Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

Is there a Moore's law for quantum computing?

There is a common wisdom according to which many technologies can progress according to some exponential law like the empirical Moore's law that was validated for over half a century with the growth of transistors number in chipsets. As a still in the making technology with a lot of potential promises, quantum computing is supposed to follow the pack and grow inexorably to maturity. The Holy Grail in that domain is a large quantum computer with thousands of errors corrected logical qubits made themselves of thousands, if not more, of physical qubits. These would enable molecular simulations as well as factoring 2048 RSA bit keys among other use cases taken from the intractable classical computing problems book. How far are we from this? Less than 15 years according to many predictions. We will see in this paper that Moore's empirical law cannot easily be translated to an equivalent in quantum computing. Qubits have various figures of merit that won't progress magically thanks to some new manufacturing technique capacity. However, some equivalents of Moore's law may be at play inside and outside the quantum realm like with quantum computers enabling technologies, cryogeny and control electronics. Algorithms, software tools and engineering also play a key role as enablers of quantum computing progress. While much of quantum computing future outcomes depends on qubit fidelities, it is progressing rather slowly, particularly at scale. We will finally see that other figures of merit will come into play and potentially change the landscape like the quality of computed results and the energetics of quantum computing. Although scientific and technological in nature, this inventory has broad business implications, on investment, education and cybersecurity related decision-making processes.Comment: 32 pages, 24 figure

Hybrid Analog-Digital Co-Processing for Scientific Computation

In the past 10 years computer architecture research has moved to more heterogeneity and less adherence to conventional abstractions. Scientists and engineers hold an unshakable belief that computing holds keys to unlocking humanity's Grand Challenges. Acting on that belief they have looked deeper into computer architecture to find specialized support for their applications. Likewise, computer architects have looked deeper into circuits and devices in search of untapped performance and efficiency. The lines between computer architecture layers---applications, algorithms, architectures, microarchitectures, circuits and devices---have blurred. Against this backdrop, a menagerie of computer architectures are on the horizon, ones that forgo basic assumptions about computer hardware, and require new thinking of how such hardware supports problems and algorithms. This thesis is about revisiting hybrid analog-digital computing in support of diverse modern workloads. Hybrid computing had extensive applications in early computing history, and has been revisited for small-scale applications in embedded systems. But architectural support for using hybrid computing in modern workloads, at scale and with high accuracy solutions, has been lacking. I demonstrate solving a variety of scientific computing problems, including stochastic ODEs, partial differential equations, linear algebra, and nonlinear systems of equations, as case studies in hybrid computing. I solve these problems on a system of multiple prototype analog accelerator chips built by a team at Columbia University. On that team I made contributions toward programming the chips, building the digital interface, and validating the chips' functionality. The analog accelerator chip is intended for use in conjunction with a conventional digital host computer. The appeal and motivation for using an analog accelerator is efficiency and performance, but it comes with limitations in accuracy and problem sizes that we have to work around. The first problem is how to do problems in this unconventional computation model. Scientific computing phrases problems as differential equations and algebraic equations. Differential equations are a continuous view of the world, while algebraic equations are a discrete one. Prior work in analog computing mostly focused on differential equations; algebraic equations played a minor role in prior work in analog computing. The secret to using the analog accelerator to support modern workloads on conventional computers is that these two viewpoints are interchangeable. The algebraic equations that underlie most workloads can be solved as differential equations, and differential equations are naturally solvable in the analog accelerator chip. A hybrid analog-digital computer architecture can focus on solving linear and nonlinear algebra problems to support many workloads. The second problem is how to get accurate solutions using hybrid analog-digital computing. The reason that the analog computation model gives less accurate solutions is it gives up representing numbers as digital binary numbers, and instead uses the full range of analog voltage and current to represent real numbers. Prior work has established that encoding data in analog signals gives an energy efficiency advantage as long as the analog data precision is limited. While the analog accelerator alone may be useful for energy-constrained applications where inputs and outputs are imprecise, we are more interested in using analog in conjunction with digital for precise solutions. This thesis gives novel insight that the trick to do so is to solve nonlinear problems where low-precision guesses are useful for conventional digital algorithms. The third problem is how to solve large problems using hybrid analog-digital computing. The reason the analog computation model can't handle large problems is it gives up step-by-step discrete-time operation, instead allowing variables to evolve smoothly in continuous time. To make that happen the analog accelerator works by chaining hardware for mathematical operations end-to-end. During computation analog data flows through the hardware with no overheads in control logic and memory accesses. The downside is then the needed hardware size grows alongside problem sizes. While scientific computing researchers have for a long time split large problems into smaller subproblems to fit in digital computer constraints, this thesis is a first attempt to consider these divide-and-conquer algorithms as an essential tool in using the analog model of computation. As we enter the post-Moore’s law era of computing, unconventional architectures will offer specialized models of computation that uniquely support specific problem types. Two prominent examples are deep neural networks and quantum computers. Recent trends in computer science research show these unconventional architectures will soon have broad adoption. In this thesis I show another specialized, unconventional architecture is to use analog accelerators to solve problems in scientific computing. Computer architecture researchers will discover other important models of computation in the future. This thesis is an example of the discovery process, implementation, and evaluation of how an unconventional architecture supports specialized workloads

Addressing the feasibility of USI-based threads scheduler on polymorphic computing system

The consistent advances in IC technology result in ever increasing number of transistors. There is more and more interest attracted on the issue of using these transistors in computing more efficiently. The CMP (Chip Multi &ndash processors) is predicted to be one of the most promising solutions for this problem in future. The heterogeneous CMP is supposed to provide more computing efficiency compared to the homogeneous CMP architecture; but it requires complex processing art for manufacturing, which makes it less competitive in the old era. Nowadays, the complicate SOC(System On Chip) manufacturing techniques are pacing fast. This is leading us inexorably to heterogeneous CMP with diverse computing style resources like general purpose CPU, GPU, FPGA, and ASIC cores. In the heterogeneous CMP architecture, the generous purpose CPU provides coverage for all computing, while the non von &ndash Neumann cores harvest energy and processing time for specific computing. The polymorphic system is defined as a heterogeneous system that enable a computing thread to be dynamically selected and mapped to multiple kinds of cores. A polymorphic thread is compiled for multiple morphisms afforded by these diverse cores. The resulting polymorphic computing systems solve two problems. (1) Polymorphic threads enable more complex, dynamic trade &ndash offs between delay and power consumption. A piecewise cobbling of multiple morphism energy &ndash delay profiles offers a richer Energy &ndash Delay(ED) profile for the entire application. This in turn helps scale the proverbial ITRS &rdquo red &ndash brick power wall &rdquo. (2) The OS scheduler not only picks a thread to run, it also chooses its morphism. Previously, the scientists and engineers prefer using the numerical E · T results to evaluate the design trade &ndash offs, which is challenged to not fit on the future mobile systems design in this thesis. In the mobile systems, whose primary role is &ldquo enhanced terminals &rdquo &ndash user interface to cloud hosted computing backbone, user satisfaction ought to be the primary goal. We propose a scheduler to target User Satisfaction Index (USI) functions. In this thesis, we develop a model for a mobile polymorphic embedded system. This model primarily abstracts the queuing process of the threads in the OS operation. We integrate a polymorphic scheduler in this model to assess the application design space offered by polymorphic computing. We explore several greedy versions of a polymorphic scheduler to improve the user satisfaction driven QoS. We build a polymorphic system simulation platform based on SystemC to validate our theoretical analysis of a polymorphic system. We evaluate our polymorphic scheduler on a variety of application mix with various metrics. We further discuss the feasibility of USI &ndash based polymorphic scheduler by identifying its strengths and weaknesses in relation to the application design space based on the simulation results

Linking image processing and numerical modeling to identify potential geohazards

Faults, along with natural fractures, may enhance production when confined within the reservoir. However, if the fault is connected to an aquifer, it may cause early water breakthrough in the reservoir. Even if they are not conductive, they pose a significant geohazard during drilling as fault slippage can cause shearing of casing/tubing leading to either sidetracking, or complete abandonment of the well. In this thesis, I propose a simplistic approximation of dynamic conductivity of faults based on steady state flow equation. I use a geometric attribute; coherence, as a proxy for fault hydraulic conductivity and in a steady state flow equation to model dynamic flow. This thesis was inspired by problems faced by several companies working the Eagle Ford shale reservoir of south Texas. Surveys often exceeds 1000 km2 and exhibit hundreds of faults. Most faults are not problematic; however, some connect with the deeper Edwards limestone aquifer. Wells that complete near these faults produce water. This algorithm can provide early water production warnings and can provide simple, easy to compute useful input in field development in the absence of the more complete datasets required more rigorous reservoir simulation implemented in commercial software. This simple tool is designed to be used in a statistical, rather than deterministic manner, identifying problematic faults by comparing their orientation and connectivity to those known to be bad by previous drilling history. The computational time is less than 17% of a more rigorous conventional reservoir simulation. The model can be updated easily as more and more dataset are available during various stages of field development by ignoring important parameters for single well production such as facies, petrophysical and flow equations. This algorithm is a fast and simple approximation that can be very useful in overall field management where one wishes to quickly identify problematic faults or fault sets

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Mapping the evolving landscape of child-computer interaction research: structures and processes of knowledge (re)production

Implementing an iterative sequential mixed methods design (Quantitative → Qualitative → Quantitative) framed within a sociology of knowledge approach to discourse, this study offers an account of the structure of the field of Child-Computer Interaction (CCI), its development over time, and the practices through which researchers have (re)structured knowledge comprising the field. Thematic structure of knowledge within the field, and its evolution over time, is quantified through implementation of a Correlated Topic Model (CTM), an automated inductive content analysis method, in analysing 4,771 CCI research papers published between 2003 and 2021. Detailed understanding of practices through which researchers (re)structure knowledge within the field, including factors influencing these practices, is obtained through thematic analysis of online workshops involving prominent contributors to the field (n=7). Strategic practices utilised by researchers in negotiating tensions impeding integration of novel concepts in the field are investigated through analysis of semantic features of retrieved papers using linear and negative binomial regression models. Contributing an extensive mapping, results portray the field of CCI as a varied research landscape, comprising 48 major themes of study, which has evolved dynamically over time. Research priorities throughout the field have been subject to influence from a range of endogenous and exogenous factors which researchers actively negotiate through research and publication practices. Tacitly structuring research practices, these factors have broadly sustained a technology-driven, novelty-dominated paradigm throughout the field which has failed to substantively progress cumulative knowledge. Through strategic negotiation of persistent tensions arising as consequence of these factors, researchers have nonetheless affected structural change within the field, contributing to a shift towards a user needs-driven agenda and progression of knowledge therein. Findings demonstrate that the field of CCI is proceeding through an intermediary phase in maturation, forming an increasingly distinct disciplinary shape and identity through the cumulative structuring effect of community members’ continued negotiation of tensions

Towards a living earth simulator

The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems. © The Author(s) 2012