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Ross, Robert

Publications and source records attributed to Ross, Robert.

At least 37 records · Page 2

Modeling I/O Performance Variability Using Conditional Variational Auto Encoders

Storage system performance modeling is crucial for efficient use of heterogeneous shared resources on leadership class computers. Variability in application performance, particularly variability arising from concurrent applications sharing I/O resources, is a major hurdle in the development of accurate performance models. We adopt a deep learning approach based on conditional variational auto encoders (CVAE) for I/O performance modeling, and use it to quantify performance variability. We illustrate our approach using the data collected on Edison, a production supercomputing system at the National Energy Research Scientific Computing Center (NERSC). The CVAE approach is investigated by comparing it to a previously proposed sensitivity-based Gaussian process (GP) model. We find that the CVAE model performs slightly better than the GP model in cases where training and testing data come from different applications, since CVAE can inherently leverage the whole data from multiple applications whereas GP partitions the data and builds separate models for each partition. Hence, the CVAE offers an alternative modeling approach that does not need preprocessing; it has enough flexibility to handle data from a wide variety of applications without changing the inference approach.

I/O perfornance variability↗

Scidac-Data: Enabling Data Driven Modeling of Exascale Computing

Here, the SciDAC-Data project is a DOE-funded initiative to analyze and exploit two decades of information and analytics that have been collected by the Fermilab data center on the organization, movement, and consumption of high energy physics (HEP) data. The project analyzes the analysis patterns and data organization that have been used by NOvA, MicroBooNE, MINERvA, CDF, D0, and other experiments to develop realistic models of HEP analysis workflows and data processing. The SciDAC-Data project aims to provide both realistic input vectors and corresponding output data that can be used to optimize and validate simulations of HEP analysis. These simulations are designed to address questions of data handling, cache optimization, and workflow structures that are the prerequisites for modern HEP analysis chains to be mapped and optimized to run on the next generation of leadership-class exascale computing facilities. We present the use of a subset of the SciDAC-Data distributions, acquired from analysis of approximately 71,000 HEP workflows run on the Fermilab data center and corresponding to over 9 million individual analysis jobs, as the input to detailed queuing simulations that model the expected data consumption and caching behaviors of the work running in high performance computing (HPC) and high throughput computing (HTC) environments. In particular we describe how the Sequential Access via Metadata (SAM) data-handling system in combination with the dCache/Enstore-based data archive facilities has been used to develop radically different models for analyzing the HEP data. We also show how the simulations may be used to assess the impact of design choices in archive facilities.

97 MATHEMATICS AND COMPUTING↗

Lightweight Provenance Service for High-Performance Computing

Provenance describes detailed information about the history of a piece of data, containing the relationships among elements such as users, processes, jobs, and workflows that contribute to the existence of data. Provenance is key to supporting many data management functionalities that are increasingly important in operations such as identifying data sources, parameters, or assumptions behind a given result; auditing data usage; or understanding details about how inputs are transformed into outputs. Despite its importance, however, provenance support is largely underdeveloped in highly parallel architectures and systems. One major challenge is the demanding requirements of providing provenance service in situ. The need to remain lightweight and to be always on often conflicts with the need to be transparent and offer an accurate catalog of details regarding the applications and systems. To tackle this challenge, we introduce a lightweight provenance service, called LPS, for high-performance computing (HPC) systems. LPS leverages a kernel instrument mechanism to achieve transparency and introduces representative execution and flexible granularity to capture comprehensive provenance with controllable overhead. Extensive evaluations and use cases have confirmed its efficiency and usability. We believe that LPS can be integrated into current and future HPC systems to support a variety of data management needs.

Dai, Dong↗

Modular HPC I/O characterization with Darshan

Contemporary high-performance computing (HPC) applications encompass a broad range of distinct I/O strategies and are often executed on a number of different compute platforms in their lifetime. These large-scale HPC platforms employ increasingly complex I/O subsystems to provide a suitable level of I/O performance to applications. Tuning I/O workloads for such a system is nontrivial, and the results generally are not portable to other HPC systems. I/O profiling tools can help to address this challenge, but most existing tools only instrument specific components within the I/O subsystem that provide a limited perspective on I/O performance. The increasing diversity of scientific applications and computing platforms calls for greater flexibililty and scope in I/O characterization.

Snyder, Shane↗

Visual Data-Analytics of Large-Scale Parallel Discrete-Event Simulations

Parallel discrete-event simulation (PDES) is an important tool in the codesign of extreme-scale systems because PDES provides a cost-effective way to evaluate designs of highperformance computing systems. Optimistic synchronization algorithms for PDES, such as Time Warp, allow events to be processed without global synchronization among the processing elements. A rollback mechanism is provided when events are processed out of timestamp order. Although optimistic synchronization protocols enable the scalability of large-scale PDES, the performance of the simulations must be tuned to reduce the number of rollbacks and provide an improved simulation runtime. To enable efficient large-scale optimistic simulations, one has to gain insight into the factors that affect the rollback behavior and simulation performance. We developed a tool for ROSS model developers that gives them detailed metrics on the performance of their large-scale optimistic simulations at varying levels of simulation granularity. Model developers can use this information for parameter tuning of optimistic simulations in order to achieve better runtime and fewer rollbacks. In this work, we instrument the ROSS optimistic PDES framework to gather detailed statistics about the simulation engine. We have also developed an interactive visualization interface that uses the data collected by the ROSS instrumentation to understand the underlying behavior of the simulation engine. The interface connects real time to virtual time in the simulation and provides the ability to view simulation data at different granularities. We demonstrate the usefulness of our framework by performing a visual analysis of the dragonfly network topology model provided by the CODES simulation framework built on top of ROSS. The instrumentation needs to minimize overhead in order to accurately collect data about the simulation performance. To ensure that the instrumentation does not introduce unnecessary overhead, we perform a scaling study that compares instrumented ROSS simulations with their noninstrumented counterparts in order to determine the amount of perturbation when running at different simulation scales.

Ross, Caitlin↗

Modeling a Million-Node Slim Fly Network Using Parallel Discrete-Event Simulation

As supercomputers close in on exascale performance, the increased number of processors and processing power translates to an increased demand on the underlying network interconnect. The Slim Fly network topology, a new lowdiameter and low-latency interconnection network, is gaining interest as one possible solution for next-generation supercomputing interconnect systems. In this paper, we present a high-fidelity Slim Fly it-level model leveraging the Rensselaer Optimistic Simulation System (ROSS) and Co-Design of Exascale Storage (CODES) frameworks. We validate our Slim Fly model with the Kathareios et al. Slim Fly model results provided at moderately sized network scales. We further scale the model size up to n unprecedented 1 million compute nodes; and through visualization of network simulation metrics such as link bandwidth, packet latency, and port occupancy, we get an insight into the network behavior at the million-node scale. We also show linear strong scaling of the Slim Fly model on an Intel cluster achieving a peak event rate of 36 million events per second using 128 MPI tasks to process 7 billion events. Detailed analysis of the underlying discrete-event simulation performance shows that a million-node Slim Fly model simulation can execute in 198 seconds on the Intel cluster.

interconnection networks↗

Impact of Data Placement on Resilience in Large-Scale Object Storage Systems

Distributed object storage architectures have become the de facto standard for high-performance storage in big data, cloud, and HPC computing. Object storage deployments using commodity hardware to reduce costs often employ object replication as a method to achieve data resilience. Repairing object replicas after failure is a daunting task for systems with thousands of servers and billions of objects, however, and it is increasingly difficult to evaluate such scenarios at scale on realworld systems. Resilience and availability are both compromised if objects are not repaired in a timely manner. In this work we leverage a high-fidelity discrete-event simulation model to investigate replica reconstruction on large-scale object storage systems with thousands of servers, billions of objects, and petabytes of data. We evaluate the behavior of CRUSH, a well-known object placement algorithm, and identify configuration scenarios in which aggregate rebuild performance is constrained by object placement policies. After determining the root cause of this bottleneck, we then propose enhancements to CRUSH and the usage policies atop it to enable scalable replica reconstruction. We use these methods to demonstrate a simulated aggregate rebuild rate of 410 GiB/s (within 5% of projected ideal linear scaling) on a 1,024-node commodity storage system. We also uncover an unexpected phenomenon in rebuild performance based on the characteristics of the data stored on the system.

Carns, Philip↗

Performance Evaluation of Darshan 3.0.0 on the Cray XC30

Abstract—Darshan is a lightweight I/O characterization tool used to gather and summarize salient I/O workload statistics from HPC applications. Darshan was designed to minimize any possible perturbations of an application’s performance, leading it to be enabled by default on a number of production HPC systems. For each file accessed by a given application, Darshan records the count and types of I/O operations performed, histograms of access sizes, cumulative timers on the amount of time spent doing I/O, and other statistical data. This type of data has proved invaluable in understanding and improving the I/O performance of HPC applications. Darshan 3.0.0 is the new modularized version of the traditional Darshan library and file format, allowing users to easily add more in-depth I/O characterization data to Darshan logs. In this work we perform an empirical evaluation of Darshan 3.0.0 to ensure that it continues to meet performance expectations for broad deployment. In particular, we evaluate the imposed overhead on instrumented I/O operations, time taken to shut down and generate corresponding Darshan log files, and resultant log file sizes for different workloads. These performance results are compared to results of Darshan 2.3.0 on the Edison XC30 system at NERSC to determine whether the new version is lightweight enough to run full-time on production HPC systems. Our evaluation shows that Darshan has limited impact on application I/O performance and can fully generate a corresponding log file for most application workloads in under two seconds.

97 MATHEMATICS AND COMPUTING↗

GraphMeta: Managing HPC Rich Metadata in Graphs

High-performance computing (HPC) systems face increasingly critical metadata management challenges, especially in the approaching exascale era. These challenges arise not only from exploding metadata volumes, but also from increasingly diverse metadata, which contains data provenance and arbitrary user-defined attributes in addition to traditional POSIX metadata. This ‘rich’ metadata is becoming critical to supporting advanced data management functionality such as data auditing and validation. In our prior work, we identified a graph-based model as a promising solution to uniformly manage HPC rich metadata due to its flexibility and generality. However, at the same time, graph-based HPC rich metadata anagement also introduces significant challenges to the underlying infrastructure. In this study, we first identify the challenges on the underlying infrastructure to support scalable, high-performance rich metadata management. Based on that, we introduce GraphMeta, a graphbased engine designed for this use case. It achieves performance scalability by introducing a new graph partitioning algorithm and a write-optimal storage engine. We evaluate GraphMeta under both synthetic and real HPC metadata workloads, compare it with other approaches, and demonstrate its advantages in terms of efficiency and usability for rich metadata management in HPC systems.

Dai, Dong↗

Storage Systems and Input/Output to Support Extreme Scale Science

Storage systems are a foundational component of computational, experimental, and observational science today. The success of Department of Energy (DOE) activities in these areas is inextricably tied to the usability, performance, and reliability of storage and input/output (I/O) technologies.

97 MATHEMATICS AND COMPUTING↗

Storage Systems and Input/Output to Support Extreme Scale Science.

Storage systems are a foundational component of computational, experimental, and observational science today. The success of Department of Energy (DOE) activities in these areas is inextricably tied to the usability, performance, and reliability of storage and input/output (I/O) technologies.

97 MATHEMATICS AND COMPUTING↗

YARNsim: Simulating Hadoop YARN

Despite the popularity of the Apache Hadoop system, its success has been limited by issues such as single points of failure, centralized job/task management, and lack of support for programming models other than MapReduce. The next generation of Hadoop, Apache Hadoop YARN, is designed to address these issues. In this paper, we propose YARNsim, a simulation system for Hadoop YARN. YARNsim is based on parallel discrete event simulation and provides protocol-level accuracy in simulating key components of YARN. YARNsim provides a virtual platform on which system architects can evaluate the design and implementation of Hadoop YARN systems. Also, application developers can tune job performance and understand the tradeoffs between different configurations, and Hadoop YARN system vendors can evaluate system efficiency under limited budgets. To demonstrate the validity of YARNsim, we use it to model two real systems and compare the experimental results from YARNsim and the real systems. The experiments include standard Hadoop benchmarks, synthetic workloads, and a bioinformatics application. The results show that the error rate is within 10% for the majority of test cases. The experiments prove that YARNsim can provide what-if analysis for system designers in a timely manner and at minimal cost compared with testing and evaluating on a real system.

Hadoop↗

RADAR: Runtime Asymmetric Data-access Driven Scientific Data Replication

Efficient I/O on large-scale spatiotemporal scientific data requires scrutiny of both the logical layout of the data (e.g., row-major vs. column-major) and the physical layout (e.g., distribution on parallel filesystems). For increasingly complex datasets, hand optimization is a difficult matter prone to error and not scalable to the increasing heterogeneity of analysis workloads. Given these factors, we present a partial data replication system called RADAR. We capture datatype- and collective-aware I/O access patterns (indicating logical access) via MPI-IO tracing and use a combination of coarse-grained and fine-grained performance modeling to evaluate and select optimized physical data distributions for the task at hand. Unlike conventional methods, we store all replica data and metadata, along with the original untouched data, under a single file container using the object abstraction in parallel filesystems. Our system results in manyfold improvements in some commonly used subvolume decomposition access patterns.Moreover, the modeling approach can determine whether such optimizations should be undertaken in the first place.

access pattern↗