Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library

Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general black-box approach for the efficient GPU acceleration of matrix−matrix multiplications where the matrix size is too large for the whole computation to be held in the GPU’s onboard memory. Second, we show how to improve the accuracy of matrix multiplications when using only single-precision GPU devices by proposing a heterogeneous computing model, whereby single- and double-precision operations are evaluated in a mixed fashion on the GPU and central processing unit, respectively. The utility of the library is illustrated for quantum chemistry with application to the acceleration of resolution-of-the-identity second-order Møller−Plesset perturbation theory calculations for molecules, which we were previously unable to treat. In particular, for the 168-atom valinomycin molecule in a cc-pVDZ basis set, we observed speedups of 13.8, 7.8, and 10.1 times for single-, double- and mixed-precision general matrix multiply (SGEMM, DGEMM, and MGEMM), respectively. The corresponding errors in the correlation energy were reduced from −10.0 to −1.2 kcal mol$^{-1}$ for SGEMM and MGEMM, respectively, while higher accuracy can be easily achieved with a different choice of cutoff parameter.Chemistry and Chemical Biolog

Exascale machines require new programming paradigms and runtimes

Extreme scale parallel computing systems will have tens of thousands of optionally accelerator-equiped nodes with hundreds of cores each, as well as deep memory hierarchies and complex interconnect topologies. Such Exascale systems will provide hardware parallelism at multiple levels and will be energy constrained. Their extreme scale and the rapidly deteriorating reliablity of their hardware components means that Exascale systems will exhibit low mean-time-between-failure values. Furthermore, existing programming models already require heroic programming and optimisation efforts to achieve high efficiency on current supercomputers. Invariably, these efforts are platform-specific and non-portable. In this paper we will explore the shortcomings of existing programming models and runtime systems for large scale computing systems. We then propose and discuss important features of programming paradigms and runtime system to deal with large scale computing systems with a special focus on data-intensive applications and resilience. Finally, we also discuss code sustainability issues and propose several software metrics that are of paramount importance for code development for large scale computing systems

The DeepHealth Toolkit: A key European free and open-source software for deep learning and computer vision ready to exploit heterogeneous HPC and cloud architectures

At the present time, we are immersed in the convergence between Big Data, High-Performance Computing and Artificial Intelligence. Technological progress in these three areas has accelerated in recent years, forcing different players like software companies and stakeholders to move quickly. The European Union is dedicating a lot of resources to maintain its relevant position in this scenario, funding projects to implement large-scale pilot testbeds that combine the latest advances in Artificial Intelligence, High-Performance Computing, Cloud and Big Data technologies. The DeepHealth project is an example focused on the health sector whose main outcome is the DeepHealth toolkit, a European unified framework that offers deep learning and computer vision capabilities, completely adapted to exploit underlying heterogeneous High-Performance Computing, Big Data and cloud architectures, and ready to be integrated into any software platform to facilitate the development and deployment of new applications for specific problems in any sector. This toolkit is intended to be one of the European contributions to the field of AI. This chapter introduces the toolkit with its main components and complementary tools, providing a clear view to facilitate and encourage its adoption and wide use by the European community of developers of AI-based solutions and data scientists working in the healthcare sector and others. iThis chapter describes work undertaken in the context of the DeepHealth project, “Deep-Learning and HPC to Boost Biomedical Applications for Health”, which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.Peer Reviewed"Article signat per 19 autors/es: Marco Aldinucci, David Atienza, Federico Bolelli, Mónica Caballero, Iacopo Colonnelli, José Flich, Jon A. Gómez, David González, Costantino Grana, Marco Grangetto, Simone Leo, Pedro López, Dana Oniga, Roberto Paredes, Luca Pireddu, Eduardo Quiñones, Tatiana Silva, Enzo Tartaglione & Marina Zapater "Postprint (author's final draft

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

We propose a novel computing runtime that exposes remote compute devices via the cross-vendor open heterogeneous computing standard OpenCL and can execute compute tasks on the MEC cluster side across multiple servers in a scalable manner. Intermittent UE connection loss is handled gracefully even if the device's IP address changes on the way. Network-induced latency is minimized by transferring data and signaling command completions between remote devices in a peer-to-peer fashion directly to the target server with a streamlined TCP-based protocol that yields a command latency of only 60 microseconds on top of network round-trip latency in synthetic benchmarks. The runtime can utilize RDMA to speed up inter-server data transfers by an additional 60% compared to the TCP-based solution. The benefits of the proposed runtime in MEC applications are demonstrated with a smartphone-based augmented reality rendering case study. Measurements show up to 19x improvements to frame rate and 17x improvements to local energy consumption when using the proposed runtime to offload AR rendering from a smartphone. Scalability to multiple GPU servers in real-world applications is shown in a computational fluid dynamics simulation, which scales with the number of servers at roughly 80% efficiency which is comparable to an MPI port of the same simulation.Comment: 13 pages, 17 figure

Gunrock: GPU Graph Analytics

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs, have presented two significant challenges to developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We characterize the performance of various optimization strategies and evaluate Gunrock's overall performance on different GPU architectures on a wide range of graph primitives that span from traversal-based algorithms and ranking algorithms, to triangle counting and bipartite-graph-based algorithms. The results show that on a single GPU, Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives and CPU shared-memory graph libraries such as Ligra and Galois, and better performance than any other GPU high-level graph library.Comment: 52 pages, invited paper to ACM Transactions on Parallel Computing (TOPC), an extended version of PPoPP'16 paper "Gunrock: A High-Performance Graph Processing Library on the GPU

Investigating Single Precision Floating General Matrix Multiply in Heterogeneous Hardware

The fundamental operation of matrix multiplication is ubiquitous across a myriad of disciplines. Yet, the identification of new optimizations for matrix multiplication remains relevant for emerging hardware architectures and heterogeneous systems. Frameworks such as OpenCL enable computation orchestration on existing systems, and its availability using the Intel High Level Synthesis compiler allows users to architect new designs for reconfigurable hardware using C/C++. Using the HARPv2 as a vehicle for exploration, we investigate the utility of several of the most notable matrix multiplication optimizations to better understand the performance portability of OpenCL and the implications for such optimizations on this and future heterogeneous architectures. Our results give targeted insights into the applicability of best practices that were for existing architectures when used on emerging heterogeneous systems

Computing large market equilibria using abstractions

Computing market equilibria is an important practical problem for market design (e.g. fair division, item allocation). However, computing equilibria requires large amounts of information (e.g. all valuations for all buyers for all items) and compute power. We consider ameliorating these issues by applying a method used for solving complex games: constructing a coarsened abstraction of a given market, solving for the equilibrium in the abstraction, and lifting the prices and allocations back to the original market. We show how to bound important quantities such as regret, envy, Nash social welfare, Pareto optimality, and maximin share when the abstracted prices and allocations are used in place of the real equilibrium. We then study two abstraction methods of interest for practitioners: 1) filling in unknown valuations using techniques from matrix completion, 2) reducing the problem size by aggregating groups of buyers/items into smaller numbers of representative buyers/items and solving for equilibrium in this coarsened market. We find that in real data allocations/prices that are relatively close to equilibria can be computed from even very coarse abstractions

Randomized Entity-wise Factorization for Multi-Agent Reinforcement Learning

Multi-agent settings in the real world often involve tasks with varying types and quantities of agents and non-agent entities; however, common patterns of behavior often emerge among these agents/entities. Our method aims to leverage these commonalities by asking the question: ``What is the expected utility of each agent when only considering a randomly selected sub-group of its observed entities?'' By posing this counterfactual question, we can recognize state-action trajectories within sub-groups of entities that we may have encountered in another task and use what we learned in that task to inform our prediction in the current one. We then reconstruct a prediction of the full returns as a combination of factors considering these disjoint groups of entities and train this ``randomly factorized" value function as an auxiliary objective for value-based multi-agent reinforcement learning. By doing so, our model can recognize and leverage similarities across tasks to improve learning efficiency in a multi-task setting. Our approach, Randomized Entity-wise Factorization for Imagined Learning (REFIL), outperforms all strong baselines by a significant margin in challenging multi-task StarCraft micromanagement settings.Comment: ICML 2021 Camera Read