting flow problems on massively parallel computers. MPSalsa has been written to enable the rigorous modeling of the complex geometry and physics found in engineering systems that exhibit coupled fluid flow, heat transfer, mass transfer, and detailed reactions. In addition, considerable effort has been made to ensure that the code makes efficient use of the computational resources of massively parallel (MP), distributed memory architectures in a way that is nearly transparent to the user. The result is the ability to simultaneously model both three-dimensional geometries and flow as well as detailed reaction chemistry in a timely manner on MT computers, an ability we believe to be unique. MPSalsa has been designed to allow the experienced researcher considerable flexibility in modeling a system. Any combination of the momentum equations, energy balance, and an arbitrary number of species mass balances can be solved. The physical and transport properties can be specified as constants, as functions, or taken from the Chemkin library and associated database. Any of the standard set of boundary conditions and source terms can be adapted by writing user functions, for which templates and examples exist

Automating Black-Box Property Based Testing

<p>Black-box property based testing tools like QuickCheck allow developers to write elegant logical specifications of their programs, while still permitting unrestricted use of the same language features and libraries that simplify writing the programs themselves. This is an improvement over unit testing because a single property can replace a large collection of test cases, and over more heavy-weight white-box testing frameworks that impose restrictions on how properties and tested code are written. In most cases the developer only needs to write a function returning a boolean, something any developer is capable of without additional training. </p> <p> This thesis aims to further lower the threshold for using property based testing by automating some problematic areas, most notably generating test data for user defined data types. Writing procedures for random test data generation by hand is time consuming and error prone, and most fully automatic algorithms give very poor random distributions for practical cases. </p><p> Several fully automatic algorithms for generating test data are presented in this thesis, along with implementations as Haskell libraries. These algorithms all fit nicely within a framework called sized functors, allowing re-usable generator definitions to be constructed automatically or by hand using a few simple combinators. </p><p> Test quality is another difficulty with property based testing. When a property fails to find a counterexample there is always some uncertainty in the strength of the property as a specification. To address this problem we introduce a black-box variant of mutation testing. Usually mutation testing involves automatically introducing errors (mutations) in the source code of a tested program to see if a test suite can detect it. Using higher order functions, we mutate functions without accessing their source code. The result is a very light-weight mutation testing procedure that automatically estimates property strength for QuickCheck properties. </p

Distributed frequent hierarchical pattern mining for robust and efficient large-scale association discovery

Field of study: Computer science.Dr. Chi-Ren Shyu, Dissertation Supervisor.Includes vita."May 2017."Frequent pattern mining is a classic data mining technique, generally applicable to a wide range of application domains, and a mature area of research. The fundamental challenge arises from the combinatorial nature of frequent itemsets, scaling exponentially with respect to the number of unique items. Apriori-based and FPTree-based algorithms have dominated the space thus far. Initial phases of this research relied on the Apriori algorithm and utilized a distributed computing environment; we proposed the Cartesian Scheduler to manage Apriori's candidate generation process. To address the limitation of bottom-up frequent pattern mining algorithms such as Apriori and FPGrowth, we propose the Frequent Hierarchical Pattern Tree (FHPTree): a tree structure and new frequent pattern mining paradigm. The classic problem is redefined as frequent hierarchical pattern mining where the goal is to detect frequent maximal pattern covers. Under the proposed paradigm, compressed representations of maximal patterns are mined using a top-down FHPTree traversal, FHPGrowth, which detects large patterns before their subsets, thus yielding significant reductions in computation time. The FHPTree memory footprint is small; the number of nodes in the structure scales linearly with respect to the number of unique items. Additionally, the FHPTree serves as a persistent, dynamic data structure to index frequent patterns and enable efficient searches. When the search space is exponential, efficient targeted mining capabilities are paramount; this is one of the key contributions of the FHPTree. This dissertation will demonstrate the performance of FHPGrowth, achieving a 300x speed up over state-of-the-art maximal pattern mining algorithms and approximately a 2400x speedup when utilizing FHPGrowth in a distributed computing environment. In addition, we allude to future research opportunities, and suggest various modifications to further optimize the FHPTree and FHPGrowth. Moreover, the methods we offer will have an impact on other data mining research areas including contrast set mining as well as spatial and temporal mining.Includes bibliographical references (pages 121-133)

Multipartite Graph Algorithms for the Analysis of Heterogeneous Data

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of biomolecules within an organism. This dissertation describes the design, implementation and application of graph algorithms, with the goal of seeking dense structure in data derived from omics experiments in order to detect latent associations between often heterogeneous entities, such as genes, diseases and phenotypes. Exact combinatorial solutions are developed and implemented, rather than relying on approximations or heuristics, even when problems are exceedingly large and/or difficult. Datasets on which the algorithms are applied include time series transcriptomic data from an experiment on the developing mouse cerebellum, gene expression data measuring acute ethanol response in the prefrontal cortex, and the analysis of a predicted protein-protein interaction network. A bipartite graph model is used to integrate heterogeneous data types, such as genes with phenotypes and microbes with mouse strains. The techniques are then extended to a multipartite algorithm to enumerate dense substructure in multipartite graphs, constructed using data from three or more heterogeneous sources, with applications to functional genomics. Several new theoretical results are given regarding multipartite graphs and the multipartite enumeration algorithm. In all cases, practical implementations are demonstrated to expand the frontier of computational feasibility

Treasure hunt : a framework for cooperative, distributed parallel optimization

Orientador: Prof. Dr. Daniel WeingaertnerCoorientadora: Profa. Dra. Myriam Regattieri DelgadoTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa : Curitiba, 27/05/2019Inclui referências: p. 18-20Área de concentração: Ciência da ComputaçãoResumo: Este trabalho propõe um framework multinível chamado Treasure Hunt, que é capaz de distribuir algoritmos de busca independentes para um grande número de nós de processamento. Com o objetivo de obter uma convergência conjunta entre os nós, este framework propõe um mecanismo de direcionamento que controla suavemente a cooperação entre múltiplas instâncias independentes do Treasure Hunt. A topologia em árvore proposta pelo Treasure Hunt garante a rápida propagação da informação pelos nós, ao mesmo tempo em que provê simutaneamente explorações (pelos nós-pai) e intensificações (pelos nós-filho), em vários níveis de granularidade, independentemente do número de nós na árvore. O Treasure Hunt tem boa tolerância à falhas e está parcialmente preparado para uma total tolerância à falhas. Como parte dos métodos desenvolvidos durante este trabalho, um método automatizado de Particionamento Iterativo foi proposto para controlar o balanceamento entre explorações e intensificações ao longo da busca. Uma Modelagem de Estabilização de Convergência para operar em modo Online também foi proposto, com o objetivo de encontrar pontos de parada com bom custo/benefício para os algoritmos de otimização que executam dentro das instâncias do Treasure Hunt. Experimentos em benchmarks clássicos, aleatórios e de competição, de vários tamanhos e complexidades, usando os algoritmos de busca PSO, DE e CCPSO2, mostram que o Treasure Hunt melhora as características inerentes destes algoritmos de busca. O Treasure Hunt faz com que os algoritmos de baixa performance se tornem comparáveis aos de boa performance, e os algoritmos de boa performance possam estender seus limites até problemas maiores. Experimentos distribuindo instâncias do Treasure Hunt, em uma rede cooperativa de até 160 processos, demonstram a escalabilidade robusta do framework, apresentando melhoras nos resultados mesmo quando o tempo de processamento é fixado (wall-clock) para todas as instâncias distribuídas do Treasure Hunt. Resultados demonstram que o mecanismo de amostragem fornecido pelo Treasure Hunt, aliado à maior cooperação entre as múltiplas populações em evolução, reduzem a necessidade de grandes populações e de algoritmos de busca complexos. Isto é especialmente importante em problemas de mundo real que possuem funções de fitness muito custosas. Palavras-chave: Inteligência artificial. Métodos de otimização. Algoritmos distribuídos. Modelagem de convergência. Alta dimensionalidade.Abstract: This work proposes a multilevel framework called Treasure Hunt, which is capable of distributing independent search algorithms to a large number of processing nodes. Aiming to obtain joint convergences between working nodes, Treasure Hunt proposes a driving mechanism that smoothly controls the cooperation between the multiple independent Treasure Hunt instances. The tree topology proposed by Treasure Hunt ensures quick propagation of information, while providing simultaneous explorations (by parents) and exploitations (by children), on several levels of granularity, regardless the number of nodes in the tree. Treasure Hunt has good fault tolerance and is partially prepared to full fault tolerance. As part of the methods developed during this work, an automated Iterative Partitioning method is proposed to control the balance between exploration and exploitation as the search progress. A Convergence Stabilization Modeling to operate in Online mode is also proposed, aiming to find good cost/benefit stopping points for the optimization algorithms running within the Treasure Hunt instances. Experiments on classic, random and competition benchmarks of various sizes and complexities, using the search algorithms PSO, DE and CCPSO2, show that Treasure Hunt boosts the inherent characteristics of these search algorithms. Treasure Hunt makes algorithms with poor performances to become comparable to good ones, and algorithms with good performances to be capable of extending their limits to larger problems. Experiments distributing Treasure Hunt instances in a cooperative network up to 160 processes show the robust scaling of the framework, presenting improved results even when fixing a wall-clock time for the instances. Results show that the sampling mechanism provided by Treasure Hunt, allied to the increased cooperation between multiple evolving populations, reduce the need for large population sizes and complex search algorithms. This is specially important on real-world problems with time-consuming fitness functions. Keywords: Artificial intelligence. Optimization methods. Distributed algorithms. Convergence modeling. High dimensionality

A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed

Dynamic programming algorithms within the NUPACK software suite enable analysis of nucleic acid sequences over complex and test tube ensembles containing arbitrary numbers of interacting strand species, serving the needs of researchers in molecular programming, nucleic acid nanotechnology, synthetic biology, and across the life sciences. Here, to enhance the underlying physical model, ensure scalability for large calculations, and achieve dramatic speedups when calculating diverse physical quantities over complex and test tube ensembles, we introduce a unified dynamic programming framework that combines three ingredients: (1) recursions that specify the dependencies between subproblems and incorporate the details of the structural ensemble and the free energy model, (2) evaluation algebras that define the mathematical form of each subproblem, (3) operation orders that specify the computational trajectory through the dependency graph of subproblems. The physical model is enhanced using new recursions that operate over the complex ensemble including coaxial and dangle stacking subensembles. The recursions are coded generically and then compiled with a quantity-specific evaluation algebra and operation order to generate an executable for each physical quantity: partition function, equilibrium base-pairing probabilities, MFE energy and proxy structure, suboptimal proxy structures, and Boltzmann sampled structures. For large complexes (e.g., 30 000 nt), scalability is achieved for partition function calculations using an overflow-safe evaluation algebra, and for equilibrium base-pairing probabilities using a backtrack-free operation order. A new blockwise operation order that treats subcomplex blocks for the complex species in a test tube ensemble enables dramatic speedups (e.g., 20–120× ) using vectorization and caching. With these performance enhancements, equilibrium analysis of substantial test tube ensembles can be performed in ≤ 1 min on a single computational core (e.g., partition function and equilibrium concentration for all complex species of up to six strands formed from two strand species of 300 nt each, or for all complex species of up to two strands formed from 80 strand species of 100 nt each). A new sampling algorithm simultaneously samples multiple structures from the complex ensemble to yield speedups of an order of magnitude or more as the number of structures increases above ≈10³. These advances are available within the NUPACK 4.0 code base (www.nupack.org) which can be flexibly scripted using the all-new NUPACK Python module