86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy

We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version is 7 times faster than the CPU version with the same power consumption. The code can scale up to the entire Summit supercomputer. For a copper system of 113, 246, 208 atoms, the code can perform one nanosecond MD simulation per day, reaching a peak performance of 86 PFLOPS (43% of the peak). Such unprecedented ability to perform MD simulation with ab initio accuracy opens up the possibility of studying many important issues in materials and molecules, such as heterogeneous catalysis, electrochemical cells, irradiation damage, crack propagation, and biochemical reactions.Comment: 29 pages, 11 figure

When parallel speedups hit the memory wall

After Amdahl's trailblazing work, many other authors proposed analytical speedup models but none have considered the limiting effect of the memory wall. These models exploited aspects such as problem-size variation, memory size, communication overhead, and synchronization overhead, but data-access delays are assumed to be constant. Nevertheless, such delays can vary, for example, according to the number of cores used and the ratio between processor and memory frequencies. Given the large number of possible configurations of operating frequency and number of cores that current architectures can offer, suitable speedup models to describe such variations among these configurations are quite desirable for off-line or on-line scheduling decisions. This work proposes new parallel speedup models that account for variations of the average data-access delay to describe the limiting effect of the memory wall on parallel speedups. Analytical results indicate that the proposed modeling can capture the desired behavior while experimental hardware results validate the former. Additionally, we show that when accounting for parameters that reflect the intrinsic characteristics of the applications, such as degree of parallelism and susceptibility to the memory wall, our proposal has significant advantages over machine-learning-based modeling. Moreover, besides being black-box modeling, our experiments show that conventional machine-learning modeling needs about one order of magnitude more measurements to reach the same level of accuracy achieved in our modeling.Comment: 24 page

Investigation into scalable energy and performance models for many-core systems

PhD ThesisIt is likely that many-core processor systems will continue to penetrate emerging embedded and high-performance applications. Scalable energy and performance models are two critical aspects that provide insights into the conflicting trade-offs between them with growing hardware and software complexity. Traditional performance models, such as Amdahl’s Law, Gustafson’s and Sun-Ni’s, have helped the research community and industry to better understand the system performance bounds with given processing resources, which is otherwise known as speedup. However, these models and their existing extensions have limited applicability for energy and/or performance-driven system optimization in practical systems. For instance, these are typically based on software characteristics, assuming ideal and homogeneous hardware platforms or limited forms of processor heterogeneity. In addition, the measurement of speedup and parallelization factors of an application running on a specific hardware platform require instrumenting the original software codes. Indeed, practical speedup and parallelizability models of application workloads running on modern heterogeneous hardware are critical for energy and performance models, as they can be used to inform design and control decisions with an aim to improve system throughput and energy efficiency. This thesis addresses the limitations by firstly developing novel and scalable speedup and energy consumption models based on a more general representation of heterogeneity, referred to as the normal form heterogeneity. A method is developed whereby standard performance counters found in modern many-core platforms can be used to derive speedup, and therefore the parallelizability of the software, without instrumenting applications. This extends the usability of the new models to scenarios where the parallelizability of software is unknown, leading to potentially Run-Time Management (RTM) speedup and/or energy efficiency optimization. The models and optimization methods presented in this thesis are validated through extensive experimentation, by running a number of different applications in wide-ranging concurrency scenarios on a number of different homogeneous and heterogeneous Multi/Many Core Processor (M/MCP) systems. These include homogeneous and heterogeneous architectures and viii range from existing off-the-shelf platforms to potential future system extensions. The practical use of these models and methods is demonstrated through real examples such as studying the effectiveness of the system load balancer. The models and methodologies proposed in this thesis provide guidance to a new opportunities for improving the energy efficiency of M/MCP systemsHigher Committee of Education Development (HCED) in Ira

A GPU-accelerated package for simulation of flow in nanoporous source rocks with many-body dissipative particle dynamics

Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and fluid-solid interactions in nano- to micro-scale shale pores, which are physically and chemically sophisticated, must be captured. To address those challenges, we present a GPU-accelerated package for simulation of flow in nano- to micro-pore networks with a many-body dissipative particle dynamics (mDPD) mesoscale model. Based on a fully distributed parallel paradigm, the code offloads all intensive workloads on GPUs. Other advancements, such as smart particle packing and no-slip boundary condition in complex pore geometries, are also implemented for the construction and the simulation of the realistic shale pores from 3D nanometer-resolution stack images. Our code is validated for accuracy and compared against the CPU counterpart for speedup. In our benchmark tests, the code delivers nearly perfect strong scaling and weak scaling (with up to 512 million particles) on up to 512 K20X GPUs on Oak Ridge National Laboratory's (ORNL) Titan supercomputer. Moreover, a single-GPU benchmark on ORNL's SummitDev and IBM's AC922 suggests that the host-to-device NVLink can boost performance over PCIe by a remarkable 40\%. Lastly, we demonstrate, through a flow simulation in realistic shale pores, that the CPU counterpart requires 840 Power9 cores to rival the performance delivered by our package with four V100 GPUs on ORNL's Summit architecture. This simulation package enables quick-turnaround and high-throughput mesoscopic numerical simulations for investigating complex flow phenomena in nano- to micro-porous rocks with realistic pore geometries

Runtime-guided mitigation of manufacturing variability in power-constrained multi-socket NUMA nodes

This work has been supported by the Spanish Government (Severo Ochoa grants SEV2015-0493, SEV-2011-00067), by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P), by Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), by the RoMoL ERC Advanced Grant (GA 321253) and the European HiPEAC Network of Excellence. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047. M. Casas is supported by the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia and the Cofund programme of the Marie Curie Actions of the 7th R&D Framework Programme of the European Union (Contract 2013 BP B 00243). This work was also partially performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-CONF-689878). Finally, the authors are grateful to the reviewers for their valuable comments, to the RoMoL team, to Xavier Teruel and Kallia Chronaki from the Programming Models group of BSC and the Computation Department of LLNL for their technical support and useful feedback.Peer ReviewedPostprint (published version