Scientific workflows in High Performance Computing ( HPC ) environments are processing large amounts of data. The storage hierarchy on HPC systems is getting deeper, driven by new technologies (NVRAMs, SSDs, etc.) There is a need for new programming abstractions that allow users to seamlessly manage data at the workflow level on multi-tiered storage systems, and provide optimal workflow performance and use of storage resources. In previous work, we introduced a software architecture Managing Data on Tiered Storage for Scientific Workflows (MaDaTS ) that used a Virtual Data Space ( VDS ) abstraction to hide the complexities of the underlying storage system while allowing users to control data management strategies. In this article, we detail the data-centric programming abstractions that allow users to manage a workflow around its data on the storage layer. The programming abstractions simplify data management for scientific workflows on multi-tiered storage systems, without affecting workflow performance or storage capacity. We measure the overheads and effectiveness introduced by the programming abstractions of MaDaTS. Our results show that these abstractions can optimally use the storage capacity in lesser capacity storage tiers, and simplify data management without adding any performance overheads.

In High Performance Computing (HPC), resources are controlled by batch systems and may not be available due to long queue waiting times, negatively impacting application deadlines. This is noticeable in low latency scientific workflows where resource planning and timely allocation are key for efficient processing. On the one hand, peak allocations guarantee the fastest possible workflows execution time, at the cost of extended queue waiting times and costly resource usage. On the other hand, dynamic allocations following specific workflow stage requirements optimizes resource usage, though it increases the total workflow makespan. To enable new scheduling strategies and features in workflows, we propose ASA: the Adaptive Scheduling Architecture, a novel scheduling method to reduce perceived queue waiting times as well as to optimize workflows resource usage. Reinforcement learning is used to estimate queue waiting times, and based on these estimates ASA pro-actively submit resource change requests, minimizing total workflow inter-stage waiting times, idle resources, and makespan. Experiments with three scientific workflows at two HPC centers show that ASA combines the best of the two aforementioned approaches, with average queue waiting time and makespan reductions of up to 10% and 2% respectively, with up to 100% prediction accuracy, while obtaining near optimal resource utilization.

Scientific workflows are increasingly transferring large amounts of data between high performance computing (HPC) systems. Even though these HPC systems are connected via high-speed dedicated networks and use dedicated data transfer nodes (DTNs), it is still difficult to predict the data transfer throughput because of variations in data transfer protocols, host configurations, performance of file systems, and overlapping workloads. In order to provide reliable performance prediction for better resource management and job scheduling, we need models for predicting data transfer throughput under real-world conditions. In this paper, we explore different machine learning approaches for building data-driven models to improve performance and prediction of large-scale data transfer throughput. In addition to the variables already collected by the network monitoring system, we also develop heuristics to derive additional metrics for improving the prediction accuracy. We use the prediction results to identify the importance of different network parameters in predicting the throughput for large-scale data transfers. Through extensive tests, we identify key network parameters, discover interesting variations among different HPC sites, and show that we can predict throughput with high accuracy. We also analyze our models and results to provide recommendations for improving the performance of big data transfers.

Today, scientific experiments and simulations produce massive amounts of heterogeneous data that need to be stored and analyzed. Given that these large datasets are stored in many files, formats and locations, how can scientists find relevant data, duplicates or similarities? In this context, we concentrate on developing algorithms to compare similarity of time series for the purpose of search, classification and clustering. For example, generating accurate patterns from climate related time series is important not only for building models for weather forecasting and climate prediction, but also for modeling and predicting the cycle of carbon, water, and energy. We developed the methodology and ran an exploratory analysis of climatic and ecosystem variables from the FLUXNET2015 dataset. The proposed combination of similarity metrics, nonlinear dimension reduction, clustering methods and validity measures for time series data has never been applied to unlabeled datasets before, and provides a process that can be easily extended to other scientific time series data. The dimensionality reduction step provides a good way to identify the optimum number of clusters, detect outliers and assign initial labels to the time series data. We evaluated multiple similarity metrics, in terms of the internal cluster validity for driver as well as response variables. While the best metric often depends on a number of factor, the Euclidean distance seems to perform well for most variables and also in terms of computational expense.

We present the design and implementation of Data Jockey, a data management system for HPC multi-tiered storage systems. As a centralized data management control plane, Data Jockey automates bulk data movement and placement for scientific workflows and integrates into existing HPC storage infrastructures. Data Jockey simplifies data management by eliminating human effort in programming complex data movements, laying datasets across multiple storage tiers when supporting complex workflows, which in turn increases the usability of multitiered storage systems emerging in modern HPC data centers. Specifically, Data Jockey presents a new data management scheme called “goal driven data management” that can automatically infer low-level bulk data movement plans from declarative high-level goal statements that come from the lifetime of iterative runs of scientific workflows. While doing so, Data Jockey aims to minimize data wait times by taking responsibility for datasets that are unused or to be used, and aggressively utilizing the capacity of the upper, higher performant storage tiers. We evaluated a prototype implementation of Data Jockey under a synthetic workload based on a year's worth of Oak Ridge Leadership Computing Facility's (OLCF) operational logs. Our evaluations suggest that Data Jockey leads to higher utilization of the upper storage tiers while minimizing the programming effort of data movement compared to human involved, per-domain adhoc data management scripts.

Qualitative user research is a human-intensive approach that draws upon ethnographic methods from social sciences to develop insights about work practices to inform software design and development. Recent advances in data science, and in particular, natural language processing (NLP), enables the derivation of machine-generated insights to augment existing techniques. Our work describes our prototype framework based in Jupyter, a software tool that supports interactive data science and scientific computing, that leverages NLP techniques to make sense of transcribed texts from user interviews. This work also serves as a starting point for incorporating data science techniques in the qualitative analyses process.

Scientific workflows are increasingly used in High Performance Computing (HPC) environments to manage complex simulation and analyses, often consuming and generating large amounts of data. However, workflow tools have limited support for managing the input, output and intermediate data. The data elements of a workflow are often managed by the user through scripts or other ad-hoc mechanisms. Technology advances for future HPC systems is redefining the memory and storage subsystem by introducing additional tiers to improve the I/O performance of data-intensive applications. These architectural changes introduce additional complexities to managing data for scientific workflows. Thus, we need to manage the scientific workflow data across the tiered storage system on HPC machines. In this paper, we present the design and implementation of MaDaTS (Managing Data on Tiered Storage for Scientific Workflows), a software architecture that manages data for scientific workflows. We introduce Virtual Data Space (VDS), an abstraction of the data in a workflow that hides the complexities of the underlying storage system while allowing users to control data management strategies. We evaluate the data management strategies with real scientific and synthetic workflows, and demonstrate the capabilities of MaDaTS. Our experiments demonstrate the flexibility, performance and scalability gains of MaDaTS as compared to the traditional approach of managing data in scientific workflows.

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterative workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechansims) that affect the performance of scientific workflows on HPC systems.

Data provenance is the lineage of a digital artifact or object. Its capture in workflow-controlled distributed applications is well studied but less is known about quality of provenance captured solely through existing control infrastructures (i.e., middleware frameworks used for high throughput computing). We study completeness of provenance in case where information is only available from the middleware layer. We use WorkQueue to validate our model. Our evaluation shows that provenance captured from a middleware framework is sufficient to represent the existence of output data and trace certain failures independent of the application semantics. We show the method's limitations as well.

Clouds are increasingly being used for running data-intensive scientific applications. Data-intensive science applications need performance, scalability and reliability. However, these can be hard to achieve in cloud environments. Intelligent strategies are required to obtain better performance, scalability and reliability on cloud platforms. In this paper, we propose a set of pipelining strategies to effectively utilize provisioned cloud resources. Our experiments on the ExoGENI cloud testbed demonstrates the effectiveness of our approach in increasing performance and reducing failures.

Visualization facilitates the understanding of scientific data both through exploration and explanation of the visualized data. Provenance also contributes to the understanding of data by containing the contributing factors behind a result. The visualization of provenance, although supported in existing workflow management systems, generally focuses on small (medium) sized provenance data, lacking techniques to deal with big data with high complexity. This paper discusses visualization techniques developed for exploration and explanation of provenance, including layout algorithm, visual style, graph abstraction techniques, and graph matching algorithm, to deal with the high complexity. We demonstrate through application to two extensively analyzed case studies that involved provenance capture and use over three year projects, the first involving provenance of a satellite imagery ingest processing pipeline and the other of provenance in a large-scale computer network testbed.