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

Treikalis, Antons; Merzky, André; Chen, Haoyuan; T, Lee; York, Darrin M.; Jha, Shantenu

doi:10.1109/icpp.2016.78

Cited by 11 publications

(10 citation statements)

References 26 publications

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“…It is worth noting that, more recently, the traditional limitations in computational resources are being overcome by advances in GPU computing (55)(56)(57)(58)(59)(60)(61)(62) and wider access to new academic supercomputers (63,64). Furthermore, replica-based free energy methods, such as BEUS, while challenging to perform, have become more accessible to the non-mathematicians by recent advances in best practices (34,65,66) and the availability of several toolsets (35,(67)(68)(69)(70)(71)(72)(73)(74). Hence, extended MD simulations and energy landscape exploration should be easier to carry out in the future by experts and non-experts alike.…”

Section: Discussionmentioning

confidence: 99%

Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer

Mayne

Toy

Carlson

et al. 2021

Molecular Cancer Research

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Author Contributions CGM, ET, and JAK conceived and designed the study. CGM performed all molecular dynamics simulations, KEC performed the ligand binding/unbinding kinetics assays, and WT and TB performed the activity assays. CGM, KEC, WT, JAK, BSK, ET, and SC performed data analysis. All authors performed data interpretation, reviewed the results, and prepared the manuscript for submission. All authors have reviewed the final version and approved the manuscript for publication.

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Section: Discussionmentioning

confidence: 99%

Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer

Mayne

Toy

Carlson

et al. 2021

Molecular Cancer Research

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“…The focus of this paper has been on the direct execution of workloads on HPC machines, but RP also serves as the runtime system for a range of other tools and libraries [27][28][29][30], many already used in production. The requirements of these tools and libraries will also motivate future research and development.…”

Section: Resultsmentioning

confidence: 99%

Using Pilot Systems to Execute Many Task Workloads on Supercomputers

Merzky

Turilli

Maldonado

et al. 2019

Lecture Notes in Computer Science

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High performance computing systems have historically been designed to support applications comprised of mostly monolithic, singlejob 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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“…Although, driven by specific application needs, each DSW is characterized by a unique execution and coordination pattern and can serve multiple applications. The four ensemble-based DSW developed using EnTK and other RCT are: EX-TASY [15], RepEx [18], HTBAC [19], and ICEBERG. Details can be found in Ref.…”

Section: Illustrative Examplesmentioning

confidence: 99%

RADICAL-Cybertools: Middleware Building Blocks for Scalable Science

Balasubramanian,

Jha,

Merzky

et al. 2019

Preprint

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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 components, their impact, and the architectural principle and software engineering underlying RCT.

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

Cited by 11 publications

References 26 publications

Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer

Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer

Using Pilot Systems to Execute Many Task Workloads on Supercomputers

RADICAL-Cybertools: Middleware Building Blocks for Scalable Science

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