funcX: A Federated Function Serving Fabric for Science

Exploding data volumes and velocities, new computational methods and platforms, and ubiquitous connectivity demand new approaches to computation in the sciences. These new approaches must enable computation to be mobile, so that, for example, it can occur near data, be triggered by events (e.g., arrival of new data), be offloaded to specialized accelerators, or run remotely where resources are available. They also require new design approaches in which monolithic applications can be decomposed into smaller components, that may in turn be executed separately and on the most suitable resources. To address these needs we present funcX---a distributed function as a service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. funcX's endpoint software can transform existing clouds, clusters, and supercomputers into function serving systems, while funcX's cloud-hosted service provides transparent, secure, and reliable function execution across a federated ecosystem of endpoints. We motivate the need for funcX with several scientific case studies, present our prototype design and implementation, show optimizations that deliver throughput in excess of 1 million functions per second, and demonstrate, via experiments on two supercomputers, that funcX can scale to more than more than 130000 concurrent workers.Comment: Accepted to ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC 2020). arXiv admin note: substantial text overlap with arXiv:1908.0490

Transparent Orchestration of Task-based Parallel Applications in Containers Platforms

This paper presents a framework to easily build and execute parallel applications in container-based distributed computing platforms in a user-transparent way. The proposed framework is a combination of the COMP Superscalar (COMPSs) programming model and runtime, which provides a straightforward way to develop task-based parallel applications from sequential codes, and containers management platforms that ease the deployment of applications in computing environments (as Docker, Mesos or Singularity). This framework provides scientists and developers with an easy way to implement parallel distributed applications and deploy them in a one-click fashion. We have built a prototype which integrates COMPSs with different containers engines in different scenarios: i) a Docker cluster, ii) a Mesos cluster, and iii) Singularity in an HPC cluster. We have evaluated the overhead in the building phase, deployment and execution of two benchmark applications compared to a Cloud testbed based on KVM and OpenStack and to the usage of bare metal nodes. We have observed an important gain in comparison to cloud environments during the building and deployment phases. This enables better adaptation of resources with respect to the computational load. In contrast, we detected an extra overhead during the execution, which is mainly due to the multi-host Docker networking.This work is partly supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316 project, by the Generalitat de Catalunya under contracts 2014-SGR-1051 and 2014-SGR-1272, and by the European Union through the Horizon 2020 research and innovation program under grant 690116 (EUBra-BIGSEA Project). Results presented in this paper were obtained using the Chameleon testbed supported by the National Science Foundation.Peer ReviewedPostprint (author's final draft

The evolution of bits and bottlenecks in a scientific workflow trying to keep up with technology: Accelerating 4D image segmentation applied to nasa data

In 2016, a team of earth scientists directly engaged a team of computer scientists to identify cyberinfrastructure (CI) approaches that would speed up an earth science workflow. This paper describes the evolution of that workflow as the two teams bridged CI and an image segmentation algorithm to do large scale earth science research. The Pacific Research Platform (PRP) and The Cognitive Hardware and Software Ecosystem Community Infrastructure (CHASE-CI) resources were used to significantly decreased the earth science workflow's wall-clock time from 19.5 days to 53 minutes. The improvement in wall-clock time comes from the use of network appliances, improved image segmentation, deployment of a containerized workflow, and the increase in CI experience and training for the earth scientists. This paper presents a description of the evolving innovations used to improve the workflow, bottlenecks identified within each workflow version, and improvements made within each version of the workflow, over a three-year time period

StreamFlow: cross-breeding cloud with HPC

Workflows are among the most commonly used tools in a variety of execution environments. Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and batch clusters. We present a novel approach to workflow execution, called StreamFlow, that complements the workflow graph with the declarative description of potentially complex execution environments, and that makes it possible the execution onto multiple sites not sharing a common data space. StreamFlow is then exemplified on a novel bioinformatics pipeline for single-cell transcriptomic data analysis workflow.Comment: 30 pages - 2020 IEEE Transactions on Emerging Topics in Computin

Conceptualization and scalable execution of big data workflows using domain-specific languages and software containers

Big Data processing, especially with the increasing proliferation of Internet of Things (IoT) technologies and convergence of IoT, edge and cloud computing technologies, involves handling massive and complex data sets on heterogeneous resources and incorporating different tools, frameworks, and processes to help organizations make sense of their data collected from various sources. This set of operations, referred to as Big Data workflows, requires taking advantage of Cloud infrastructures’ elasticity for scalability. In this article, we present the design and prototype implementation of a Big Data workflow approach based on the use of software container technologies, message-oriented middleware (MOM), and a domain-specific language (DSL) to enable highly scalable workflow execution and abstract workflow definition. We demonstrate our system in a use case and a set of experiments that show the practical applicability of the proposed approach for the specification and scalable execution of Big Data workflows. Furthermore, we compare our proposed approach’s scalability with that of Argo Workflows – one of the most prominent tools in the area of Big Data workflows – and provide a qualitative evaluation of the proposed DSL and overall approach with respect to the existing literature.publishedVersio

Conceptualization and scalable execution of big data workflows using domain-specific languages and software containers

Big Data processing, especially with the increasing proliferation of Internet of Things (IoT) technologies and convergence of IoT, edge and cloud computing technologies, involves handling massive and complex data sets on heterogeneous resources and incorporating different tools, frameworks, and processes to help organizations make sense of their data collected from various sources. This set of operations, referred to as Big Data workflows, requires taking advantage of Cloud infrastructures’ elasticity for scalability. In this article, we present the design and prototype implementation of a Big Data workflow approach based on the use of software container technologies, message-oriented middleware (MOM), and a domain-specific language (DSL) to enable highly scalable workflow execution and abstract workflow definition. We demonstrate our system in a use case and a set of experiments that show the practical applicability of the proposed approach for the specification and scalable execution of Big Data workflows. Furthermore, we compare our proposed approach’s scalability with that of Argo Workflows – one of the most prominent tools in the area of Big Data workflows – and provide a qualitative evaluation of the proposed DSL and overall approach with respect to the existing literature.publishedVersio

Sciunits: Reusable Research Objects

Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. In this paper, we present the sciunit, a reusable research object in which aggregated content is recomputable. We describe a Git-like client that efficiently creates, stores, and repeats sciunits. We show through analysis that sciunits repeat computational experiments with minimal storage and processing overhead. Finally, we provide an overview of sharing and reproducible cyberinfrastructure based on sciunits gaining adoption in the domain of geosciences

Big data workflows: Locality-aware orchestration using software containers

The emergence of the Edge computing paradigm has shifted data processing from centralised infrastructures to heterogeneous and geographically distributed infrastructures. Therefore, data processing solutions must consider data locality to reduce the performance penalties from data transfers among remote data centres. Existing Big Data processing solutions provide limited support for handling data locality and are inefficient in processing small and frequent events specific to the Edge environments. This article proposes a novel architecture and a proof-of-concept implementation for software container-centric Big Data workflow orchestration that puts data locality at the forefront. The proposed solution considers the available data locality information, leverages long-lived containers to execute workflow steps, and handles the interaction with different data sources through containers. We compare the proposed solution with Argo Workflows and demonstrate a significant performance improvement in the execution speed for processing the same data units. Finally, we carry out experiments with the proposed solution under different configurations and analyze individual aspects affecting the performance of the overall solution.publishedVersio