Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Workflow management”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Accelerating Scientific Workflows on HPC Platforms with In Situ Processing

Scientific workflows drive most modern large-scale science breakthroughs by allowing scientists to define their computations as a set of jobs executed in a given order based on their data dependencies. Workflow management systems (WMSs) have become key to automating scientific workflows-executing computational jobs and orchestrating data transfers between those jobs running on complex high-performance computing (HPC) platforms. Traditionally, WMSs use files to communicate between jobs: a job writes out files that are read by other jobs. However, HPC machines face a growing gap between their storage and compute capabilities. To address that concern, the scientific community has adopted a new approach called in situ, which bypasses costly parallel filesystem I/O operations with faster in-memory or in-network communications. When using in situ approaches, communication and computations can be interleaved. In this work, we leverage the Decaf in situ dataflow framework to accelerate task-based scientific workflows managed by the Pegasus WMS, by replacing file communications with faster MPI messaging. We propose a new execution engine that uses Decaf to manage communications within a sub-workflow (i.e., set of jobs) to optimize inter-job communications. We consider two workflows in this study: (i) a synthetic workflow that benchmarks and compares file- and MPI-based communication; and (ii) a realistic bioinformatics workflow that computes mu-tational overlaps in the human genome. Experiments show that in situ communication can improve the bioinformatics workflow execution time by 22% to 30% compared with file communication. Our results motivate further opportunities and challenges for bridging traditional WMSs with in situ frameworks.

Decaf↗
DOE OSTI2024

Enabling Low-Overhead HT-HPC Workflows at Extreme Scale using GNU Parallel

GNU Parallel is a versatile and powerful tool for process parallelization widely used in scientific computing. This paper demonstrates its effective application in high-performance computing (HPC) environments, particularly focusing on its scalability and efficiency in executing large-scale high-throughput high-performance computing (HT-HPC) workflows. Through real-world examples, we highlight GNU Parallel’s performance across various HPC workloads, including GPU computing, container-based workloads, and node-local NVMe storage. Our results on two leading supercomputers, OLCF’s Frontier and NERSC’s Perlmutter, showcase GNU Parallel’s rapid process dispatching ability and its capacity to maintain low overhead even at extreme scales. We explore GNU Parallel’s application in massive parallel file transfers using a scheduled Data Transfer Node (DTN) cluster, emphasizing its broad utility in diverse scientific workflows. Beyond its direct application as a viable workflow manager, GNU Parallel can be employed in conjunction with other workflow systems as a "last-mile" parallelizing driver and as a quick prototyping tool to design and extract parallel profiles from application executions. We then argue that the potential for GNU Parallel to transform workflow management at extreme scales is substantial, paving the way for more efficient and effective scientific discoveries.

Maheshwari, Ketan↗
DOE OSTI2022

A New Integrated Analysis Suite for Fast-Ion Study in KSTAR

Here, an integrated workflow for fast-ion analysis was developed by adapting the One Modeling Framework for Integrated Task (OMFIT) workflow manager to support a standard and unified analysis platform for KSTAR users. The newly established analysis suite offers a graphical user interface–based workflow to enable users to readily access and handle experimental data archived in various data formats and servers. Further, users can analyze the data by importing modules designed for conducting certain tasks, such as profile fitting, equilibrium reconstruction, and postprocessing of tokamak data. The procedures for preparing the inputs for fast-ion simulations are streamlined by a common workflow manager, which enables the parallel processing of various tasks to efficiently analyze large fast-ion datasets. The OMFIT platform comprises a flexible Python-based application that enables users to freely manipulate the Python scripts for applications that are unavailable in the standard workflow. The framework also offers mapping tools to translate the output data into the Integrated Modeling and Analysis Suite format to maintain application compatibility for future ITER burning plasma experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Performance Characterization and Provenance of Distributed Task-based Workflows on HPC Platforms

Understanding performance and provenance of task-based workflows poses significant challenges, particularly in distributed configurations where resources are shared by multiple applications. Task-based workflow management systems further complicate performance predictability because of their dynamicity that subtly alters task execution order from run to run. In this paper we propose a layered characterization framework for performance and task provenance for Dask.distributed workflows running on high-performance computing (HPC) platforms. It collects data from jobs, the workflow management system, and the operating system to aid in understanding the performance of these workflows. Our approach encompasses three main contributions: first, an extension of Dask.distributed to capture high-fidelity task provenance using Mochi data services; second, the adaptation of the established HPC I/O characterization tool Darshan to gather high-fidelity I/O data, thereby enhancing the granularity of our analysis; and third, a framework to combine and process the collected data and provide helpful insights into performance characterization and reproducibility, alongside our lessons learned.

Dask↗
NASA NTRS2018

Integration of Information Management System, Workflow and Computational Tools Enabling Multiscale Modeling Within an ICME Paradigm

With the increased emphasis on reducing the cost and time to market of new materials, the need for analytical tools that enable the virtual design and optimization of materials throughout their processing - internal structure - property - performance envelope, along with the capturing and storing of the associated material and model information across its lifecycle, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Fortunately, material information management systems and physics-based multiscale modeling methods have kept pace with the growing user demands. Herein, recent efforts to develop a set of Python functions that exchange information between NASA GRC's Integrated multiscale Micromechanics Analysis Code (ImMAC) software toolset and its Integrated Computational Materials Engineering (ICME), Granta MI® database schema is presented. The goal is to enable seamless coupling between both test data and simulation data, which is captured and tracked automatically within Granta MI®, with full model pedigree information. These tools, and this type of linkage, are foundational to realizing the full potential of ICME, in which materials processing, microstructure, properties, and performance are coupled to enable application-driven design and optimization of materials and structures.

multiscale modeling; Micromechanics; Computational↗
DOE OSTI2022

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗
DOE OSTI2019

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗
DOE OSTI2024

Enabling HPC Scientific Workflows for Serverless

The convergence of edge computing, big data analytics, and AI with traditional scientific calculations is increasingly being adopted in HPC workflows. Workflow management systems are crucial for managing and orchestrating these complex computational tasks. However, it is difficult to identify patterns within the growing population of HPC workflows. Serverless has emerged as a novel computing paradigm, offering dynamic resource allocation, quick response time, fine-grained resource management and auto-scaling. In this paper, we propose a framework to enable HPC scientific workflows on serverless. Our approach integrates a widely used traditional HPC workflow generator with an HPC serverless workflow management system to create benchmark suites of scientific workflows with diverse characteristics. These workflows can be executed on different serverless platforms. We comprehensively compare executing workflows on traditional local containers and serverless computing platforms. Our results show that serverless can reduce CPU and memory usage respectively by 78.11% and 73.92% without compromising performance.

Andrei da silva, Anderson↗
NASA NTRSDate not supplied

Data Integrity Challenges in NASA Giovanni

The Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) is an online tool developed by the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), one of 12 NASA Science Mission Directorate Data Centers (DAACs) to analyze and visualize NASA remote sensing and model data without downloading data and software. As of this writing, over 2000 Earth satellite and model variables are available in Giovanni, including several well-known NASA satellite missions (e.g., TRMM, GPM) and projects (e.g., MERRA-2, GPCP). There are twenty-two plots provided by Giovanni that can be used to analyze, compare, and explore Earth data across disciplines. Results can be shared with colleagues and downloaded for further analysis. Giovanni has helped publish over 3000 referral papers over the years. As open science policies roll in, data integrity has become a major challenge for Giovanni and other tools. For integrity, both data and workflows must be transparent. FAIR-compliant data, including input, intermediate, and result products, as well as their associated statistics, metadata, and information, are needed. The NASA Data Product Development Guide for Data Producers provides a key resource on how to develop FAIR-compliant data products. Data quality information is also needed from data producers and analysis services like Giovanni. The workflow part is quite challenging and requires workflow management improvements, such as recording workflows and making them available to users. In this presentation, we will discuss the data integrity challenges in Giovanni.

data analysis, visualization↗
DOE OSTI2019

Producing Madgraph5_aMC@NLO gridpacks and using TensorFlow GPU resources in the CMS HTCondor Global Pool

The CMS experiment has an HTCondor Global Pool, composed of more than 200K CPU cores available for Monte Carlo production and the analysis of da.The submission of user jobs to this pool is handled by either CRAB, the standard workflow management tool used by CMS users to submit analysis jobs requiring event processing of large amounts of data, or by CMS Connect, a service focused on final stage condor-like analysis jobs and applications that already have a workflow job manager in place. The latest scenario canbring cases in which workflows need further adjustments in order to efficiently work in a globally distributed pool of resources. For instance, the generation of matrix elements for high energy physics processes via Madgraph5_aMC@NLO and the usage of tools not (yet) fully supported by the CMS software, such as Ten-sorFlow with GPUsupport, are tasks with particular requirements. A special adaption, either at the pool factory level (advertising GPU resources) or at the execute level (e.g: to handle special parameters that describe certain needs for the remote execute nodes during submission) is needed in order to adequately work in the CMS global pool. This contribution describes the challenges and efforts performed towards adaptingsuch workflows so they can properly profit from the Global Pool via CMS Connect.

Bockelman, Brian Paul↗
DOE OSTI2025

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative’s FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

AiiDA-INQ plugin

The AiiDA-INQ plugin will allow the INQ code developed at the lab to utilize the AiiDA workflow manager which enables high-throughput workflows. This includes provenance tracking, restart capabilities, job calculators, and other capabilities

Keilbart, NathanD↗
DOE OSTI2025

Enabling Command-and-Control in Advanced In Situ Workflows

Scientific discovery is progressing towards autonomous science with the combination of scientific instruments, high-performance computing, and artificial intelligence in complex workflows. This evolution introduces new requirements for managing scientific workflows, including feedback loops, near real-time constraints, and the ability to dynamically control workflow execution. In situ workflows that analyze and visualize data as it is generated are well-suited to satisfy stringent time constraints and their iterative nature offers greater opportunities for command-and-control. However, only a few of the many workflow management systems available have been specifically designed to manage in situ workflows and often lack support for automated feedback loops that allow analysis and visualization components to interact with the main scientific data producer. To address this need, we present in this paper how to add command-and-control capabilities to a workflow management system. We identify the functional design requirements of such a command-and-control system, detail its architecture, interface, and core mechanisms, and illustrate how advanced in situ workflows can leverage command-and-control in three use cases: graceful termination with checkpoint, dynamic and adaptive data reduction, and event-triggered analysis.

Mehta, Kshitij [ORNL] (ORCID:0000000297149981)↗
DOE OSTI2022

A low-cost centralized HVAC control system solution for energy savings, load shedding, and improved maintenance

University campuses rely on centralized controls for managing and optimizing complex HVAC systems in larger buildings. However, most campuses also have many smaller buildings with packaged HVAC systems controlled by a stand-alone thermostat. Even when these distributed and often overlooked systems have modern programmable thermostats, they cannot be centrally monitored or controlled, and they are typically not programmed adequately. This paper describes the implementation of a low-cost centralized control solution for these systems serving smaller campus buildings, mostly under 5,000 sf and representative of light commercial spaces. Thanks to advances in technology spurred by residential and commercial IoT developments, simple networked thermostat solutions exist that can easily replace original thermostats, and, connect these systems to a web-based portal for monitoring and control. We show that, with small customizations, these platforms can be integrated into facility management workflows. Beyond the energy savings potential from improved scheduling and closer management of these systems, there are significant advantages for maintenance crews since these systems can now be monitored on smart phones or tablets. A grid-responsive load-shedding program has also been implemented for additional cost savings. The networked thermostats can also be connected to additional systems such as economizer controls for improved ventilation management and energy savings. With data from these systems integrated centrally, it can also be used for improved analytics and fault detection. A toolkit has been developed to share the program with other campuses, whether for energy savings, improved management of ventilation, or a more proactive maintenance approach.

Fauchier-Magnan, Nicolas↗
DOE OSTI2024

Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows

The 2024 Workflows Community Summit report presents the outcomes of a three-day international gathering that brought together 109 experts from 18 countries to discuss future trends and challenges in scientific workflows. The summit focused on six key areas: time-sensitive workflows, convergence of AI and HPC workflows, multi-facility workflows, heterogeneous HPC environments, user experience and interfaces, and FAIR computational workflows. Discussions highlighted emerging challenges such as integrating AI with traditional HPC, managing workflows across diverse facilities, addressing heterogeneity in computing environments, and ensuring workflows are findable, accessible, interoperable, and reusable (FAIR). The report outlines recent advances, ongoing challenges, and provides recommendations for each topic area, emphasizing the need for standardization, improved interoperability, and the development of more sophisticated tools and frameworks to support the evolving landscape of scientific workflows in the era of exascale computing and AI integration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Myna

The additive manufacturing (AM) community has been developing digital factory tools over the past decade to better leverage the multi-modal process data coming out of the advanced manufacturing process. As a result, numerous databases of additive manufacturing process data exist in the literature and in the archival storage of disparate research groups. While some efforts have been made to create a standard ontology for storing and sharing AM data, in practice a variety of data structures are used to store AM build data, even within a single institution. This causes many problems for maintainability and extensibility when attempting to integrate computational modeling tools with experimental data to either validate models or to provide further insight into results and trends. Myna is a Python-based framework that aims to decrease the effort needed to connect individual computational models to the variety of AM process data that exist in different research groups and institutions. This type of software is sometimes referred to as "middleware" or “glueware,” in that it connects disparate databases and applications into a single computational ecosystem. Instead of maintaining unique interfaces between each application and each database, developers can create a single interface from each application to Myna and thereby gain access to the implemented database connections. Similarly, developing a database connection in Myna provides access to the developed simulation applications. This framework greatly simplifies the maintainability of model applications that rely on experimental data. Using external simulation tools, users will also be able to run pre-configured workflows using the built-in workflow manager. Several examples of input files are provided with Myna for different workflows, including melt pool geometry predictions and detailed melt pool and solidification microstructure predictions.

Knapp, GerryL. [Oak Ridge National Laboratory (ORN↗
NASA NTRS2007

Collaborative Resource Allocation

Collaborative Resource Allocation Networking Environment (CRANE) Version 0.5 is a prototype created to prove the newest concept of using a distributed environment to schedule Deep Space Network (DSN) antenna times in a collaborative fashion. This program is for all space-flight and terrestrial science project users and DSN schedulers to perform scheduling activities and conflict resolution, both synchronously and asynchronously. Project schedulers can, for the first time, participate directly in scheduling their tracking times into the official DSN schedule, and negotiate directly with other projects in an integrated scheduling system. A master schedule covers long-range, mid-range, near-real-time, and real-time scheduling time frames all in one, rather than the current method of separate functions that are supported by different processes and tools. CRANE also provides private workspaces (both dynamic and static), data sharing, scenario management, user control, rapid messaging (based on Java Message Service), data/time synchronization, workflow management, notification (including emails), conflict checking, and a linkage to a schedule generation engine. The data structure with corresponding database design combines object trees with multiple associated mortal instances and relational database to provide unprecedented traceability and simplify the existing DSN XML schedule representation. These technologies are used to provide traceability, schedule negotiation, conflict resolution, and load forecasting from real-time operations to long-range loading analysis up to 20 years in the future. CRANE includes a database, a stored procedure layer, an agent-based middle tier, a Web service wrapper, a Windows Integrated Analysis Environment (IAE), a Java application, and a Web page interface.

Wang, Yeou-Fang↗
DOE OSTI2017

BASTet: Shareable and Reproducible Analysis and Visualization of Mass Spectrometry Imaging Data via OpenMSI

Mass spectrometry imaging (MSI) is a transformative imaging method that supports the untargeted, quantitative measurement of the chemical composition and spatial heterogeneity of complex samples with broad applications in life sciences, bioenergy, and health. While MSI data can be routinely collected, its broad application is currently limited by the lack of easily accessible analysis methods that can process data of the size, volume, diversity, and complexity generated by MSI experiments. The development and application of cutting-edge analytical methods is a core driver in MSI research for new scientific discoveries, medical diagnostics, and commercial-innovation. However, the lack of means to share, apply, and reproduce analyses hinders the broad application, validation, and use of novel MSI analysis methods. To address this central challenge, we introduce the Berkeley Analysis and Storage Toolkit (BASTet), a novel framework for shareable and reproducible data analysis that supports standardized data and analysis interfaces, integrated data storage, data provenance, workflow management, and a broad set of integrated tools. Based on BASTet, we describe the extension of the OpenMSI mass spectrometry imaging science gateway to enable web-based sharing, reuse, analysis, and visualization of data analyses and derived data products. Here, we demonstrate the application of BASTet and OpenMSI in practice to identify and compare characteristic substructures in the mouse brain based on their chemical composition measured via MSI.

97 MATHEMATICS AND COMPUTING↗