arXiv subjects

Matteo Turilli

Publications and source records attributed to Matteo Turilli.

48 records · Page 3Linked to original sources

arXiv2019

Designing Workflow Systems Using Building Blocks

We suggest there is a need for a fresh perspective on the design and development of workflow systems and argue for a building blocks approach. We outline a description of this approach and define the properties of software building blocks. We discuss RADICAL-Cybertools as one implementation of the building blocks concept, showing how they have been designed and developed in accordance with this approach. Four case studies are presented, covering a dozen science problems. We discuss how RADICAL-Cybertools have been used to develop new workflow systems capabilities and integrated to enhance existing ones, illustrating the applicability and potential of software building blocks. In doing so, we have begun an investigation of an alternative approach to thinking about the design and implementation of workflow systems.

cs.SE↗

arXiv2019

RADICAL-Cybertools: Middleware Building Blocks for Scalable Science

RADICAL-Cybertools (RCT) are a set of software systems that serve as middleware to develop efficient and effective tools for scientific computing. Specifically, RCT enable executing many-task applications at extreme scale and on a variety of computing infrastructures. RCT are building blocks, designed to work as stand-alone systems, integrated among themselves or integrated with third-party systems. RCT enables innovative science in multiple domains, including but not limited to biophysics, climate science and particle physics, consuming hundreds of millions of core hours. This paper provides an overview of RCT systems, their impact, and the architectural principles and software engineering underlying RCT

cs.SE↗

arXiv2018

Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations

The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of computational chemistry, surmounting which could revolutionize drug design and provide the platform for patient-specific medicine. Recent evidence suggests that molecular dynamics (MD) can achieve useful predictive accuracy (< 1 kcal/mol). For this predictive accuracy to impact clinical decision making, binding free energy computational campaigns must provide results rapidly and without loss of accuracy. This demands advances in algorithms, scalable software systems, and efficient utilization of supercomputing resources. We introduce a framework called HTBAC, designed to support accurate and scalable drug binding affinity calculations, while marshaling large simulation campaigns. We show that HTBAC supports the specification and execution of free-energy protocols at scale. This paper makes three main contributions: (1) shows the importance of adaptive execution for ensemble-based free energy protocols to improve binding affinity accuracy; (2) presents and characterizes HTBAC -- a software system that enables the scalable and adaptive execution of binding affinity protocols at scale; and (3) for a widely used free-energy protocol (TIES), shows improvements in the accuracy of simulations for a fixed amount of resource, or reduced resource consumption for a fixed accuracy as a consequence of adaptive execution.

cs.DC↗

arXiv2018

Synapse: Synthetic Application Profiler and Emulator

Motivated by the need to emulate workload execution characteristics on high-performance and distributed heterogeneous resources, we introduce Synapse. Synapse is used as a proxy application (or "representative application") for real workloads, with the advantage that it can be tuned in different ways and dimensions, and also at levels of granularity that are not possible with real applications. Synapse has a platform-independent application profiler, and has the ability to emulate profiled workloads on a variety of resources. Experiments show that the automated profiling performed using Synapse captures an application's characteristics with high fidelity. The emulation of an application using Synapse can reproduce the application's execution behavior in the original run-time environment, and can also reproduce those behaviors on different run-time environments.

cs.DC↗

arXiv2018

Using Pilot Systems to Execute Many Task Workloads on Supercomputers

High performance computing systems have historically been designed to support applications comprised of mostly monolithic, single-job workloads. Pilot systems decouple workload specification, resource selection, and task execution via job placeholders and late-binding. Pilot systems help to satisfy the resource requirements of workloads comprised of multiple tasks. RADICAL-Pilot (RP) is a modular and extensible Python-based pilot system. In this paper we describe RP's design, architecture and implementation, and characterize its performance. RP is capable of spawning more than 100 tasks/second and supports the steady-state execution of up to 16K concurrent tasks. RP can be used stand-alone, as well as integrated with other application-level tools as a runtime system.

cs.DC↗

arXiv2018

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications

Many scientific problems require multiple distinct computational tasks to be executed in order to achieve a desired solution. We introduce the Ensemble Toolkit (EnTK) to address the challenges of scale, diversity and reliability they pose. We describe the design and implementation of EnTK, characterize its performance and integrate it with two distinct exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of two use case implementations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) implementing dedicated abstractions to support the description and execution of ensemble applications; (ii) support for execution on heterogeneous computing infrastructures; (iii) efficient scalability up to O(10^4) tasks; and (iv) fault tolerance. We discuss novel computational capabilities that EnTK enables and the scientific advantages arising thereof. We propose EnTK as an important addition to the suite of tools in support of production scientific computing.

cs.DC↗

arXiv2018

High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols.

cs.DC↗

arXiv2018

Towards General Distributed Resource Selection

The advantages of distributing workloads and utilizing multiple distributed resources are now well established. The type and degree of heterogeneity of distributed resources is increasing, and thus determining how to distribute the workloads becomes increasingly difficult, in particular with respect to the selection of suitable resources. We formulate and investigate the resource selection problem in a way that it is agnostic of specific task and resource properties, and which is generalizable to range of metrics. Specifically, we developed a model to describe the requirements of tasks and to estimate the cost of running that task on an arbitrary resource using baseline measurements from a reference machine. We integrated our cost model with the Condor matchmaking algorithm to enable resource selection. Experimental validation of our model shows that it provides execution time estimates with 157-171% error on XSEDE resources and 18-31% on OSG resources. We use the task execution cost model to select resources for a bag-of-tasks of up to 1024 GROMACS MD simulations across the target resources. Experiments show that using the model's estimates reduces the workload's time-to-completion up to ~85% when compared to the random distribution of workload across the same resources.

cs.DC↗

arXiv2018

Design and Performance Characterization of RADICAL-Pilot on Titan

Many extreme scale scientific applications have workloads comprised of a large number of individual high-performance tasks. The Pilot abstraction decouples workload specification, resource management, and task execution via job placeholders and late-binding. As such, suitable implementations of the Pilot abstraction can support the collective execution of large number of tasks on supercomputers. We introduce RADICAL-Pilot (RP) as a portable, modular and extensible Python-based Pilot system. We describe RP's design, architecture and implementation. We characterize its performance and show its ability to scalably execute workloads comprised of thousands of MPI tasks on Titan--a DOE leadership class facility. Specifically, we investigate RP's weak (strong) scaling properties up to 131K (65K) cores and 4096 (16384) 32 core tasks. RADICAL-Pilot can be used stand-alone, as well as integrated with other tools as a runtime system.

cs.DC↗

arXiv2017

High-Throughput Computing on High-Performance Platforms: A Case Study

The computing systems used by LHC experiments has historically consisted of the federation of hundreds to thousands of distributed resources, ranging from small to mid-size resource. In spite of the impressive scale of the existing distributed computing solutions, the federation of small to mid-size resources will be insufficient to meet projected future demands. This paper is a case study of how the ATLAS experiment has embraced Titan---a DOE leadership facility in conjunction with traditional distributed high- throughput computing to reach sustained production scales of approximately 52M core-hours a years. The three main contributions of this paper are: (i) a critical evaluation of design and operational considerations to support the sustained, scalable and production usage of Titan; (ii) a preliminary characterization of a next generation executor for PanDA to support new workloads and advanced execution modes; and (iii) early lessons for how current and future experimental and observational systems can be integrated with production supercomputers and other platforms in a general and extensible manner.

cs.DC↗

arXiv2016

A Comprehensive Perspective on Pilot-Job Systems

Pilot-Job systems play an important role in supporting distributed scientific computing. They are used to consume more than 700 million CPU hours a year by the Open Science Grid communities, and by processing up to 1 million jobs a day for the ATLAS experiment on the Worldwide LHC Computing Grid. With the increasing importance of task-level parallelism in high-performance computing, Pilot-Job systems are also witnessing an adoption beyond traditional domains. Notwithstanding the growing impact on scientific research, there is no agreement upon a definition of Pilot-Job system and no clear understanding of the underlying abstraction and paradigm. Pilot-Job implementations have proliferated with no shared best practices or open interfaces and little interoperability. Ultimately, this is hindering the realization of the full impact of Pilot-Jobs by limiting their robustness, portability, and maintainability. This paper offers a comprehensive analysis of Pilot-Job systems critically assessing their motivations, evolution, properties, and implementation. The three main contributions of this paper are: (i) an analysis of the motivations and evolution of Pilot-Job systems; (ii) an outline of the Pilot abstraction, its distinguishing logical components and functionalities, its terminology, and its architecture pattern; and (iii) the description of core and auxiliary properties of Pilot-Jobs systems and the analysis of seven exemplar Pilot-Job implementations. Together, these contributions illustrate the Pilot paradigm, its generality, and how it helps to address some challenges in distributed scientific computing.

cs.DC↗

arXiv2016

Integrating Abstractions to Enhance the Execution of Distributed Applications

One of the factors that limits the scale, performance, and sophistication of distributed applications is the difficulty of concurrently executing them on multiple distributed computing resources. In part, this is due to a poor understanding of the general properties and performance of the coupling between applications and dynamic resources. This paper addresses this issue by integrating abstractions representing distributed applications, resources, and execution processes into a pilot-based middleware. The middleware provides a platform that can specify distributed applications, execute them on multiple resource and for different configurations, and is instrumented to support investigative analysis. We analyzed the execution of distributed applications using experiments that measure the benefits of using multiple resources, the late-binding of scheduling decisions, and the use of backfill scheduling.

cs.DC↗