Workflows are critical for scientific discovery. However, the sophistication, heterogeneity, and scale of workflows make building, testing, and optimizing them increasingly challenging. Furthermore, their complexity and heterogeneity make performance reproducibility hard. In this paper, we propose workflow mini-apps as a tool to address the challenges in building and testing workflows while controlling the fidelity of representing real-world workflows. Workflow mini-apps are deployed and run on various HPC systems and architectures without workflow-specific constraints. We offer insight into their design and implementation, providing an analysis of their performance and reproducibility. Workflow mini-apps thus advance the science of workflows by providing simple, portable, and managed (fidelity) representations of otherwise complex and difficult-to-control real workflows.

Heterogeneous workflows represent a promising approach for overcoming traditional application performance limitations and to accelerate scientific insight on high-performance computing (HPC) platforms. As HPC platforms grow in size and complexity, managing and optimizing workflow resources while maximizing scientific output assumes vital importance. Optimal workflow resource allocation requires high-quality and timely information about the state of the hardware resources, the status of the pending tasks, the performance of the tasks that have already been executed, and the current status of the workflow itself. A robust performance observability framework that captures and delivers this information can fundamentally improve the quality of decision-making within the workflow system, setting the stage for the adaptive execution of workflow tasks. We propose the use of SOMA, a service-based performance observability framework for such HPC workflows. With the RADICAL-Pilot runtime system as a development vehicle, SOMA demonstrates that service-based architectures coupled with an appropriate data model can serve the performance monitoring needs of large-scale ensemble workflows in a low-overhead fashion. Effective observability of workflow performance requires exporting, storing, and analyzing several types of performance data from across the application and workflow software stacks. Our study finds significant benefits in integrating observability frameworks as first-class citizens within an HPC workflow software stack. In this paper, we demonstrate how SOMA can simultaneously observe the performance states of the individual tasks, system hardware, and the workflow as a whole. Such information can then be employed to calculate better resource allocation and task configuration.

It is generally desirable for high-performance computing (HPC) applications to be portable between HPC systems, for example to make use of more performant hardware, make effective use of allocations, and to co-locate compute jobs with large datasets. Unfortunately, moving scientific applications between HPC systems is challenging for various reasons, most notably that HPC systems have different HPC schedulers. We introduce PSI/J, a job management abstraction API intended to simplify the construction of software components and applications that are portable over various HPC scheduler implementations. We argue that such a system is both necessary and that no viable alternative currently exists. We analyze similar notable APIs and attempt to determine the factors that influenced their evolution and adoption by the HPC community. We base the design of PSI/J on that analysis. We describe how PSI/J has been integrated in three workflow systems and one application, and also show via experiments that PSI/J imposes minimal overhead.

Scientific computing communities increasingly run their experiments using complex data- and compute-intensive workflows that utilize distributed and heterogeneous architectures targeting numerical simulations and machine learning, often executed on the Department of Energy Leadership Computing Facilities (LCFs). We argue that a principled, systematic approach to implementing FAIR principles at scale, including fine-grained metadata extraction and organization, can help with the numerous challenges to performance reproducibility posed by such workflows. We extract workflow patterns, propose a set of tools to manage the entire life cycle of performance metadata, and aggregate them in an HPC-ready framework for reproducibility (RECUP). We describe the challenges in making these tools interoperable, preliminary work, and lessons learned from this experiment.

We describe the design, implementation and performance of the RADICAL-Pilot task overlay (RAPTOR). RAPTOR enables the execution of heterogeneous tasks-i.e., functions and executables with arbitrary duration-on HPC platforms, pro-viding high throughput and high resource utilization. RAPTOR supports the high throughput virtual screening requirements of DOE's National Virtual Biotechnology Laboratory effort to find therapeutic solutions for COVID-19. RAPTOR has been used on 8300 compute nodes to sustain 144M/hour docking hits, and to screen 1011 ligands. To the best of our knowledge, both the throughput rate and aggregated number of executed tasks are a factor of two greater than previously reported in literature. RAPTOR represents important progress towards improvement of computational drug discovery, in terms of size of libraries screened, and for the possibility of generating training data fast enough to serve the last generation of docking surrogate models.

The importance of ensemble computing is well established. However, executing ensembles at scale introduces interesting performance fluctuations that have not been well investigated. In this paper, we trace our experience uncovering performance fluctuations of ensemble applications (primarily constituting a workflow of GROMACS tasks), and unsuccessful attempts, so far, at trying to discern the underlying cause(s) of performance fluctuations. Is the failure to discern the causative or contributing factors a failure of capability? Or imagination? Do the fluctuations have their genesis in some inscrutable aspect of the system or software? Does it warrant a fundamental reassessment and rethinking of how we assume and conceptualize performance reproducibility? Answers to these questions are not straightforward, nor are they immediate or obvious. We conclude with a discussion about the performance of ensemble applications and ruminate over the implications for how we define and measure application performance.

Machine learning (ML)-based steering can improve the performance of ensemble-based simulations by allowing for online selection of more scientifically meaningful computations. We present DeepDriveMD, a framework for ML-driven steering of scientific simulations that we have used to achieve orders-of-magnitude improvements in molecular dynamics (MD) performance via effective coupling of ML and HPC on large parallel computers. We discuss the design of DeepDriveMD and characterize its performance. We demonstrate that DeepDriveMD can achieve between 100-1000× acceleration for protein folding simulations relative to other methods, as measured by the amount of simulated time performed, while covering the same conformational landscape as quantified by the states sampled during a simulation. Experiments are performed on leadership-class platforms on up to 1020 nodes. The results establish DeepDriveMD as a high-performance framework for ML-driven HPC simulation scenarios, that supports diverse MD simulation and ML back-ends, and which enables new scientific insights by improving the length and time scales accessible with current computing capacity.

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 pilot-enabled runtime system. We describe RP's design, architecture and implementation. We characterize its performance and show its ability to scalably execute workloads comprised of tens of thousands heterogeneous tasks on DOE and NSF leadership-class HPC platforms. Specifically, we investigate RP's weak/strong scaling with CPU/GPU, single/multi core, (non)MPI tasks and Python functions when using most of ORNL Summit and TACC Frontera. RADICAL-Pilot can be used stand-alone, as well as the runtime for third-party workflow systems.

The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2–3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silico methodologies need to be improved both to select better lead compounds, so as to improve the efficiency of later stages in the drug discovery protocol, and to identify those lead compounds more quickly. No known methodological approach can deliver this combination of higher quality and speed. Here, we describe an Integrated Modeling PipEline for COVID Cure by Assessing Better LEads (IMPECCABLE) that employs multiple methodological innovations to overcome this fundamental limitation. We also describe the computational framework that we have developed to support these innovations at scale, and characterize the performance of this framework in terms of throughput, peak performance, and scientific results. We show that individual workflow components deliver 100 × to 1000 × improvement over traditional methods, and that the integration of methods, supported by scalable infrastructure, speeds up drug discovery by orders of magnitudes. IMPECCABLE has screened ∼ 1011 ligands and has been used to discover a promising drug candidate. These capabilities have been used by the US DOE National Virtual Biotechnology Laboratory and the EU Centre of Excellence in Computational Biomedicine.

Ecological sciences are using imagery from a variety of sources to monitor and survey populations and ecosystems. Very High Resolution (VHR) satellite imagery provide an effective dataset for large scale surveys. Convolutional Neural Networks have successfully been employed to analyze such imagery and detect large animals. As the datasets increase in volume, O(TB), and number of images, O(1k), utilizing High Performance Computing (HPC) resources becomes necessary. In this paper, we investigate a task-parallel data-driven workflows design to support imagery analysis pipelines with heterogeneous tasks on HPC. We analyze the capabilities of each design when processing a dataset of 3,000 VHR satellite images for a total of 4~TB. We experimentally model the execution time of the tasks of the image processing pipeline. We perform experiments to characterize the resource utilization, total time to completion, and overheads of each design. Based on the model, overhead and utilization analysis, we show which design approach to is best suited in scientific pipelines with similar characteristics.

The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. Quantifying the strength of these interactions (the so called `binding affinity') is a grand challenge of computational chemistry, surmounting which could revolutionize drug design and provide the platform for patient specific medicine. Recently, evidence from blind challenge predictions and retrospective validation studies has suggested that molecular dynamics (MD) can now achieve useful predictive accuracy ( 1 kcal/mol) This accuracy is sufficient to greatly accelerate hit to lead and lead optimization. To translate these advances in predictive accuracy so as to impact clinical and/or industrial decision making requires that binding free energy results must be turned around on reduced timescales without loss of accuracy. This demands advances in algorithms, scalable software systems, and intelligent and efficient utilization of supercomputing resources. This work is motivated by the real world problem of providing insight from drug candidate data on a time scale that is as short as possible. Specifically, we reproduce results from a collaborative project between UCL and GlaxoSmithKline to study a congeneric series of drug candidates binding to the BRD4 protein - inhibitors of which have shown promising preclinical efficacy in pathologies ranging from cancer to inflammation. We demonstrate the use of a framework called HTBAC, designed to support the aforementioned requirements of accurate and rapid drug binding affinity calculations. HTBAC facilitates the execution of the numbers of simulations while supporting the adaptive execution of algorithms. Furthermore, HTBAC enables the selection of simulation parameters during runtime which can, in principle, optimize the use of computational resources whilst producing results within a target uncertainty.

We suggest there is a need for a fresh perspective on the design and development of middleware for high-performance workflows and workflow systems. We argue for a building blocks approach, outline a description of this approach and define their properties. 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. We discuss three case-studies where RADICAL-Cybertools have been used to develop new workflow systems capabilities and in-tegrated to enhance existing ones, illustrating the potential and promise of the building blocks approach.

Traditionally, the ATLAS experiment at Large Hadron Collider (LHC) has utilized distributed resources as provided by the Worldwide LHC Computing Grid (WLCG) to support data distribution, data analysis and simulations. For example, the ATLAS experiment uses a geographically distributed grid of approximately 200,000 cores continuously (250 000 cores at peak), (over 1,000 million core-hours per year) to process, simulate, and analyze its data (todays total data volume of ATLAS is more than 300 PB). After the early success in discovering a new particle consistent with the long-awaited Higgs boson, ATLAS is continuing the precision measurements necessary for further discoveries. Planned high-luminosity LHC upgrade and related ATLAS detector upgrades, that are necessary for physics searches beyond Standard Model, pose serious challenge for ATLAS computing. Data volumes are expected to increase at higher energy and luminosity, causing the storage and computing needs to grow at a much higher pace than the flat budget technology evolution (see Fig. 1). The need for simulation and analysis will overwhelm the expected capacity of WLCG computing facilities unless the range and precision of physics studies will be curtailed.

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 results must be turned around 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 adaptive free-energy protocols at scale and with minimal overheads on NCSA Blue Waters. We validate the results obtained and show how adaptivity can be used to improve accuracy while reducing resource consumption of TIES, a widely used free-energy protocol.

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 exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of the two use case imple-mentations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) imple-menting 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(104) tasks; and (iv) task-level 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.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: As such, HTBAC advances the state of the art of binding affinity calculations and protocols. HTBAC provides the platform to enable scientists to study a wide range of cancer drugs and candidate ligands in order to support personalized clinical decision making based on genome sequencing and drug discovery.

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 re-source. 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.

Resource selection and task placement for distributed execution poses conceptual and implementation difficulties. Although resource selection and task placement are at the core of many tools and workflow systems, the methods are ad hoc rather than being based on models. Consequently, partial and non-interoperable implementations proliferate. We address both the conceptual and implementation difficulties by experimentally characterizing diverse modalities of resource selection and task placement. We compare the architectures and capabilities of two systems: the AIMES middleware and Swift workflow scripting language and runtime. We integrate these systems to enable the distributed execution of Swift workflows on Pilot-Jobs managed by the AIMES middleware. Our experiments characterize and compare alternative execution strategies by measuring the time to completion of heterogeneous uncoupled workloads executed at diverse scale and on multiple resources. We measure the adverse effects of pilot fragmentation and early binding of tasks to resources and the benefits of backfill scheduling across pilots on multiple resources. We then use this insight to execute a multi-stage workflow across five production-grade resources. We discuss the importance and implications for other tools and workflow systems

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.

This paper details the state of the art, the design, development and deployment of the EGI Federated Cloud platform, an e-infrastructure offering scalable and flexible models of utilization to the European research community. While continuing support for the traditional High Throughput Computing model, the EGI Cloud Platform extends its reach to other models of utilization such as long-lived services and on demand computation. Following a two-year period of development, the EGI Federated Cloud platform was officially launched in May 2014 offering resources provided by trusted academic and research organisations from within the user communities and consistently with their standard funding regime. Since then, the use cases supported have significantly increased both in total number and diversity of model of service required, validating both the choice of enforcing cloud technology agnosticism and of supporting service mobility and portability by means of open standards. These design choices have also allowed for the inclusion of commercial cloud providers into an infrastructure previously supported only by academic institutions. This contributes to a wider goal of funding agencies to create economic and social impact from supported research activities.

Cloud Computing provides an optimal infrastructure to utilise and share both computational and data resources whilst allowing a pay-per-use model, useful to cost-effectively manage hardware investment or to maximise its utilisation. Cloud Computing also offers transitory access to scalable amounts of computational resources, something that is particularly important due to the time and financial constraints of many user communities. The growing number of communities that are adopting large public cloud resources such as Amazon Web Services [1] or Microsoft Azure [2] proves the success and hence usefulness of the Cloud Computing paradigm. Nonetheless, the typical use cases for public clouds involve non-business critical applications, particularly where issues around security of utilization of applications or deposited data within shared public services are binding requisites. In this paper, a use case is presented illustrating how the integration of Trusted Computing technologies into an available cloud infrastructure -- Eucalyptus -- allows the security-critical energy industry to exploit the flexibility and potential economical benefits of the Cloud Computing paradigm for their business-critical applications.

This paper proposes a , the "ambit' of an action, that allows the degree of distribution of an action in a multiagent system to be quantified without regard to its functionality. It demonstrates the use of that notion in the design, analysis and implementation of dynamically-reconfigurable multi-agent systems. It distinguishes between the extensional (or system) view and intensional (or agent-based) view of such a system and shows how, using the notion of ambit, the step-wise derivation paradigm of formal methods can be used to derive the latter from the former. In closing it addresses the manner in which these ideas inform studies in the ethics of systems of artificial agents.