arXiv subjects

Dong Dai

Publications and source records attributed to Dong Dai.

30 records · Page 2Linked to original sources

arXiv2024

DGAP: Efficient Dynamic Graph Analysis on Persistent Memory

Dynamic graphs, featuring continuously updated vertices and edges, have grown in importance for numerous real-world applications. To accommodate this, graph frameworks, particularly their internal data structures, must support both persistent graph updates and rapid graph analysis simultaneously, leading to complex designs to orchestrate `fast but volatile' and `persistent but slow' storage devices. Emerging persistent memory technologies, such as Optane DCPMM, offer a promising alternative to simplify the designs by providing data persistence, low latency, and high IOPS together. In light of this, we propose DGAP, a framework for efficient dynamic graph analysis on persistent memory. Unlike traditional dynamic graph frameworks, which combine multiple graph data structures (e.g., edge list or adjacency list) to achieve the required performance, DGAP utilizes a single mutable Compressed Sparse Row (CSR) graph structure with new designs for persistent memory to construct the framework. Specifically, DGAP introduces a \textit{per-section edge log} to reduce write amplification on persistent memory; a \textit{per-thread undo log} to enable high-performance, crash-consistent rebalancing operations; and a data placement schema to minimize in-place updates on persistent memory. Our extensive evaluation results demonstrate that DGAP can achieve up to $3.2\times$ better graph update performance and up to $3.77\times$ better graph analysis performance compared to state-of-the-art dynamic graph frameworks for persistent memory, such as XPGraph, LLAMA, and GraphOne.

cs.DS↗

arXiv2023

PROV-IO+: A Cross-Platform Provenance Framework for Scientific Data on HPC Systems

Data provenance, or data lineage, describes the life cycle of data. In scientific workflows on HPC systems, scientists often seek diverse provenance (e.g., origins of data products, usage patterns of datasets). Unfortunately, existing provenance solutions cannot address the challenges due to their incompatible provenance models and/or system implementations. In this paper, we analyze four representative scientific workflows in collaboration with the domain scientists to identify concrete provenance needs. Based on the first-hand analysis, we propose a provenance framework called PROV-IO+, which includes an I/O-centric provenance model for describing scientific data and the associated I/O operations and environments precisely. Moreover, we build a prototype of PROV-IO+ to enable end-to-end provenance support on real HPC systems with little manual effort. The PROV-IO+ framework can support both containerized and non-containerized workflows on different HPC platforms with flexibility in selecting various classes of provenance. Our experiments with realistic workflows show that PROV-IO+ can address the provenance needs of the domain scientists effectively with reasonable performance (e.g., less than 3.5% tracking overhead for most experiments). Moreover, PROV-IO+ outperforms a state-of-the-art system (i.e., ProvLake) in our experiments.

cs.DC↗

arXiv2023

ClusterLog: Clustering Logs for Effective Log-based Anomaly Detection

With the increasing prevalence of scalable file systems in the context of High Performance Computing (HPC), the importance of accurate anomaly detection on runtime logs is increasing. But as it currently stands, many state-of-the-art methods for log-based anomaly detection, such as DeepLog, have encountered numerous challenges when applied to logs from many parallel file systems (PFSes), often due to their irregularity and ambiguity in time-based log sequences. To circumvent these problems, this study proposes ClusterLog, a log pre-processing method that clusters the temporal sequence of log keys based on their semantic similarity. By grouping semantically and sentimentally similar logs, this approach aims to represent log sequences with the smallest amount of unique log keys, intending to improve the ability of a downstream sequence-based model to effectively learn the log patterns. The preliminary results of ClusterLog indicate not only its effectiveness in reducing the granularity of log sequences without the loss of important sequence information but also its generalizability to different file systems' logs.

cs.DC↗

arXiv2023

IOPathTune: Adaptive Online Parameter Tuning for Parallel File System I/O Path

Parallel file systems contain complicated I/O paths from clients to storage servers. An efficient I/O path requires proper settings of multiple parameters, as the default settings often fail to deliver optimal performance, especially for diverse workloads in the HPC environment. Existing tuning strategies have shortcomings in being adaptive, timely, and flexible. We propose IOPathTune, which adaptively tunes PFS I/O Path online from the client side without characterizing the workloads, doing expensive profiling, and communicating with other machines. We implemented IOPathTune on Lustre and leveraged CloudLab to conduct the evaluations on 20 different Filebench workloads in three different scenarios. We observed either on-par or better performance than the default configuration, as high as 231% on standalone executions. IOPathTune also delivers 89.57% better overall performance than CAPES in multiple client executions.

cs.DC↗

arXiv2020

RLScheduler: An Automated HPC Batch Job Scheduler Using Reinforcement Learning

Today high-performance computing (HPC) platforms are still dominated by batch jobs. Accordingly, effective batch job scheduling is crucial to obtain high system efficiency. Existing HPC batch job schedulers typically leverage heuristic priority functions to prioritize and schedule jobs. But, once configured and deployed by the experts, such priority functions can hardly adapt to the changes of job loads, optimization goals, or system settings, potentially leading to degraded system efficiency when changes occur. To address this fundamental issue, we present RLScheduler, an automated HPC batch job scheduler built on reinforcement learning. RLScheduler relies on minimal manual interventions or expert knowledge, but can learn high-quality scheduling policies via its own continuous 'trial and error'. We introduce a new kernel-based neural network structure and trajectory filtering mechanism in RLScheduler to improve and stabilize the learning process. Through extensive evaluations, we confirm that RLScheduler can learn high-quality scheduling policies towards various workloads and various optimization goals with relatively low computation cost. Moreover, we show that the learned models perform stably even when applied to unseen workloads, making them practical for production use.

cs.DC↗

arXiv2018

Client-side Straggler-Aware I/O Scheduler for Object-based Parallel File Systems

Object-based parallel file systems have emerged as promising storage solutions for high-performance computing (HPC) systems. Despite the fact that object storage provides a flexible interface, scheduling highly concurrent I/O requests that access a large number of objects still remains as a challenging problem, especially in the case when stragglers (storage servers that are significantly slower than others) exist in the system. An efficient I/O scheduler needs to avoid possible stragglers to achieve low latency and high throughput. In this paper, we introduce a log-assisted straggler-aware I/O scheduling to mitigate the impact of storage server stragglers. The contribution of this study is threefold. First, we introduce a client-side, log-assisted, straggler-aware I/O scheduler architecture to tackle the storage straggler issue in HPC systems. Second, we present three scheduling algorithms that can make efficient decision for scheduling I/Os while avoiding stragglers based on such an architecture. Third, we evaluate the proposed I/O scheduler using simulations, and the simulation results have confirmed the promise of the newly introduced straggler-aware I/O scheduler.

cs.DC↗

arXiv2018

A Software-Defined Approach for QoS Control in High-Performance Computing Storage Systems

High-performance computing (HPC) storage systems become increasingly critical to scientific applications given the data-driven discovery paradigm shift. As a storage solution for large-scale HPC systems, dozens of applications share the same storage system, and will compete and can interfere with each other. Application interference can dramatically degrade the overall storage system performance. Therefore, developing a flexible and effective storage solution to assure a certain level of resources per application, i.e. the Quality-of-Service (QoS) support, is critical. One of the common solution to achieve QoS assurance for storage systems is using provisioning technique~\cite{3}. Provisioning refers to the ability of providing certain amount of resources for applications and expected workloads. However, provisioning has limitations such as requiring the detailed knowledge of the expected workloads. In addition, the storage workloads are transient hence expensive to be satisfied. Due to these limitations, providing QoS storage systems through provisioning is challenging. In this research, a software-defined approach~\cite{0} is proposed as a flexible solution to achieve QoS guarantee for storage systems. The driving force of using a software-defined approach instead of the traditional approaches, is that it has the ability to enable a more flexible, scalable, and efficient platform. For example, if any changes occurred in the system, it does not necessarily need to re-configure thousands of devices; instead, with re-configuring a logically centralized component, other devices will be automatically notified.

cs.DC↗

arXiv2018

A Cross-Layer Solution in Scientific Workflow System for Tackling Data Movement Challenge

Scientific applications in HPC environment are more com-plex and more data-intensive nowadays. Scientists usually rely on workflow system to manage the complexity: simply define multiple processing steps into a single script and let the work-flow systems compile it and schedule all tasks accordingly. Numerous workflow systems have been proposed and widely used, like Galaxy, Pegasus, Taverna, Kepler, Swift, AWE, etc., to name a few examples. Traditionally, scientific workflow systems work with parallel file systems, like Lustre, PVFS, Ceph, or other forms of remote shared storage systems. As such, the data (including the intermediate data generated during workflow execution) need to be transferred back and forth between compute nodes and storage systems, which introduces a significant performance bottleneck on I/O operations. Along with the enlarging perfor-mance gap between CPU and storage devices, this bottleneck is expected to be worse. Recently, we have introduced a new concept of Compute-on-Data-Path to allow tasks and data binding to be more efficient to reduce the data movement cost. To workflow systems, the key is to exploit the data locality in HPC storage hierarchy: if the datasets are stored in compute nodes, near the workflow tasks, then the task can directly access them with better performance with less network usage. Several recent studies have been done regarding building such a shared storage system, utilizing compute node resources, to serve HPC workflows with locality, such as Hercules [1] and WOSS [2] etc. In this research, we further argue that providing a compute-node side storage system is not sufficient to fully exploit data locality. A cross-layer solution combining storage system, compiler, and runtime is necessary. We take Swift/T [3], a workflow system for data-intensive applications, as a prototype platform to demonstrate such a cross-layer solution

cs.DC↗

arXiv2018

Bayesian Model Averaging with Exponentiated Least Square Loss

The model averaging problem is to average multiple models to achieve a prediction accuracy not much worse than that of the best single model in terms of mean squared error. It is known that if the models are misspecified, model averaging is superior to model selection. Specifically, let $n$ be the sample size, then the worst case regret of the former decays at a rate of $O(1/n)$ while the worst case regret of the latter decays at a rate of $O(1/\sqrt{n})$. The recently proposed $Q$-aggregation algorithm \citep{DaiRigZhang12} solves the model averaging problem with the optimal regret of $O(1/n)$ both in expectation and in deviation; however it suffers from two limitations: (1) for continuous dictionary, the proposed greedy algorithm for solving $Q$-aggregation is not applicable; (2) the formulation of $Q$-aggregation appears ad hoc without clear intuition. This paper examines a different approach to model averaging by considering a Bayes estimator for deviation optimal model averaging by using exponentiated least squares loss. We establish a primal-dual relationship of this estimator and that of $Q$-aggregation and propose new greedy procedures that satisfactorily resolve the above mentioned limitations of $Q$-aggregation.

math.ST↗

arXiv2017

Rare Disease Physician Targeting: A Factor Graph Approach

In rare disease physician targeting, a major challenge is how to identify physicians who are treating diagnosed or underdiagnosed rare diseases patients. Rare diseases have extremely low incidence rate. For a specified rare disease, only a small number of patients are affected and a fractional of physicians are involved. The existing targeting methodologies, such as segmentation and profiling, are developed under mass market assumption. They are not suitable for rare disease market where the target classes are extremely imbalanced. The authors propose a graphical model approach to predict targets by jointly modeling physician and patient features from different data spaces and utilizing the extra relational information. Through an empirical example with medical claim and prescription data, the proposed approach demonstrates better accuracy in finding target physicians. The graph representation also provides visual interpretability of relationship among physicians and patients. The model can be extended to incorporate more complex dependency structures. This article contributes to the literature of exploring the benefit of utilizing relational dependencies among entities in healthcare industry.

stat.ML↗

arXiv2013

Aggregation of Affine Estimators

We consider the problem of aggregating a general collection of affine estimators for fixed design regression. Relevant examples include some commonly used statistical estimators such as least squares, ridge and robust least squares estimators. Dalalyan and Salmon (2012) have established that, for this problem, exponentially weighted (EW) model selection aggregation leads to sharp oracle inequalities in expectation, but similar bounds in deviation were not previously known. While results indicate that the same aggregation scheme may not satisfy sharp oracle inequalities with high probability, we prove that a weaker notion of oracle inequality for EW that holds with high probability. Moreover, using a generalization of the newly introduced $Q$-aggregation scheme we also prove sharp oracle inequalities that hold with high probability. Finally, we apply our results to universal aggregation and show that our proposed estimator leads simultaneously to all the best known bounds for aggregation, including $\ell_q$-aggregation, $q \in (0,1)$, with high probability.

math.ST↗

arXiv2012

Deviation optimal learning using greedy Q-aggregation

Given a finite family of functions, the goal of model selection aggregation is to construct a procedure that mimics the function from this family that is the closest to an unknown regression function. More precisely, we consider a general regression model with fixed design and measure the distance between functions by the mean squared error at the design points. While procedures based on exponential weights are known to solve the problem of model selection aggregation in expectation, they are, surprisingly, sub-optimal in deviation. We propose a new formulation called Q-aggregation that addresses this limitation; namely, its solution leads to sharp oracle inequalities that are optimal in a minimax sense. Moreover, based on the new formulation, we design greedy Q-aggregation procedures that produce sparse aggregation models achieving the optimal rate. The convergence and performance of these greedy procedures are illustrated and compared with other standard methods on simulated examples.

math.ST↗