The PGAS model is well suited for executing irregular applications on cluster-based systems, due to its efficient support for short, one-sided messages. However, there are currently two major limitations faced by PGAS applications. The first relates to scalability: despite the availability of APIs that support non-blocking operations in special cases, many PGAS operations on remote locations are synchronous by default, which can lead to long-latency stalls and poor scalability. The second relates to productivity: while it is simpler for the developer to express all communications at a fine-grained granularity that is natural to the application, experiments have shown that such a natural expression results in performance that is 20x slower than more efficient but less productive code that requires manual message aggregation and termination detection. In this paper, we introduce a new programming system for PGAS applications, in which point-to-point remote operations can be expressed as fine-grained asynchronous actor messages. In this approach, the programmer does not need to worry about programming complexities related to message aggregation and termination detection. Our approach can also be viewed as extending the classical Bulk Synchronous Parallelism model with fine-grained asynchronous communications within a phase or superstep. We believe that our approach offers a desirable point in the productivity-performance space for PGAS applications, with more scalable performance and higher productivity relative to past approaches. Specifically, for seven irregular mini-applications from the Bale benchmark suite executed using 2048 cores in the NERSC Cori system, our approach shows geometric mean performance improvements of >=20x relative to standard PGAS versions (UPC and OpenSHMEM) while maintaining comparable productivity to those versions.
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Runtime verification or runtime monitoring equips safety-critical cyber-physical systems to augment design assurance measures and ensure operational safety and security. Cyber-physical systems have interaction failures, attack surfaces, and attack vectors resulting in unanticipated hazards and loss scenarios. These interaction failures pose challenges to runtime verification regarding monitoring specifications and monitoring placements for in-time detection of hazards. We develop a well-formed workflow model that connects system theoretic process analysis, commonly referred to as STPA, hazard causation information to lower-level runtime monitoring to detect hazards at the operational phase. Specifically, our model follows the DepDevOps paradigm to provide evidence and insights to runtime monitoring on what to monitor, where to monitor, and the monitoring context. We demonstrate and evaluate the value of multilevel monitors by injecting hazards on an autonomous emergency braking system model.
In this paper we present a proof system that operates on graphs instead of formulas. Starting from the well-known relationship between formulas and cographs, we drop the cograph-conditions and look at arbitrary undirected) graphs. This means that we lose the tree structure of the formulas corresponding to the cographs, and we can no longer use standard proof theoretical methods that depend on that tree structure. In order to overcome this difficulty, we use a modular decomposition of graphs and some techniques from deep inference where inference rules do not rely on the main connective of a formula. For our proof system we show the admissibility of cut and a generalization of the splitting property. Finally, we show that our system is a conservative extension of multiplicative linear logic with mix, and we argue that our graphs form a notion of generalized connective.
A determinantal point process (DPP) on a collection of $M$ items is a model, parameterized by a symmetric kernel matrix, that assigns a probability to every subset of those items. Recent work shows that removing the kernel symmetry constraint, yielding nonsymmetric DPPs (NDPPs), can lead to significant predictive performance gains for machine learning applications. However, existing work leaves open the question of scalable NDPP sampling. There is only one known DPP sampling algorithm, based on Cholesky decomposition, that can directly apply to NDPPs as well. Unfortunately, its runtime is cubic in $M$, and thus does not scale to large item collections. In this work, we first note that this algorithm can be transformed into a linear-time one for kernels with low-rank structure. Furthermore, we develop a scalable sublinear-time rejection sampling algorithm by constructing a novel proposal distribution. Additionally, we show that imposing certain structural constraints on the NDPP kernel enables us to bound the rejection rate in a way that depends only on the kernel rank. In our experiments we compare the speed of all of these samplers for a variety of real-world tasks.
Industrial Control Systems (ICSs) rely on insecure protocols and devices to monitor and operate critical infrastructure. Prior work has demonstrated that powerful attackers with detailed system knowledge can manipulate exchanged sensor data to deteriorate performance of the process, even leading to full shutdowns of plants. Identifying those attacks requires iterating over all possible sensor values, and running detailed system simulation or analysis to identify optimal attacks. That setup allows adversaries to identify attacks that are most impactful when applied on the system for the first time, before the system operators become aware of the manipulations. In this work, we investigate if constrained attackers without detailed system knowledge and simulators can identify comparable attacks. In particular, the attacker only requires abstract knowledge on general information flow in the plant, instead of precise algorithms, operating parameters, process models, or simulators. We propose an approach that allows single-shot attacks, i.e., near-optimal attacks that are reliably shutting down a system on the first try. The approach is applied and validated on two use cases, and demonstrated to achieve comparable results to prior work, which relied on detailed system information and simulations.
Data collection and research methodology represents a critical part of the research pipeline. On the one hand, it is important that we collect data in a way that maximises the validity of what we are measuring, which may involve the use of long scales with many items. On the other hand, collecting a large number of items across multiple scales results in participant fatigue, and expensive and time consuming data collection. It is therefore important that we use the available resources optimally. In this work, we consider how a consideration for theory and the associated causal/structural model can help us to streamline data collection procedures by not wasting time collecting data for variables which are not causally critical for subsequent analysis. This not only saves time and enables us to redirect resources to attend to other variables which are more important, but also increases research transparency and the reliability of theory testing. In order to achieve this streamlined data collection, we leverage structural models, and Markov conditional independency structures implicit in these models to identify the substructures which are critical for answering a particular research question. In this work, we review the relevant concepts and present a number of didactic examples with the hope that psychologists can use these techniques to streamline their data collection process without invalidating the subsequent analysis. We provide a number of simulation results to demonstrate the limited analytical impact of this streamlining.
In this paper we get error bounds for fully discrete approximations of infinite horizon problems via the dynamic programming approach. It is well known that considering a time discretization with a positive step size $h$ an error bound of size $h$ can be proved for the difference between the value function (viscosity solution of the Hamilton-Jacobi-Bellman equation corresponding to the infinite horizon) and the value function of the discrete time problem. However, including also a spatial discretization based on elements of size $k$ an error bound of size $O(k/h)$ can be found in the literature for the error between the value functions of the continuous problem and the fully discrete problem. In this paper we revise the error bound of the fully discrete method and prove, under similar assumptions to those of the time discrete case, that the error of the fully discrete case is in fact $O(h+k)$ which gives first order in time and space for the method. This error bound matches the numerical experiments of many papers in the literature in which the behaviour $1/h$ from the bound $O(k/h)$ have not been observed.
Numerical solution of heterogeneous Helmholtz problems presents various computational challenges, with descriptive theory remaining out of reach for many popular approaches. Robustness and scalability are key for practical and reliable solvers in large-scale applications, especially for large wave number problems. In this work we explore the use of a GenEO-type coarse space to build a two-level additive Schwarz method applicable to highly indefinite Helmholtz problems. Through a range of numerical tests on a 2D model problem, discretised by finite elements on pollution-free meshes, we observe robust convergence, iteration counts that do not increase with the wave number, and good scalability of our approach. We further provide results showing a favourable comparison with the DtN coarse space. Our numerical study shows promise that our solver methodology can be effective for challenging heterogeneous applications.
Molecular dynamics (MD) has long been the \emph{de facto} choice for modeling complex atomistic systems from first principles, and recently deep learning become a popular way to accelerate it. Notwithstanding, preceding approaches depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called ScoreMD by directly estimating the gradient of the log density of molecular conformations. Moreover, we analyze that diffusion processes highly accord with the principle of enhanced sampling in MD simulations, and is therefore a perfect match to our sequential conformation generation task. That is, ScoreMD perturbs the molecular structure with a conditional noise depending on atomic accelerations and employs conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that the molecule is kinetic instead of static, which no prior studies strictly consider. To solve this challenge, we introduce a equivariant geometric Transformer as a score function in the diffusion process to calculate the corresponding gradient. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperforms state-of-the-art baselines on MD17 and isomers of C7O2H10. This research provides new insights into the acceleration of new material and drug discovery.
Computing a maximum independent set (MaxIS) is a fundamental NP-hard problem in graph theory, which has important applications in a wide spectrum of fields. Since graphs in many applications are changing frequently over time, the problem of maintaining a MaxIS over dynamic graphs has attracted increasing attention over the past few years. Due to the intractability of maintaining an exact MaxIS, this paper aims to develop efficient algorithms that can maintain an approximate MaxIS with an accuracy guarantee theoretically. In particular, we propose a framework that maintains a $(\frac{\Delta}{2} + 1)$-approximate MaxIS over dynamic graphs and prove that it achieves a constant approximation ratio in many real-world networks. To the best of our knowledge, this is the first non-trivial approximability result for the dynamic MaxIS problem. Following the framework, we implement an efficient linear-time dynamic algorithm and a more effective dynamic algorithm with near-linear expected time complexity. Our thorough experiments over real and synthetic graphs demonstrate the effectiveness and efficiency of the proposed algorithms, especially when the graph is highly dynamic.
We describe a cognitive architecture intended to solve a wide range of problems based on the five identified principles of brain activity, with their implementation in three subsystems: logical-probabilistic inference, probabilistic formal concepts, and functional systems theory. Building an architecture involves the implementation of a task-driven approach that allows defining the target functions of applied applications as tasks formulated in terms of the operating environment corresponding to the task, expressed in the applied ontology. We provide a basic ontology for a number of practical applications as well as for the subject domain ontologies based upon it, describe the proposed architecture, and give possible examples of the execution of these applications in this architecture.
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