Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

A Maximum Satisfiability Based Approach to Bi-Objective Boolean Optimization

Many real-world problem settings give rise to NP-hard combinatorial optimization problems. This results in a need for non-trivial algorithmic approaches for finding optimal solutions to such problems. Many such approaches—ranging from probabilistic and meta-heuristic algorithms to declarative programming—have been presented for optimization problems with a single objective. Less work has been done on approaches for optimization problems with multiple objectives. We present BiOptSat, an exact declarative approach for finding so-called Pareto-optimal solutions to bi-objective optimization problems. A bi-objective optimization problem arises for example when learning interpretable classifiers and the size, as well as the classification error of the classifier should be taken into account as objectives. Using propositional logic as a declarative programming language, we seek to extend the progress and success in maximum satisfiability (MaxSAT) solving to two objectives. BiOptSat can be viewed as an instantiation of the lexicographic method and makes use of a single SAT solver that is preserved throughout the entire search procedure. It allows for solving three tasks for bi-objective optimization: finding a single Pareto-optimal solution, finding one representative solution for each Pareto point, and enumerating all Pareto-optimal solutions. We provide an open-source implementation of five variants of BiOptSat, building on different algorithms proposed for MaxSAT. Additionally, we empirically evaluate these five variants, comparing their runtime performance to that of three key competing algorithmic approaches. The empirical comparison in the contexts of learning interpretable decision rules and bi-objective set covering shows practical benefits of our approach. Furthermore, for the best-performing variant of BiOptSat, we study the effects of proposed refinements to determine their effectiveness

A Comparison of Lex Bounds for Multiset Variables in Constraint Programming

Set and multiset variables in constraint programming have typically been represented using subset bounds. However, this is a weak representation that neglects potentially useful information about a set such as its cardinality. For set variables, the length-lex (LL) representation successfully provides information about the length (cardinality) and position in the lexicographic ordering. For multiset variables, where elements can be repeated, we consider richer representations that take into account additional information. We study eight different representations in which we maintain bounds according to one of the eight different orderings: length-(co)lex (LL/LC), variety-(co)lex (VL/VC), length-variety-(co)lex (LVL/LVC), and variety-length-(co)lex (VLL/VLC) orderings. These representations integrate together information about the cardinality, variety (number of distinct elements in the multiset), and position in some total ordering. Theoretical and empirical comparisons of expressiveness and compactness of the eight representations suggest that length-variety-(co)lex (LVL/LVC) and variety-length-(co)lex (VLL/VLC) usually give tighter bounds after constraint propagation. We implement the eight representations and evaluate them against the subset bounds representation with cardinality and variety reasoning. Results demonstrate that they offer significantly better pruning and runtime.Comment: 7 pages, Proceedings of the Twenty-Fifth AAAI Conference on Artificial Intelligence (AAAI-11

An improved multi-parametric programming algorithm for flux balance analysis of metabolic networks

Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to mass-balance constraints. A variety of cell functions in response to environmental stimuli can be quantified using flux balance analysis by parameterizing the linear program with respect to extracellular conditions. However, for most large, genome-scale metabolic networks of practical interest, the resulting parametric problem has multiple and highly degenerate optimal solutions, which are computationally challenging to handle. An improved multi-parametric programming algorithm based on active-set methods is introduced in this paper to overcome these computational difficulties. Degeneracy and multiplicity are handled, respectively, by introducing generalized inverses and auxiliary objective functions into the formulation of the optimality conditions. These improvements are especially effective for metabolic networks because their stoichiometry matrices are generally sparse; thus, fast and efficient algorithms from sparse linear algebra can be leveraged to compute generalized inverses and null-space bases. We illustrate the application of our algorithm to flux balance analysis of metabolic networks by studying a reduced metabolic model of Corynebacterium glutamicum and a genome-scale model of Escherichia coli. We then demonstrate how the critical regions resulting from these studies can be associated with optimal metabolic modes and discuss the physical relevance of optimal pathways arising from various auxiliary objective functions. Achieving more than five-fold improvement in computational speed over existing multi-parametric programming tools, the proposed algorithm proves promising in handling genome-scale metabolic models.Comment: Accepted in J. Optim. Theory Appl. First draft was submitted on August 4th, 201

MaxSAT-Based Bi-Objective Boolean Optimization

Peer reviewe

A study on set variable representations in constraint programming

Il lavoro presentato in questa tesi si colloca nel contesto della programmazione con vincoli, un paradigma per modellare e risolvere problemi di ricerca combinatoria che richiedono di trovare soluzioni in presenza di vincoli. Una vasta parte di questi problemi trova naturale formulazione attraverso il linguaggio delle variabili insiemistiche. Dal momento che il dominio di tali variabili può essere esponenziale nel numero di elementi, una rappresentazione esplicita è spesso non praticabile. Recenti studi si sono quindi focalizzati nel trovare modi efficienti per rappresentare tali variabili. Pertanto si è soliti rappresentare questi domini mediante l'uso di approssimazioni definite tramite intervalli (d'ora in poi rappresentazioni), specificati da un limite inferiore e un limite superiore secondo un'appropriata relazione d'ordine. La recente evoluzione della ricerca sulla programmazione con vincoli sugli insiemi ha chiaramente indicato che la combinazione di diverse rappresentazioni permette di raggiungere prestazioni di ordini di grandezza superiori rispetto alle tradizionali tecniche di codifica. Numerose proposte sono state fatte volgendosi in questa direzione. Questi lavori si differenziano su come è mantenuta la coerenza tra le diverse rappresentazioni e su come i vincoli vengono propagati al fine di ridurre lo spazio di ricerca. Sfortunatamente non esiste alcun strumento formale per paragonare queste combinazioni. Il principale obiettivo di questo lavoro è quello di fornire tale strumento, nel quale definiamo precisamente la nozione di combinazione di rappresentazioni facendo emergere gli aspetti comuni che hanno caratterizzato i lavori precedenti. In particolare identifichiamo due tipi possibili di combinazioni, una forte ed una debole, definendo le nozioni di coerenza agli estremi sui vincoli e sincronizzazione tra rappresentazioni. Il nostro studio propone alcune interessanti intuizioni sulle combinazioni esistenti, evidenziandone i limiti e svelando alcune sorprese. Inoltre forniamo un'analisi di complessità della sincronizzazione tra minlex, una rappresentazione in grado di propagare in maniera ottimale vincoli lessicografici, e le principali rappresentazioni esistenti