arXiv subjects

Bartosz Balis

Publications and source records attributed to Bartosz Balis.

9 recordsLinked to original sources

arXiv2026

From Research Question to Scientific Workflow: Leveraging Agentic AI for Science Automation

Scientific workflow systems automate execution -- scheduling, fault tolerance, resource management -- but not the semantic translation that precedes it. Scientists still manually convert research questions into workflow specifications, a task requiring both domain knowledge and infrastructure expertise. We propose an agentic architecture that closes this gap through three layers: an LLM interprets natural language into structured intents (semantic layer); validated generators produce reproducible workflow DAGs (deterministic layer); and domain experts author ``Skills'': markdown documents encoding vocabulary mappings, parameter constraints, and optimization strategies (knowledge layer). This decomposition confines LLM non-determinism to intent extraction: identical intents always yield identical workflows. We implement and evaluate the architecture on the 1000 Genomes population genetics workflow and Hyperflow WMS running on Kubernetes. In an ablation study on 150 queries, Skills raise full-match intent accuracy from 44% to 83%; skill-driven deferred workflow generation reduces data transfer by 92\%; and the end-to-end pipeline completes queries on Kubernetes with LLM overhead below 15 seconds and cost under $0.001 per query.

cs.AI↗

arXiv2025

A Terminology for Scientific Workflow Systems

The term scientific workflow has evolved over the last two decades to encompass a broad range of compositions of interdependent compute tasks and data movements. It has also become an umbrella term for processing in modern scientific applications. Today, many scientific applications can be considered as workflows made of multiple dependent steps, and hundreds of workflow management systems (WMSs) have been developed to manage and run these workflows. However, no turnkey solution has emerged to address the diversity of scientific processes and the infrastructure on which they are implemented. Instead, new research problems requiring the execution of scientific workflows with some novel feature often lead to the development of an entirely new WMS. A direct consequence is that many existing WMSs share some salient features, offer similar functionalities, and can manage the same categories of workflows but also have some distinct capabilities. This situation makes researchers who develop workflows face the complex question of selecting a WMS. This selection can be driven by technical considerations, to find the system that is the most appropriate for their application and for the resources available to them, or other factors such as reputation, adoption, strong community support, or long-term sustainability. To address this problem, a group of WMS developers and practitioners joined their efforts to produce a community-based terminology of WMSs. This paper summarizes their findings and introduces this new terminology to characterize WMSs. This terminology is composed of fives axes: workflow characteristics, composition, orchestration, data management, and metadata capture. Each axis comprises several concepts that capture the prominent features of WMSs. Based on this terminology, this paper also presents a classification of 23 existing WMSs according to the proposed axes and terms.

cs.DC↗

arXiv2024

Towards observability of scientific applications

As software systems increase in complexity, conventional monitoring methods struggle to provide a comprehensive overview or identify performance issues, often missing unexpected problems. Observability, however, offers a holistic approach, providing methods and tools that gather and analyze detailed telemetry data to uncover hidden issues. Originally developed for cloud-native systems, modern observability is less prevalent in scientific computing, particularly in HPC clusters, due to differences in application architecture, execution environments, and technology stacks. This paper proposes and evaluates an end-to-end observability solution tailored for scientific computing in HPC environments. We address several challenges, including collection of application-level metrics, instrumentation, context propagation, and tracing. We argue that typical dashboards with charts are not sufficient for advanced observability-driven analysis of scientific applications. Consequently, we propose a different approach based on data analysis using DataFrames and a Jupyter environment. The proposed solution is implemented and evaluated on two medical scientific pipelines running on an HPC cluster.

cs.DC↗

arXiv2024

Towards cloud-native scientific workflow management

Cloud-native is an approach to building and running scalable applications in modern cloud infrastructures, with the Kubernetes container orchestration platform being often considered as a fundamental cloud-native building block. In this paper, we evaluate alternative execution models for scientific workflows in Kubernetes. We compare the simplest job-based model, its variant with task clustering, and finally we propose a cloud-native model based on microservices comprising auto-scalable worker-pools. We implement the proposed models in the HyperFlow workflow management system, and evaluate them using a large Montage workflow on a Kubernetes cluster. The results indicate that the proposed cloud-native worker-pools execution model achieves best performance in terms of average cluster utilization, resulting in a nearly 20\% improvement of the workflow makespan compared to the best-performing job-based model. However, better performance comes at the cost of significantly higher complexity of the implementation and maintenance. We believe that our experiments provide a valuable insight into the performance, advantages and disadvantages of alternative cloud-native execution models for scientific workflows.

cs.DC↗

arXiv2023

Serverless Computing for Scientific Applications

Serverless computing has become an important model in cloud computing and influenced the design of many applications. Here, we provide our perspective on how the recent landscape of serverless computing for scientific applications looks like. We discuss the advantages and problems with serverless computing for scientific applications, and based on the analysis of existing solutions and approaches, we propose a science-oriented architecture for a serverless computing framework that is based on the existing designs. Finally, we provide an outlook of current trends and future directions.

cs.DC↗

arXiv2023

Workflows Community Summit 2022: A Roadmap Revolution

Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a cloud-based data preprocessing pipeline to multi-facility instrument-to-edge-to-HPC computational workflows. Given the changing landscape of scientific computing and the evolving needs of emerging scientific applications, it is paramount that the development of novel scientific workflows and system functionalities seek to increase the efficiency, resilience, and pervasiveness of existing systems and applications. Specifically, the proliferation of machine learning/artificial intelligence (ML/AI) workflows, need for processing large scale datasets produced by instruments at the edge, intensification of near real-time data processing, support for long-term experiment campaigns, and emergence of quantum computing as an adjunct to HPC, have significantly changed the functional and operational requirements of workflow systems. Workflow systems now need to, for example, support data streams from the edge-to-cloud-to-HPC enable the management of many small-sized files, allow data reduction while ensuring high accuracy, orchestrate distributed services (workflows, instruments, data movement, provenance, publication, etc.) across computing and user facilities, among others. Further, to accelerate science, it is also necessary that these systems implement specifications/standards and APIs for seamless (horizontal and vertical) integration between systems and applications, as well as enabling the publication of workflows and their associated products according to the FAIR principles. This document reports on discussions and findings from the 2022 international edition of the Workflows Community Summit that took place on November 29 and 30, 2022.

cs.DC↗

arXiv2021

A Community Roadmap for Scientific Workflows Research and Development

The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projects partnered to bring the international workflows community together. This paper reports on discussions and findings from two virtual "Workflows Community Summits" (January and April, 2021). The overarching goals of these workshops were to develop a view of the state of the art, identify crucial research challenges in the workflows community, articulate a vision for potential community efforts, and discuss technical approaches for realizing this vision. To this end, participants identified six broad themes: FAIR computational workflows; AI workflows; exascale challenges; APIs, interoperability, reuse, and standards; training and education; and building a workflows community. We summarize discussions and recommendations for each of these themes.

cs.DC↗

arXiv2021

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

cs.DC↗

arXiv2020

Serverless Containers -- rising viable approach to Scientific Workflows

Increasing popularity of the serverless computing approach has led to the emergence of new cloud infrastructures working in Container-as-a-Service (CaaS) model like AWS Fargate, Google Cloud Run, or Azure Container Instances. They introduce an innovative approach to running cloud containers where developers are freed from managing underlying resources. In this paper, we focus on evaluating capabilities of elastic containers and their usefulness for scientific computing in the scientific workflow paradigm using AWS Fargate and Google Cloud Run infrastructures. For experimental evaluation of our approach, we extended HyperFlow engine to support these CaaS platform, together with adapting four real-world scientific workflows composed of several dozen to over a hundred of tasks organized into a dependency graph. We used these workflows to create cost-performance benchmarks and flow execution plots, measuring delays, elasticity, and scalability. The experiments proved that serverless containers can be successfully applied for scientific workflows. Also, the results allow us to gain insights on specific advantages and limits of such platforms.

cs.DC↗