Mastering the scales: A survey on the benefits of multiscale computing software

Electronic supplementary material is available online at https://doi.org/10.6084/m9. figshare.c.4352660.© 2019 The Authors. In the last few decades, multiscale modeling has emerged as one of the dominant modeling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modeling paradigm is now accompanied by a vibrant ecosystem of multiscale computing software (MCS) which promise to address many challenges in the development of multiscale applications. In this paper, we define the common steps in the multiscale application development process and investigate to what degree a set of 22 representative MCS tools enhance each development step. We observe several gaps in the features provided by MCS tools, specially for application deployment and the preparation and management of production runs. In addition, we find that many MCS tools are tailored to a particular multiscale computing pattern, even though they are otherwise application agnostic. We conclude that the gaps we identify are characteristic of a field that is still maturing and features that enhance the deployment and production steps of multiscale application development are desirable for the long term success of MCS in its application fields.The European Union’s Horizon 2020 research, innovation programme under grant agreement and the project “Task-based load balancing and auto-tuning in particle simulations”European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 800925 and 671564; ‘Task-based load balancing and auto-tuning in particle simulations’ project (TaLPas), grant no. 01IH16008B

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Target Acquisition in Multiscale Electronic Worlds

Since the advent of graphical user interfaces, electronic information has grown exponentially, whereas the size of screen displays has stayed almost the same. Multiscale interfaces were designed to address this mismatch, allowing users to adjust the scale at which they interact with information objects. Although the technology has progressed quickly, the theory has lagged behind. Multiscale interfaces pose a stimulating theoretical challenge, reformulating the classic target-acquisition problem from the physical world into an infinitely rescalable electronic world. We address this challenge by extending Fitts’ original pointing paradigm: we introduce the scale variable, thus defining a multiscale pointing paradigm. This article reports on our theoretical and empirical results. We show that target-acquisition performance in a zooming interface must obey Fitts’ law, and more specifically, that target-acquisition time must be proportional to the index of difficulty. Moreover, we complement Fitts’ law by accounting for the effect of view size on pointing performance, showing that performance bandwidth is proportional to view size, up to a ceiling effect. The first empirical study shows that Fitts’ law does apply to a zoomable interface for indices of difficulty up to and beyond 30 bits, whereas classical Fitts’ law studies have been confined in the 2-10 bit range. The second study demonstrates a strong interaction between view size and task difficulty for multiscale pointing, and shows a surprisingly low ceiling. We conclude with implications of these findings for the design of multiscale user interfaces

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

MPWide: a light-weight library for efficient message passing over wide area networks

We present MPWide, a light weight communication library which allows efficient message passing over a distributed network. MPWide has been designed to connect application running on distributed (super)computing resources, and to maximize the communication performance on wide area networks for those without administrative privileges. It can be used to provide message-passing between application, move files, and make very fast connections in client-server environments. MPWide has already been applied to enable distributed cosmological simulations across up to four supercomputers on two continents, and to couple two different bloodflow simulations to form a multiscale simulation.Comment: accepted by the Journal Of Open Research Software, 13 pages, 4 figures, 1 tabl

Ithemal: Accurate, Portable and Fast Basic Block Throughput Estimation using Deep Neural Networks

Predicting the number of clock cycles a processor takes to execute a block of assembly instructions in steady state (the throughput) is important for both compiler designers and performance engineers. Building an analytical model to do so is especially complicated in modern x86-64 Complex Instruction Set Computer (CISC) machines with sophisticated processor microarchitectures in that it is tedious, error prone, and must be performed from scratch for each processor generation. In this paper we present Ithemal, the first tool which learns to predict the throughput of a set of instructions. Ithemal uses a hierarchical LSTM--based approach to predict throughput based on the opcodes and operands of instructions in a basic block. We show that Ithemal is more accurate than state-of-the-art hand-written tools currently used in compiler backends and static machine code analyzers. In particular, our model has less than half the error of state-of-the-art analytical models (LLVM's llvm-mca and Intel's IACA). Ithemal is also able to predict these throughput values just as fast as the aforementioned tools, and is easily ported across a variety of processor microarchitectures with minimal developer effort.Comment: Published at 36th International Conference on Machine Learning (ICML) 201