arXiv subjects

Andre Merzky

Publications and source records attributed to Andre Merzky.

36 records · Page 2Linked to original sources

arXiv2021

ExaWorks: Workflows for Exascale

Exascale computers will offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight. These software combinations and integrations, however, are difficult to achieve due to challenges of coordination and deployment of heterogeneous software components on diverse and massive platforms. We present the ExaWorks project, which can address many of these challenges: ExaWorks is leading a co-design process to create a workflow software development Toolkit (SDK) consisting of a wide range of workflow management tools that can be composed and interoperate through common interfaces. We describe the initial set of tools and interfaces supported by the SDK, efforts to make them easier to apply to complex science challenges, and examples of their application to exemplar cases. Furthermore, we discuss how our project is working with the workflows community, large computing facilities as well as HPC platform vendors to sustainably address the requirements of workflows at the exascale.

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arXiv2021

Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening

We propose a benchmark to study surrogate model accuracy for protein-ligand docking. We share a dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million "in-stock" molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. Our work shows surrogate docking models have six orders of magnitude more throughput than standard docking protocols on the same supercomputer node types. We demonstrate the power of high-speed surrogate models by running each target against 1 billion molecules in under a day (50k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate ML models as a pre-filter. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01\% of detecting the underlying best scoring 0.1\% of compounds. Our analysis of the speedup explains that to screen more molecules under a docking paradigm, another order of magnitude speedup must come from model accuracy rather than computing speed (which, if increased, will not anymore alter our throughput to screen molecules). We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100x or even 1000x faster than current techniques.

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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

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arXiv2020

Scalable HPC and AI Infrastructure for COVID-19 Therapeutics

COVID-19 has claimed more 1 million lives and resulted in over 40 million infections. There is an urgent need to identify drugs that can inhibit SARS-CoV-2. In response, the DOE recently established the Medical Therapeutics project as part of the National Virtual Biotechnology Laboratory, and tasked it with creating the computational infrastructure and methods necessary to advance therapeutics development. We discuss innovations in computational infrastructure and methods that are accelerating and advancing drug design. Specifically, we describe several methods that integrate artificial intelligence and simulation-based approaches, and the design of computational infrastructure to support these methods at scale. We discuss their implementation and characterize their performance, and highlight science advances that these capabilities have enabled.

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arXiv2020

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

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 silicomethodologies need to be improved to better select lead compounds that can proceed to later stages of the drug discovery protocol accelerating the entire process. No single methodological approach can achieve the necessary accuracy with required efficiency. Here we describe multiple algorithmic innovations to overcome this fundamental limitation, development and deployment of computational infrastructure at scale integrates multiple artificial intelligence and simulation-based approaches. Three measures of performance are:(i) throughput, the number of ligands per unit time; (ii) scientific performance, the number of effective ligands sampled per unit time and (iii) peak performance, in flop/s. The capabilities outlined here have been used in production for several months as the workhorse of the computational infrastructure to support the capabilities of the US-DOE National Virtual Biotechnology Laboratory in combination with resources from the EU Centre of Excellence in Computational Biomedicine.

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arXiv2019

Characterizing the Performance of Executing Many-tasks on Summit

Many scientific workloads are comprised of many tasks, where each task is an independent simulation or analysis of data. The execution of millions of tasks on heterogeneous HPC platforms requires scalable dynamic resource management and multi-level scheduling. RADICAL-Pilot (RP) -- an implementation of the Pilot abstraction, addresses these challenges and serves as an effective runtime system to execute workloads comprised of many tasks. In this paper, we characterize the performance of executing many tasks using RP when interfaced with JSM and PRRTE on Summit: RP is responsible for resource management and task scheduling on acquired resource; JSM or PRRTE enact the placement of launching of scheduled tasks. Our experiments provide lower bounds on the performance of RP when integrated with JSM and PRRTE. Specifically, for workloads comprised of homogeneous single-core, 15 minutes-long tasks we find that: PRRTE scales better than JSM for > O(1000) tasks; PRRTE overheads are negligible; and PRRTE supports optimizations that lower the impact of overheads and enable resource utilization of 63% when executing O(16K), 1-core tasks over 404 compute nodes.

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arXiv2019

Middleware Building Blocks for Workflow Systems

This paper describes a building blocks approach to the design of scientific workflow systems. We discuss RADICAL-Cybertools as one implementation of the building blocks concept, showing how they are designed and developed in accordance with this approach. This paper offers three main contributions: (i) showing the relevance of the design principles underlying the building blocks approach to support scientific workflows on high performance computing platforms; (ii) illustrating a set of building blocks that enable multiple points of integration, "unifying" conceptual reasoning across otherwise very different tools and systems; and (iii) case studies discussing how RADICAL-Cybertools are integrated with existing workflow, workload, and general purpose computing systems and used to develop domain-specific workflow systems.

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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

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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.

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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.

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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.

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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.

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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.

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arXiv2016

Synapse: Synthetic Application Profiler and Emulator

We introduce Synapse motivated by the needs to estimate and emulate workload execution characteristics on high-performance and distributed heterogeneous resources. Synapse has a platform independent application profiler, and the ability to emulate profiled workloads on a variety of heterogeneous resources. Synapse is used as a proxy application (or "representative application") for real workloads, with the added advantage that it can be tuned at arbitrary levels of granularity in ways that are simply not possible using real applications. Experiments show that automated profiling using Synapse represents application characteristics with high fidelity. Emulation using Synapse can reproduce the application behavior in the original runtime environment, as well as reproducing properties when used in a different run-time environments.

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arXiv2016

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations

Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The next set of simulation parameters are based upon the outcome of the exchanges. Typically RE functionality is integrated into the molecular simulation software package. A primary motivation of the tight integration of RE functionality with simulation codes has been performance. This is limiting at multiple levels. First, advances in the RE methodology are tied to the molecular simulation code. Consequently these advances remain confined to the molecular simulation code for which they were developed. Second, it is difficult to extend or experiment with novel RE algorithms, since expertise in the molecular simulation code is typically required. In this paper, we propose the RepEx framework which address these aforementioned shortcomings of existing approaches, while striking the balance between flexibility (any RE scheme) and scalability (tens of thousands of replicas) over a diverse range of platforms. RepEx is designed to use a pilot-job based runtime system and support diverse RE Patterns and Execution Modes. RE Patterns are concerned with synchronization mechanisms in RE simulation, and Execution Modes with spatial and temporal mapping of workload to the CPU cores. We discuss how the design and implementation yield the following primary contributions of the RepEx framework: (i) its ability to support different RE schemes independent of molecular simulation codes, (ii) provide the ability to execute different exchange schemes and replica counts independent of the specific availability of resources, (iii) provide a runtime system that has first-class support for task-level parallelism, and (iv) required scalability along multiple dimensions.

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arXiv2012

Grid Computing: The Next Decade -- Report and Summary

The evolution of the global scientific cyberinfrastructure (CI) has, over the last 10+ years, led to a large diversity of CI instances. While specialized, competing and alternative CI building blocks are inherent to a healthy ecosystem, it also becomes apparent that the increasing degree of fragmentation is hindering interoperation, and thus limiting collaboration, which is essential for modern science communities often spanning international groups and multiple disciplines (but even 'small sciences', with smaller and localized communities, are often embedded into the larger scientific ecosystem, and are increasingly dependent on the availability of CI.) There are different reasons why fragmentation occurs, on technical and social level. But also, it is apparent that the current funding model for creating CI components largely fails to aid the transition from research to production, by mixing CS research and IT engineering challenges into the same funding strategies. The 10th anniversary of the EU funded project 'Grid Lab' (which was an early and ambitious attempt on providing a consolidated and science oriented cyberinfrastructure software stack to a specific science community) was taken as an opportunity to invite international leaders and early stage researchers in grid computing and e-Science from Europe, America and Asia, and, together with representatives of the EU and US funding agencies, to discuss the fundamental aspects of CI evolution, and to contemplate the options for a more coherent, more coordinated approach to the global evolution of CI. This open document represents the results of that workshop - including a draft of a mission statement and a proposal for a blueprint process - to inform the wider community as well as to encourage external experts to provide their feedback and comments.

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arXiv2012

P*: A Model of Pilot-Abstractions

Pilot-Jobs support effective distributed resource utilization, and are arguably one of the most widely-used distributed computing abstractions - as measured by the number and types of applications that use them, as well as the number of production distributed cyberinfrastructures that support them. In spite of broad uptake, there does not exist a well-defined, unifying conceptual model of Pilot-Jobs which can be used to define, compare and contrast different implementations. Often Pilot-Job implementations are strongly coupled to the distributed cyber-infrastructure they were originally designed for. These factors present a barrier to extensibility and interoperability. This pa- per is an attempt to (i) provide a minimal but complete model (P*) of Pilot-Jobs, (ii) establish the generality of the P* Model by mapping various existing and well known Pilot-Job frameworks such as Condor and DIANE to P*, (iii) derive an interoperable and extensible API for the P* Model (Pilot-API), (iv) validate the implementation of the Pilot-API by concurrently using multiple distinct Pilot-Job frameworks on distinct production distributed cyberinfrastructures, and (v) apply the P* Model to Pilot-Data.

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