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Scheduling Operations for Massive Heterogeneous Clusters

High-performance computing (HPC) programming has become increasingly difficult with the advent of hybrid supercomputers consisting of multicore CPUs and accelerator boards such as the GPU. Manual tuning of software to achieve high performance on this type of machine has been performed by programmers. This is needlessly difficult and prone to being invalidated by new hardware, new software, or changes in the underlying code. A system was developed for task-based representation of programs, which when coupled with a scheduler and runtime system, allows for many benefits, including higher performance and utilization of computational resources, easier programming and porting, and adaptations of code during runtime. The system consists of a method of representing computer algorithms as a series of data-dependent tasks. The series forms a graph, which can be scheduled for execution on many nodes of a supercomputer efficiently by a computer algorithm. The schedule is executed by a dispatch component, which is tailored to understand all of the hardware types that may be available within the system. The scheduler is informed by a cluster mapping tool, which generates a topology of available resources and their strengths and communication costs. Software is decoupled from its hardware, which aids in porting to future architectures. A computer algorithm schedules all operations, which for systems of high complexity (i.e., most NASA codes), cannot be performed optimally by a human. The system aids in reducing repetitive code, such as communication code, and aids in the reduction of redundant code across projects. It adds new features to code automatically, such as recovering from a lost node or the ability to modify the code while running. In this project, the innovators at the time of this reporting intend to develop two distinct technologies that build upon each other and both of which serve as building blocks for more efficient HPC usage. First is the scheduling and dynamic execution framework, and the second is scalable linear algebra libraries that are built directly on the former.

Humphrey, John↗

Cloud-Based Numerical Weather Prediction for Near Real-Time Forecasting and Disaster Response

The use of cloud computing resources continues to grow within the public and private sector components of the weather enterprise as users become more familiar with cloud‐computing concepts, and competition among service providers continues to reduce costs and other barriers to entry. Cloud resources can also provide capabilities similar to high‐performance computing environments, supporting multi‐node systems required for near real‐time, regional weather predictions. Referred to as "Infrastructure as a Service", or IaaS, the use of cloud-based computing hardware in an on‐demand payment system allows for rapid deployment of a modeling system in environments lacking access to a large, supercomputing infrastructure. Use of IaaS capabilities to support regional weather prediction may be of particular interest to developing countries that have not yet established large supercomputing resources, but would otherwise benefit from a regional weather forecasting capability. Recently, collaborators from NASA Marshall Space Flight Center and Ames Research Center have developed a scripted, on‐demand capability for launching the NOAA/NWS Science and Training Resource Center (STRC) Environmental Modeling System (EMS), which includes pre‐compiled binaries of the latest version of the Weather Research and Forecasting (WRF) model. The WRF‐EMS provides scripting for downloading appropriate initial and boundary conditions from global models, along with higher‐resolution vegetation, land surface, and sea surface temperature data sets provided by the NASA Short‐term Prediction Research and Transition (SPoRT) Center. This presentation will provide an overview of the modeling system capabilities and benchmarks performed on the Amazon Elastic Compute Cloud (EC2) environment. In addition, the presentation will discuss future opportunities to deploy the system in support of weather prediction in developing countries supported by NASA's SERVIR Project, which provides capacity building activities in environmental monitoring and prediction across a growing number of regional hubs throughout the world. Capacity‐building applications that extend numerical weather prediction to developing countries are intended to provide near real‐time applications to benefit public health, safety, and economic interests, but may have a greater impact during disaster events by providing a source for local predictions of weather‐related hazards, or impacts that local weather events may have during the recovery phase.

Molthan, Andrew↗

Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

KINETICS↗

The TESS Science Processing Operations Center

The Transiting Exoplanet Survey Satellite (TESS) will conduct a search for Earth's closest cousins starting in early 2018 and is expected to discover approximately 1,000 small planets with R(sub p) less than 4 (solar radius) and measure the masses of at least 50 of these small worlds. The Science Processing Operations Center (SPOC) is being developed at NASA Ames Research Center based on the Kepler science pipeline and will generate calibrated pixels and light curves on the NASA Advanced Supercomputing Division's Pleiades supercomputer. The SPOC will also search for periodic transit events and generate validation products for the transit-like features in the light curves. All TESS SPOC data products will be archived to the Mikulski Archive for Space Telescopes (MAST).

Jenkins, Jon M.↗

Digital Technologies at NASA for Science and Engineering

While scientific and engineering advancements used to rely primarily on theoretical studies and physical experiments, today digital technology enabled by petaflops-scale supercomputers is an equal, if not a greater, contributor to such achievements. In addition, computational modeling and simulation serves as a predictive tool that is not otherwise available. As a result, the use of high performance computing is integral to NASA's work in all mission areas such as space exploration, aeronautics, and scientific discovery. But traditional supercomputing alone is not sufficient for all of the space agency's needs. The success of many NASA missions depends on solving complex computing challenges, some of which are NP-hard (decision theory) if using classical solution methods. Quantum computing promises an unprecedented ability to solve such intractable problems by harnessing quantum mechanical effects such as tunneling, superposition, and entanglement. Another disruptive digital technology is neuromorphic computing that uses brain-inspired lessons to generate new architectures that are much more energy efficient, and capable of massive parallel processing and learning in-situ. Finally, with large amounts of observational and computational data sets, the opportunities of big data and data analytics can be leveraged to enable deep learning and knowledge discovery - it's all a massive digital transformation. This talk will be an overview how NASA utilizes digital technologies for its science and engineering efforts.

Biswas, Rupak↗

Methodology and Application of HPC I/O Characterization with MPIProf and IOT

Combining the strengths of MPIProf and IOT, an efficient and systematic method is devised for I/O characterization at the per-job, per-rank, per-file and per-call levels of HPC programs running on the NASA Advanced Supercomputing Center. This method is applied to answer four I/O questions in this paper. A total of 13 MPI programs and 15 cases, ranging from 24 to 5968 ranks, are analyzed to establish the I/O landscape from answers to the four questions. Four of the 13 programs use MPI I/O and the behavior of their collective writes depends on the specific implementation of the MPI library used. The SGI MPT library, the prevailing MPI library for our systems, was found to gather small writes from a large number of ranks to perform larger writes by a small subset of collective buffering ranks. The number of collective buffering ranks invoked by MPT depends on the Lustre stripe count and the number of nodes used for the run. A demonstration of varying the stripe count to achieve double-digit speedup of one program's I/O was presented. Another program, which concurrently opens private files by all ranks and could potentially create a heavy load on the Lustre servers, was identified. The ability to systematically characterize I/O for a large number of programs running on a supercomputer, seek I/O optimization opportunity and identify programs that could cause a high load and instability on the filesystems is important for pursuing exascale in a real production environment.

Characterization↗

CFD Simulations of the Space Launch System Ascent Aerodynamics and Booster Separation

This paper presents details of Computational Fluid Dynamic modeling of the Space Launch System during ascent. The primary focus of the paper is the flow simulation of the vehicle during ascent using the Overflow Navier-Stokes code. Computations of 739 first-stage flight conditions covering a range of Mach numbers, angles of attack, and roll angles were computed. The overset grid system contained 375 million grid points, and over 28 mil- lion CPU hours were used in the simulations. The simulations were run on the Pleiades supercomputer at the NASA Advanced Supercomputer Center at Ames Research Center. The data products from this work include integrated line-loads, surface pressure coefficients, venting pressures, and protuberance air-loads. Detailed comparisons were made of the aerodynamic performance predicted by Overflow and the wind-tunnel derived aero- dynamic database. A small number of the cases were run with two different turbulence models and with two differencing schemes. These results were used to quantify the sensitivity to the choice of the turbulence model and to the differencing scheme. The paper also introduces an effort to use the inviscid, unstructured Cartesian solver Cart3D to compute the aerodynamics during booster separation. Adaptive mesh refinement is being used to enable accurate simulations of sixteen booster-separation-motor plumes. The use of this tool is explored in preparation for building a booster-separation aerodynamic database.

Ascent Aerodynamics↗

High-Performance Computing Optimization for Aladyn – Adaptive Neural Network Molecular Dynamics Mini-Application

This report provides a description and performance evaluation of the optimization techniques for high performance computing (HPC) implementation of the open source Computational Materials mini-application Aladyn (https://github.com/nasa/aladyn). Aladyn is a basic molecular dynamics code written in FORTRAN 2003, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. While achieving orders of magnitude faster computational performance than DFT, the ANN-based approach was still very computationally demanding compared to the conventional approach of using empirically fitted energy functions. After its initial development, Aladyn was evaluated and optimized by experts at the NASA Advanced Supercomputing (NAS) division to exploit modern supercomputer architectures. The code has been optimized for execution on multicore central processing units (CPUs), including Intel® Skylake microarchitecture, and on graphic accelerators, such as Nvidia® V100 graphic processing units (GPUs), using Open Multi-Processing (OpenMP) and Open Accelerators (OpenACC) programming interfaces. The optimization achieved a speedup of 4.7 times the baseline version on CPU performance and an additional 2.4 times on CPU+GPU performance. Atomistic computer simulations are a fundamental tool in materials research to model material properties form physics-based first principles. Atomic interaction, governed by Quantum Mechanics (QM) require sophisticated and highly computationally demanding mathematical models to calculate [1]. Classical methods use approximate functional forms, empirically fitted through a set of variable parameters to emulate atomic energies as direct functions of atomic coordinates [2]. While empirical potentials are computationally much simpler, allowing simulations of large-scale systems of up to a trillion (1012) atoms [3], they are substantially less accurate compared to quantum calculations and applicable only to very specific atomic configurations or predefined crystallographic phases. A recently suggested approach is to use heuristic machine learning methods [4], such as those based on Adaptive Neural Networks (ANNs) to predict atomic energies, after being trained on a sufficiently large database of QM-calculated structures [5,6]. This approach reduces significantly the computational complexity, allowing for simulations of orders of magnitude larger systems compared to QM-based methods without compromising accuracy. Still, compared to classical methods using empirical energy functions, ANN methods remain two- to three orders of magnitude more computationally demanding. Hence, the computational cost of simulations, together with the need for extensive training of ANNs, still makes the practical implementation of ANN-based methods quite challenging. The purpose of the Aladyn mini-application software [7], available as open source at https://github.com/nasa/aladyn, is to be a testbed for exploring possible optimization strategies to develop highly scalable parallel algorithms for ANN-based atomistic simulations. Aladyn is aimed at utilizing the architecture of the high-end modern highperformance computing (HPC) hardware based on multicore central processing units (CPUs) equipped with graphic processing unit (GPU) accelerators. Specifically, the goal is to optimize the performance on a single HPC compute node, before implementing scaling to multi-node parallelization using message passing interface (MPI). At the same time, the open source code of Aladyn can serve as a training model for students and professors in academia.

Yamakov, Vesselin I.↗

NASA Advanced Computing Environment for Science and Engineering

High-fidelity modeling, simulation, and analysis, enabled by supercomputing, are becoming increasingly important to NASA’s broad spectrum of missions. This paper describes NASA’s advanced supercomputing environment at Ames Research Center that is geared toward solving the space agency’s most challenging science and engineering problems.

Biswas, Rupak↗

The Evolution of NASA’s High-End Computing Capabilities

For over 35 years, the NASA Advanced Supercomputing (NAS) Division at Ames Research Center has housed and managed the U.S. space agency’s largest supercomputing assets. Focused on high-end computing technologies, efficient operations, and user success, the NAS Division has worked with industry to deploy a series of highly successful systems that enable scientific and engineering achievements across NASA. The complementary role of the High-End Computing Capability (HECC) project is evolving to meet NASA’s future challenges in returning to the Moon as a pathway to Mars, while continuing exciting research in aeronautics, space exploration, and Earth science.

Thigpen, William↗

Particle Interaction Physics Model Formulation for Plume-Surface Interaction Erosion and Cratering

The Predictive Simulation Capability development team of the STMD Game Changing Development sponsored PSI project is implementing computational simulation capability for the efficient and accurate prediction of Plume-Surface Interaction induced surface erosion and cratering in Martian and Lunar environments. The status of the Focus Area 3 of the PSI project in the generation and efficient application of accurate soil particle composition modeling in the Gas-Granular Flow Solver (GGFS) computational framework is presented. The process of constitutive closure model database generation using DEM particle interaction modeling for capturing the effects of irregular particle shape and poly-disperse mixture distribution effects is outlined. This capability has now been ported to NASA supercomputer assets and NASA engineers successfully demonstrated technology and skillset transfer in model generation for spherical and irregularly shaped, mono-disperse and bi-disperse mixture compositions. Assessment of the computational efficiency and practicality of the academic serially executed DEM tools on NASA supercomputers identified the need to migrate to a DEM framework capable of performing parallel simulations in a simultaneous process orchestrated in an automated setup, execution, database extraction, and dataset delivery ready for application simulations. The LIGGGHTS DEM toolset has been selected as the most suitable tool to migrate the DEM simulations. Once the soil model generation process is implemented, models capturing the shape and poly-dispersity effects will be generated to perform much refined validation simulations against the experiments performed under the PSI project. The application readiness of the soil models currently operational in GGFS was presented for the example of a full scale, 3-D simulation of the plume induced erosion and crater formation of the Apollo LM at an elevation of 5m above ground in a low pressure, near vacuum background.

Peter A Liever↗

Particle Interaction Physics Model Formulation for Plume-Surface Interaction Erosion and Cratering

The Predictive Simulation Capability development team of the STMD Game Changing Development sponsored PSI project is implementing computational simulation capability for the efficient and accurate prediction of Plume-Surface Interaction induced surface erosion and cratering in Martian and Lunar environments. The status of the Focus Area 3 of the PSI project in the generation and efficient application of accurate soil particle composition modeling in the Gas-Granular Flow Solver (GGFS) computational framework is presented. The process of constitutive closure model database generation using DEM particle interaction modeling for capturing the effects of irregular particle shape and poly-disperse mixture distribution effects is outlined. This capability has now been ported to NASA supercomputer assets and NASA engineers successfully demonstrated technology and skillset transfer in model generation for spherical and irregularly shaped, mono-disperse and bi-disperse mixture compositions. Assessment of the computational efficiency and practicality of the academic serially executed DEM tools on NASA supercomputers identified the need to migrate to a DEM framework capable of performing parallel simulations in a simultaneous process orchestrated in an automated setup, execution, database extraction, and dataset delivery ready for application simulations. The LIGGGHTS DEM toolset has been selected as the most suitable tool to migrate the DEM simulations. Once the soil model generation process is implemented, models capturing the shape and poly-dispersity effects will be generated to perform much refined validation simulations against the experiments performed under the PSI project. The application readiness of the soil models currently operational in GGFS was presented for the example of a full scale, 3-D simulation of the plume induced erosion and crater formation of the Apollo LM at an elevation of 5m above ground in a low pressure, near vacuum background.

Peter A Liever↗

Web-based Visualization and Analytics of Petascale Data: Equity as a Tide that Lifts All Boats

Scientists generate petabytes of data daily to help uncover environmental trends or behaviors that are hard to predict. For example, understanding climate simulations based on the long-term average of temperature, precipitation, and other environmental variables is essential to predicting and establishing root causes of future undesirable scenarios and assessing possible mitigation strategies. While supercomputer centers provide a powerful infrastructure for generating petabytes of simulation output, accessing and analyzing these datasets interactively remains challenging on multiple fronts. This paper presents an approach to managing, visualizing, and analyzing petabytes of data within a browser on equipment ranging from the top NASA supercomputer to commodity hardware like a laptop. Our novel data fabric abstraction layer allows user-friendly querying of scientific information while hid-ing the complexities of dealing with file systems or cloud services.We also optimize network utilization while streaming from petas-cale repositories through state-of-the-art progressive compression algorithms. Based on this abstraction, we provide customizable dashboards that can be accessed from any device with any inter-net connection, enabling interactive visual analysis of vast amounts of data to a wide range of users - from top scientists with access to leadership-class computing environments to undergraduate students of disadvantaged backgrounds from minority-serving institutions. We focus on NASA’s use of petascale climate datasets as an example of particular societal impact and, therefore, a case where achieving equity in science participation is critical. We validate our approach by improving the ability of climate scientists to visually explore their data via two fully interactive dashboards. We further validate our approach by deploying the dashboards and simplified training materials in the classroom at a minority-serving institution.These dashboards, released in simplified form to the general public, contribute significantly to a broader push to democratize the access and use of climate data.

Data visualization↗

Energy Innovation Hubs: A Home for Scientific Collaboration

Secretary Chu will host a live, streaming Q&A session with the directors of the Energy Innovation Hubs on Tuesday, March 6, at 2:15 p.m. EST. The directors will be available for questions regarding their teams' work and the future of American energy. Ask your questions in the comments below, or submit them on Facebook, Twitter (@energy), or send an e-mail to newmedia@hq.doe.gov, prior or during the live event. Dr. Hank Foley is the director of the Greater Philadelphia Innovation Cluster for Energy-Efficient Buildings, which is pioneering new data intensive techniques for designing and operating energy efficient buildings, including advanced computer modeling. Dr. Douglas Kothe is the director of the Consortium for Advanced Simulation of Light Water Reactors, which uses powerful supercomputers to create "virtual" reactors that will help improve the safety and performance of both existing and new nuclear reactors. Dr. Nathan Lewis is the director of the Joint Center for Artificial Photosynthesis, which focuses on how to produce fuels from sunlight, water, and carbon dioxide. The Energy Innovation Hubs are major integrated research centers, with researchers from many different institutions and technical backgrounds. Each hub is focused on a specific high priority goal, rapidly accelerating scientific discoveries and shortening the path from laboratory innovation to technological development and commercial deployment of critical energy technologies. Ask your questions in the comments below, or submit them on Facebook, Twitter (@energy), or send an e-mail to newmedia@energy.gov, prior or during the live event. The Energy Innovation Hubs are major integrated research centers, with researchers from many different institutions and technical backgrounds. Each Hub is focused on a specific high priority goal, rapidly accelerating scientific discoveries and shortening the path from laboratory innovation to technological development and commercial deployment of critical energy technologies. Dr. Hank Holey is the director of the Greater Philadelphia Innovation Cluster for Energy-Efficient Buildings, which is pioneering new data intensive techniques for designing and operating energy efficient buildings, including advanced computer modeling. Dr. Douglas Kothe is the director of the Modeling and Simulation for Nuclear Reactors Hub, which uses powerful supercomputers to create "virtual" reactors that will help improve the safety and performance of both existing and new nuclear reactors. Dr. Nathan Lewis is the director of the Joint Center for Artificial Photosynthesis Hub, which focuses on how to produce biofuels from sunlight, water, and carbon dioxide.

13 HYDRO ENERGY↗

HPC Usage Behavior Analysis and Performance Estimation with Machine Learning Techniques

Most researchers with little high performance computing (HPC) experience have difficulties productively using the supercomputing resources. To address this issue, we investigated usage behaviors of the world s fastest academic Kraken supercomputer, and built a knowledge-based recommendation system to improve user productivity. Six clustering techniques, along with three cluster validation measures, were implemented to investigate the underlying patterns of usage behaviors. Besides manually defining a category for very large job submissions, six behavior categories were identified, which cleanly separated the data intensive jobs and computational intensive jobs. Then, job statistics of each behavior category were used to develop a knowledge-based recommendation system that can provide users with instructions about choosing appropriate software packages, setting job parameter values, and estimating job queuing time and runtime. Experiments were conducted to evaluate the performance of the proposed recommendation system, which included 127 job submissions by users from different research fields. Great feedback indicated the usefulness of the provided information. The average runtime estimation accuracy of 64.2%, with 28.9% job termination rate, was achieved in the experiments, which almost doubled the average accuracy in the Kraken dataset.

Zhang, Hao↗

Build Less Code, Deliver More Science: An Experience Report on Composing Scientific Environments using Component-based and Commodity Software Platforms

Modern scientific software is daunting in its diversity and complexity. From massively parallel simulations running on the world’s largest supercomputers, to visualizations and user support environments that manage ever growing complex data collections, the challenges for software engineers are plentiful. While high performance simulators are necessarily specialized codes to maximize performance on specific supercomputer architectures, we argue the vast majority of supporting infrastructure, data management and analysis tools can leverage commodity open source and component-based technologies. This approach can significantly drive down the effort and costs of building complex, collaborative scientific user environments, as well as increase their reliability and extensibility. In this paper we describe our experiences in creating an initial user environment for scientists involved in modeling the detailed effects of climate change on the environment of selected geographical regions. Our approach composes the user environment using the Velo scientific knowledge management platform and the MeDICi Integration Framework for scientific workflows. These established platforms leverage component-based technologies and extend commodity open source platforms with abstractions and capabilities that make them amenable for broad use in science. Using this approach we were able to deliver an operational user environment capable of running thousands of simulations in a 7 month period, and achieve significant software reuse.

Gorton, Ian↗

MASSIVE HYBRID PARALLELISM FOR FULLY IMPLICIT MULTIPHYSICS

As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided.

97 MATHEMATICS AND COMPUTING↗

SCORPIO: A Scalable Two-Phase Parallel I/O Library With Application To A Large Scale Subsurface Simulator

Inefficient parallel I/O is known to be a major bottleneck among scientific applications employed on supercomputers as the number of processor cores grows into the thousands. Our prior experience indicated that parallel I/O libraries such as HDF5 that rely on MPI-IO do not scale well beyond 10K processor cores, especially on parallel file systems (like Lustre) with single point of resource contention. Our previous optimization efforts for a massively parallel multi-phase and multi-component subsurface simulator (PFLOTRAN) led to a two-phase I/O approach at the application level where a set of designated processes participate in the I/O process by splitting the I/O operation into a communication phase and a disk I/O phase. The designated I/O processes are created by splitting the MPI global communicator into multiple sub-communicators. The root process in each sub-communicator is responsible for performing the I/O operations for the entire group and then distributing the data to rest of the group. This approach resulted in over 25X speedup in HDF I/O read performance and 3X speedup in write performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar supercomputer. This research describes the design and development of a general purpose parallel I/O library, SCORPIO (SCalable block-ORiented Parallel I/O) that incorporates our optimized two-phase I/O approach. The library provides a simplified higher level abstraction to the user, sitting atop existing parallel I/O libraries (such as HDF5) and implements optimized I/O access patterns that can scale on larger number of processors. Performance results with standard benchmark problems and PFLOTRAN indicate that our library is able to maintain the same speedups as before with the added flexibility of being applicable to a wider range of I/O intensive applications.

High Performance Computing↗