There are many science applications that require scalable task-level parallelism, support for flexible execution and coupling of ensembles of simulations. Most high-performance system software and middleware, however, are designed to support the execution and optimization of single tasks. Motivated by the missing capabilities of these computing systems and the increasing importance of task-level parallelism, we introduce the Ensemble toolkit which has the following application development features: (i) abstractions that enable the expression of ensembles as primary entities, and (ii) support for ensemble-based execution patterns that capture the majority of application scenarios. Ensemble toolkit uses a scalable pilot-based runtime system that decouples workload execution and resource management details from the expression of the application, and enables the efficient and dynamic execution of ensembles on heterogeneous computing resources. We investigate three execution patterns and characterize the scalability and overhead of Ensemble toolkit for these patterns. We investigate scaling properties for up to O(1000) concurrent ensembles and O(1000) cores and find linear weak and strong scaling behaviour.
Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free energy landscapes for conformational and chemical transitions. However, daunting challenges remain in efficiently getting such simulations to scale to the very large number of replicas required to address problems in state spaces beyond two dimensions. The development of enabling technology to carry out such simulations is in its infancy, and thus it remains an open question as to which applications demand extension into higher dimensions. In the present work, we explore this problem space by applying asynchronous Hamiltonian replica exchange molecular dynamics with a combined quantum mechanical/molecular mechanical potential to explore the conformational space for a simpleribonucleoside , using a newly developed software framework capable of executing >3,000 replicas with only enough resources to run 2,000 simultaneously, which may not be possible with traditional synchronous replica exchange approaches. Our results demonstrate 1.) the necessity of high dimensional sampling simulations for biological systems, even as simple as as a single ribonucleoside, 2.) the utility of asynchronous exchange protocols in managing simultaneous resource requirements expected in high dimensional sampling simulations. It is expected that more complicated systems will only increase in computational demand and complexity and thus the reported asynchronous approach may be increasingly beneficial in order to make such applications available to a broad range of computational scientists.
No abstract
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
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