Performance of computationally intensive parameter sweep applications on Internet‐based Grids of computers: the mapping of molecular potential energy hypersurfaces

Reyes, Sebastián C.; Muñoz‐Caro, Camelia; Niño, Alfonso; Badía, Rosa M.; María, José

doi:10.1002/cpe.1114

Cited by 10 publications

(9 citation statements)

References 39 publications

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“…C++ has been selected because, apart from being an efficient language, it has useful object oriented characteristics such as encapsulation, inheritance and polymorphism [32]. The program is intended to compute the G matrix elements from the structural results of potential energy hypersurface mappings obtained in computational Grid environments [27]. These mappings can be obtained using the available standard electronic structure codes.…”

Section: Program Descriptionmentioning

confidence: 99%

“…Thus, we develop and implement accurate numerical differentiation algorithms for the computation of the kinetic terms in the framework of the rovibrational G matrix. A software system is designed to apply this methodology to the large sets of molecular structures generated in the previously described [27] mapping of potential energy hypersurfaces in computational Grid environments. Vibrational motions described by curvilinear, internal coordinates are considered.…”

Section: Introductionmentioning

confidence: 99%

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Accurate Numerical Computation of Rovibrational G Matrices in Molecules of Arbitrary Size

Castro

Niño

Muñoz‐Caro

Computational Science and Its Applications – ICCSA 2008

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Abstract. In this work we present a methodology for the accurate numerical computation of the rovibrational G matrix in any molecule. A C++ program is developed to apply this methodology. Using polymorphism, the program can handle the output of any of the available electronic structure codes. The objective is to compute the kinetic contribution to the rovibrational Hamiltonian from the results of molecular structure scans, performed in heterogeneous and distributed systems such as Internet-based Grids of computers. The numerical derivatives needed to compute the G matrix in curvilinear, internal coordinates are obtained from an adapted Richardson extrapolation. The procedure is optimized to maximize the number of significant digits in the derivatives. Using the program, we compute the vibrational kinetic terms for several simultaneous torsional motions in Glycolaldehyde, Methyl formate and Ethyl methyl ether. The results show the existence of an important coupling among the torsional vibration modes.

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Section: Program Descriptionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Accurate Numerical Computation of Rovibrational G Matrices in Molecules of Arbitrary Size

Castro

Niño

Muñoz‐Caro

Computational Science and Its Applications – ICCSA 2008

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“…The data are generated from molecular electronic structure (ab initio) calculations. The goal is to collect the information obtained in molecular hypersurface scans performed in computational Grid environments as described in [9]. The different structures defining the scan are generated as a function of vibrational coordinates.…”

Section: Molecular Spectroscopic Simulations Markupmentioning

confidence: 99%

“…This approach has been used to accurately simulate rovibrational spectra in semi-rigid and non-rigid molecules, see for instance [6], [7], [8], and references therein. To deal with problems of large size, a methodology for the automatic mapping of potential energy hypersurfaces has been developed for working on Internet-based Grids of computers [9]. Here, a set of different molecular structures are generated and submitted for computation in the Grid and the results are collected in a single file.…”

Section: Introductionmentioning

confidence: 99%

MSSML: A Molecular Spectroscopic Simulations Markup Language for Rovibrational Studies

Díaz

Reyes

Muñoz‐Caro

et al.

Computational Science and Its Applications – ICCSA 2008

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Abstract. This work presents the development of an XML based language for the standardization of the information needed to build molecular rovibrational hamiltonians. This Molecular Spectroscopic Simulations Markup Language (MSSML) allows to collect and represent in a unified way the information obtained from electronic structure calculations performed in heterogeneous distributed systems, such as Internet-based Grids of computers. This standard language will permit the use of a web (Grid) services approach to automate the simulation of rovibrational spectra.

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“…• Química Teórica En ciencias moleculares, se dispone de ejemplos que utilizan técnicas híbridas de dinámica molecular y Monte Carlo, lo que implica el afinado de varios parámetros [12], [13], [14], [15]. Otro ejemplo, es la obtención de la hipersuperficie de energía potencial molecular [16]. También se encuentran simulaciones, usando el simulador Monte Carlo de microfisiología celular MCell, que permiten representar reacciones químicas o la difusión de moléculas en espacios 3-D complejos [17].…”

Section: • Bioinformáticaunclassified

Desarrollo de un workflow genérico para el modelado de problemas de barrido paramétrico en sistemas distribuidos

Reyes Ávila

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This work presents the development and experimental validation of a generic workflow model applicable to any parameter sweep problem: the Parameter Sweep Scientific Workflow (PSWF) model. As part of it, a model for the monitoring and management of scientific workflows on distributed systems is developed. This model, Star Superscalar Status (SsTAT), is applicable to the StarSs programming model family. PSWF and SsTAT can be used by the scientific community as a reference for solving problems using the parameter sweep strategy. As an integral part of the work, the treatment of the parameter sweep problem is formalized. This is achieved by developing a general solution based on the PSNSS (Parameter Sweep Nested Summation Symbol) algorithm, using both the original sequential and a concurrent approach. Both versions are implemented and validated, showing its applicability to all automatable PSWF lifecycle phases. Load testing shows that large-scale parameter sweep problems can efficiently be addressed with the proposed approach. In addition, the SsTAT monitoring and management generic model is instantiated for a Grid environment. Thus, an operational implementation of SsTAT based on GRIDSs, GSTAT (GRID Superscalar Status), is developed. A series of tests performed on an actual heterogeneous Grid of computers shows that GSTAT can appropriately develop their functionality even in an environment so demanding as that. As a practical case, the model proposed here is applied to determining the molecular potential energy hypersurfaces. For this purpose, a specific instance of the workflow, called PSHYP (Parameter Sweep Hypersurfaces), is created. En este trabajo se presenta el desarrollo y validación experimental de un modelo de workflow genérico, aplicable a cualquier problema de barrido de parámetros, denominado Parameter Sweep Scientific Workflow (PSWF). Asimismo, se diseña y prueba un modelo de monitorización y gestión de workflows científicos, en sistemas distribuidos, designado como SsTAT (Star Superscalar Status) que es aplicable a la familia de modelos de programación Star Superscalar (StarSs). Los modelos PSWF y SsTAT pueden ser utilizados por la comunidad científica como referencia a la hora de resolver problemas mediante la estrategia de barrido de parámetros. Como parte integral del trabajo se formaliza el tratamiento del problema del barrido de parámetros, desarrollándose una solución general concretada en el algoritmo PSNSS (Parameter Sweep Nested Summation Symbol) en su versión secuencial y concurrente. Ambas versiones se implementan y validan, mostrándose su aplicabilidad a todas las fases automatizables del ciclo de vida PSWF. Mediante la realización de varias pruebas de carga se comprueba que el tratamiento de problemas de barrido de parámetros de gran envergadura puede abordarse eficientemente con la aproximación propuesta. A su vez, el modelo genérico de monitorización y gestión SsTAT se particulariza para un entorno Grid, generándose una implementación operativa del mismo, basada en GRIDSs, denominada GSTAT (GRID Superscalar Status). La realización de una serie de pruebas sobre un Grid real de computadores heterogéneo muestra que GSTAT desarrolla apropiadamente sus funciones incluso en un entorno tan exigente como este. Como caso práctico, se aplica el modelo aquí propuesto a la obtención de la hipersuperficie de energía potencial molecular generando a tal efecto un workflow específico denominado PSHYP (Parameter Sweep Hypersurfaces)

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Performance of computationally intensive parameter sweep applications on Internet‐based Grids of computers: the mapping of molecular potential energy hypersurfaces

Cited by 10 publications

References 39 publications

Accurate Numerical Computation of Rovibrational G Matrices in Molecules of Arbitrary Size

Accurate Numerical Computation of Rovibrational G Matrices in Molecules of Arbitrary Size

MSSML: A Molecular Spectroscopic Simulations Markup Language for Rovibrational Studies

Desarrollo de un workflow genérico para el modelado de problemas de barrido paramétrico en sistemas distribuidos

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