Finite difference methods fengshui: alignment through a mathematics of arrays

Numerous scientific-computational domains make use of array data. The core computing of the numerical methods and the algorithms involved is related to multi-dimensional array manipulation. Memory layout and the access patterns of that data are crucial to the optimal performance of the array-based computations. As we move towards exascale computing, writing portable code for efficient data parallel computations is increasingly requiring an abstract productive working environment. To that end, we present the design of a framework for optimizing scientific array-based computations, building a case study for a Partial Differential Equations solver. By embedding the Mathematics of Arrays formalism in the Magnolia programming language, we assemble a software stack capable of abstracting the continuous high-level application layer from the discrete formulation of the collective array-based numerical methods and algorithms and the final detailed low-level code. The case study lays the groundwork for achieving optimized memory layout and efficient computations while preserving a stable abstraction layer independent of underlying algorithms and changes in the architecture.Peer ReviewedPostprint (author's final draft

Scalable electronic structure methods to solve the Kohn-Sham equation

From the single hydrogen to proteins in the hundreds of thousands of kilodaltons, scientists can use the electronic structure of interacting atoms to predict their material properties. Knowing the material properties through solving the electronic structure problem, would allow for the controlled prediction and corresponding design of materials. The Kohn-Sham equations, based on density functional theory, transform a many-body problem impossible to solve for anything but the smallest molecules, into a practical problem which can be used to predict material properties. Although KSDFT scales as the cube of the number of electrons in the system, there are additional well documented approximations to further reduce the number of electrons, such as the pseudopotential method. The incoming exascale era will lead to unavoidable challenges in solving the Kohn-Sham equations. These challenges include communication and hardware considerations. Old paradigms, epitomized by repeated series of globally forced synchronization points, will give way to new breeds of algorithms to maximizing scaling performance while maintaining portability. This thesis focuses on the solution to Kohn-Sham DFT in real space at scale. Key to this effort is a parallel treatment of numerical elements involving the Rayleigh-Ritz method. At minimum, the Rayleigh-Ritz projection requires a number of distributed matrix vector operations equal to the number of electrons solved for in a system. Furthermore, the projection requires that number, squared and then halved, of dot products. The memory cost for such an algorithm also grows very large quickly, and explicit intelligent management is not an option. I demonstrate the computational requirements for the various steps in solving for the electronic structure problem for both large and small molecular systems. This thesis also discusses opportunities in real space Kohn-Sham DFT to further utilize floating point optimized hardware the with higher order stencils.Chemical Engineerin

A Phase-Type Distribution for the Sum of Two Concatenated Markov Processes Application to the Analysis Survival in Bladder Cancer

[EN] Stochastic processes are useful and important for modeling the evolution of processes that take different states over time, a situation frequently found in fields such as medical research and engineering. In a previous paper and within this framework, we developed the sum of two independent phase-type (PH)-distributed variables, each of them being associated with a Markovian process of one absorbing state. In that analysis, we computed the distribution function, and its associated survival function, of the sum of both variables, also PH-distributed. In this work, in one more step, we have developed a first approximation of that distribution function in order to avoid the calculation of an inverse matrix for the possibility of a bad conditioning of the matrix, involved in the expression of the distribution function in the previous paper. Next, in a second step, we improve this result, giving a second, more accurate approximation. Two numerical applications, one with simulated data and the other one with bladder cancer data, are used to illustrate the two proposed approaches to the distribution function. We compare and argue the accuracy and precision of each one of them by means of their error bound and the application to real data of bladder cancer.This paper has been supported by the Generalitat Valenciana grant AICO/2020/114.García Mora, MB.; Santamaria Navarro, C.; Rubio Navarro, G. (2020). A Phase-Type Distribution for the Sum of Two Concatenated Markov Processes Application to the Analysis Survival in Bladder Cancer. Mathematics. 8(12):1-15. https://doi.org/10.3390/math8122099S115812Rodríguez, J., Lillo, R. E., & Ramírez-Cobo, P. (2015). Failure modeling of an electrical N-component framework by the non-stationary Markovian arrival process. Reliability Engineering & System Safety, 134, 126-133. doi:10.1016/j.ress.2014.10.020García‐Mora, B., Santamaría, C., & Rubio, G. (2020). Markovian modeling for dependent interrecurrence times in bladder cancer. Mathematical Methods in the Applied Sciences, 43(14), 8302-8310. doi:10.1002/mma.6593Montoro-Cazorla, D., & Pérez-Ocón, R. (2014). Matrix stochastic analysis of the maintainability of a machine under shocks. Reliability Engineering & System Safety, 121, 11-17. doi:10.1016/j.ress.2013.07.002Fackrell, M. (2008). Modelling healthcare systems with phase-type distributions. Health Care Management Science, 12(1), 11-26. doi:10.1007/s10729-008-9070-yGarg, L., McClean, S., Meenan, B. J., & Millard, P. (2011). Phase-Type Survival Trees and Mixed Distribution Survival Trees for Clustering Patients’ Hospital Length of Stay. Informatica, 22(1), 57-72. doi:10.15388/informatica.2011.314Marshall, A. H., & McClean, S. I. (2003). Conditional phase-type distributions for modelling patient length of stay in hospital. International Transactions in Operational Research, 10(6), 565-576. doi:10.1111/1475-3995.00428Marshall, A. H., & McClean, S. I. (2004). Using Coxian Phase-Type Distributions to Identify Patient Characteristics for Duration of Stay in Hospital. Health Care Management Science, 7(4), 285-289. doi:10.1007/s10729-004-7537-zFackrell, M. (2012). A semi-infinite programming approach to identifying matrix-exponential distributions. International Journal of Systems Science, 43(9), 1623-1631. doi:10.1080/00207721.2010.549582García-Mora, B., Santamaría, C., Rubio, G., & Pontones, J. L. (2013). Computing survival functions of the sum of two independent Markov processes: an application to bladder carcinoma treatment. International Journal of Computer Mathematics, 91(2), 209-220. doi:10.1080/00207160.2013.765560Kenney, C., & Laub, A. J. (1989). Condition Estimates for Matrix Functions. SIAM Journal on Matrix Analysis and Applications, 10(2), 191-209. doi:10.1137/0610014Jackson, C. H. (2011). Multi-State Models for Panel Data: ThemsmPackage forR. Journal of Statistical Software, 38(8). doi:10.18637/jss.v038.i08Mullin, L., & Raynolds, J. (2014). Scalable, Portable, Verifiable Kronecker Products on Multi-scale Computers. Studies in Computational Intelligence, 111-129. doi:10.1007/978-3-319-04280-0_1

Understanding Quantum Technologies 2022

Understanding Quantum Technologies 2022 is a creative-commons ebook that provides a unique 360 degrees overview of quantum technologies from science and technology to geopolitical and societal issues. It covers quantum physics history, quantum physics 101, gate-based quantum computing, quantum computing engineering (including quantum error corrections and quantum computing energetics), quantum computing hardware (all qubit types, including quantum annealing and quantum simulation paradigms, history, science, research, implementation and vendors), quantum enabling technologies (cryogenics, control electronics, photonics, components fabs, raw materials), quantum computing algorithms, software development tools and use cases, unconventional computing (potential alternatives to quantum and classical computing), quantum telecommunications and cryptography, quantum sensing, quantum technologies around the world, quantum technologies societal impact and even quantum fake sciences. The main audience are computer science engineers, developers and IT specialists as well as quantum scientists and students who want to acquire a global view of how quantum technologies work, and particularly quantum computing. This version is an extensive update to the 2021 edition published in October 2021.Comment: 1132 pages, 920 figures, Letter forma

Communication-Efficient Probabilistic Algorithms: Selection, Sampling, and Checking

Diese Dissertation behandelt drei grundlegende Klassen von Problemen in Big-Data-Systemen, für die wir kommunikationseffiziente probabilistische Algorithmen entwickeln. Im ersten Teil betrachten wir verschiedene Selektionsprobleme, im zweiten Teil das Ziehen gewichteter Stichproben (Weighted Sampling) und im dritten Teil die probabilistische Korrektheitsprüfung von Basisoperationen in Big-Data-Frameworks (Checking). Diese Arbeit ist durch einen wachsenden Bedarf an Kommunikationseffizienz motiviert, der daher rührt, dass der auf das Netzwerk und seine Nutzung zurückzuführende Anteil sowohl der Anschaffungskosten als auch des Energieverbrauchs von Supercomputern und der Laufzeit verteilter Anwendungen immer weiter wächst. Überraschend wenige kommunikationseffiziente Algorithmen sind für grundlegende Big-Data-Probleme bekannt. In dieser Arbeit schließen wir einige dieser Lücken. Zunächst betrachten wir verschiedene Selektionsprobleme, beginnend mit der verteilten Version des klassischen Selektionsproblems, d. h. dem Auffinden des Elements von Rang $k$ in einer großen verteilten Eingabe. Wir zeigen, wie dieses Problem kommunikationseffizient gelöst werden kann, ohne anzunehmen, dass die Elemente der Eingabe zufällig verteilt seien. Hierzu ersetzen wir die Methode zur Pivotwahl in einem schon lange bekannten Algorithmus und zeigen, dass dies hinreichend ist. Anschließend zeigen wir, dass die Selektion aus lokal sortierten Folgen – multisequence selection – wesentlich schneller lösbar ist, wenn der genaue Rang des Ausgabeelements in einem gewissen Bereich variieren darf. Dies benutzen wir anschließend, um eine verteilte Prioritätswarteschlange mit Bulk-Operationen zu konstruieren. Später werden wir diese verwenden, um gewichtete Stichproben aus Datenströmen zu ziehen (Reservoir Sampling). Schließlich betrachten wir das Problem, die global häufigsten Objekte sowie die, deren zugehörige Werte die größten Summen ergeben, mit einem stichprobenbasierten Ansatz zu identifizieren. Im Kapitel über gewichtete Stichproben werden zunächst neue Konstruktionsalgorithmen für eine klassische Datenstruktur für dieses Problem, sogenannte Alias-Tabellen, vorgestellt. Zu Beginn stellen wir den ersten Linearzeit-Konstruktionsalgorithmus für diese Datenstruktur vor, der mit konstant viel Zusatzspeicher auskommt. Anschließend parallelisieren wir diesen Algorithmus für Shared Memory und erhalten so den ersten parallelen Konstruktionsalgorithmus für Aliastabellen. Hiernach zeigen wir, wie das Problem für verteilte Systeme mit einem zweistufigen Algorithmus angegangen werden kann. Anschließend stellen wir einen ausgabesensitiven Algorithmus für gewichtete Stichproben mit Zurücklegen vor. Ausgabesensitiv bedeutet, dass die Laufzeit des Algorithmus sich auf die Anzahl der eindeutigen Elemente in der Ausgabe bezieht und nicht auf die Größe der Stichprobe. Dieser Algorithmus kann sowohl sequentiell als auch auf Shared-Memory-Maschinen und verteilten Systemen eingesetzt werden und ist der erste derartige Algorithmus in allen drei Kategorien. Wir passen ihn anschließend an das Ziehen gewichteter Stichproben ohne Zurücklegen an, indem wir ihn mit einem Schätzer für die Anzahl der eindeutigen Elemente in einer Stichprobe mit Zurücklegen kombinieren. Poisson-Sampling, eine Verallgemeinerung des Bernoulli-Sampling auf gewichtete Elemente, kann auf ganzzahlige Sortierung zurückgeführt werden, und wir zeigen, wie ein bestehender Ansatz parallelisiert werden kann. Für das Sampling aus Datenströmen passen wir einen sequentiellen Algorithmus an und zeigen, wie er in einem Mini-Batch-Modell unter Verwendung unserer im Selektionskapitel eingeführten Bulk-Prioritätswarteschlange parallelisiert werden kann. Das Kapitel endet mit einer ausführlichen Evaluierung unserer Aliastabellen-Konstruktionsalgorithmen, unseres ausgabesensitiven Algorithmus für gewichtete Stichproben mit Zurücklegen und unseres Algorithmus für gewichtetes Reservoir-Sampling. Um die Korrektheit verteilter Algorithmen probabilistisch zu verifizieren, schlagen wir Checker für grundlegende Operationen von Big-Data-Frameworks vor. Wir zeigen, dass die Überprüfung zahlreicher Operationen auf zwei „Kern“-Checker reduziert werden kann, nämlich die Prüfung von Aggregationen und ob eine Folge eine Permutation einer anderen Folge ist. Während mehrere Ansätze für letzteres Problem seit geraumer Zeit bekannt sind und sich auch einfach parallelisieren lassen, ist unser Summenaggregations-Checker eine neuartige Anwendung der gleichen Datenstruktur, die auch zählenden Bloom-Filtern und dem Count-Min-Sketch zugrunde liegt. Wir haben beide Checker in Thrill, einem Big-Data-Framework, implementiert. Experimente mit absichtlich herbeigeführten Fehlern bestätigen die von unserer theoretischen Analyse vorhergesagte Erkennungsgenauigkeit. Dies gilt selbst dann, wenn wir häufig verwendete schnelle Hash-Funktionen mit in der Theorie suboptimalen Eigenschaften verwenden. Skalierungsexperimente auf einem Supercomputer zeigen, dass unsere Checker nur sehr geringen Laufzeit-Overhead haben, welcher im Bereich von $2\,\%$ liegt und dabei die Korrektheit des Ergebnisses nahezu garantiert wird

Resilience-Building Technologies: State of Knowledge -- ReSIST NoE Deliverable D12

This document is the first product of work package WP2, "Resilience-building and -scaling technologies", in the programme of jointly executed research (JER) of the ReSIST Network of Excellenc

New Data Structures and Algorithms for Logic Synthesis and Verification

The strong interaction between Electronic Design Automation (EDA) tools and Complementary Metal-Oxide Semiconductor (CMOS) technology contributed substantially to the advancement of modern digital electronics. The continuous downscaling of CMOS Field Effect Transistor (FET) dimensions enabled the semiconductor industry to fabricate digital systems with higher circuit density at reduced costs. To keep pace with technology, EDA tools are challenged to handle both digital designs with growing functionality and device models of increasing complexity. Nevertheless, whereas the downscaling of CMOS technology is requiring more complex physical design models, the logic abstraction of a transistor as a switch has not changed even with the introduction of 3D FinFET technology. As a consequence, modern EDA tools are fine tuned for CMOS technology and the underlying design methodologies are based on CMOS logic primitives, i.e., negative unate logic functions. While it is clear that CMOS logic primitives will be the ultimate building blocks for digital systems in the next ten years, no evidence is provided that CMOS logic primitives are also the optimal basis for EDA software. In EDA, the efficiency of methods and tools is measured by different metrics such as (i) the result quality, for example the performance of a digital circuit, (ii) the runtime and (iii) the memory footprint on the host computer. With the aim to optimize these metrics, the accordance to a specific logic model is no longer important. Indeed, the key to the success of an EDA technique is the expressive power of the logic primitives handling and solving the problem, which determines the capability to reach better metrics. In this thesis, we investigate new logic primitives for electronic design automation tools. We improve the efficiency of logic representation, manipulation and optimization tasks by taking advantage of majority and biconditional logic primitives. We develop synthesis tools exploiting the majority and biconditional expressiveness. Our tools show strong results as compared to state-of-the-art academic and commercial synthesis tools. Indeed, we produce the best results for several public benchmarks. On top of the enhanced synthesis power, our methods are the natural and native logic abstraction for circuit design in emerging nanotechnologies, where majority and biconditional logic are the primitive gates for physical implementation. We accelerate formal methods by (i) studying properties of logic circuits and (ii) developing new frameworks for logic reasoning engines. We prove non-trivial dualities for the property checking problem in logic circuits. Our findings enable sensible speed-ups in solving circuit satisfiability. We develop an alternative Boolean satisfiability framework based on majority functions. We prove that the general problem is still intractable but we show practical restrictions that can be solved efficiently. Finally, we focus on reversible logic where we propose a new equivalence checking approach. We exploit the invertibility of computation and the functionality of reversible gates in the formulation of the problem. This enables one order of magnitude speed up, as compared to the state-of-the-art solution. We argue that new approaches to solve EDA problems are necessary, as we have reached a point of technology where keeping pace with design goals is tougher than ever