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Eric J. Bylaska - One of the best experts on this subject based on the ideXlab platform.
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NWChem: scalable parallel Computational Chemistry
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011Co-Authors: H.j.j. Van Dam, Eric J. Bylaska, Tjerk P Straatsma, W. A. De Jong, Niranjan Govind, Karol Kowalski, Marat ValievAbstract:NWChem is a general purpose Computational Chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient Computational Chemistry code with high parallel scalability. NWChem is a modern, open source, Computational Chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This codemore » design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in Computational Chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose Computational Chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.« less
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Advances in Scalable Computational Chemistry: NWChem
Annual Reports in Computational Chemistry, 2011Co-Authors: Tjerk P Straatsma, Eric J. Bylaska, H.j.j. Van Dam, W. A. De Jong, N. Govind, K. Kowalski, M. ValievAbstract:Abstract NWChem is the highly scalable Computational Chemistry software package developed by the Molecular Sciences Software group for the Environmental Molecular Sciences Laboratory. The software provides a wide range of capabilities for quantum mechanical and classical mechanical modeling and simulation of chemical and biological systems. The software infrastructure has been designed to facilitate the rapid development and integration of new application modules with a convenient mechanism to enable large-scale computations that rely on a combination of methodologies to be used. Built using the partitioned global address space-based Global Arrays programming model, the design of the software separates the architecture-dependent communication layer from the Computational Chemistry modules. This results in a highly portable code in which only a relatively small part of the code needs to be ported to new computer architectures.
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Utilizing high performance computing for Chemistry: parallel Computational Chemistry.
Physical chemistry chemical physics : PCCP, 2010Co-Authors: Wibe A. De Jong, Eric J. Bylaska, Niranjan Govind, Karol Kowalski, Curtis L. Janssen, Thomas J. J. Müller, Ida M. B. Nielsen, Hubertus Van Dam, Valera Veryazov, Roland LindhAbstract:Parallel hardware has become readily available to the Computational Chemistry research community. This perspective will review the current state of parallel Computational Chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum Chemistry methodologies, algorithms, and software development will also be discussed.
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High performance Computational Chemistry: an overview of NWChem a distributed parallel application
2000Co-Authors: Ricky a. Kendall, Jeffrey a. Nichols, Eric J. Bylaska, David E Bernholdt, Theresa L. Windus, Michel Dupuis, George I. Fann, Jialin Ju, Tjerk P Straatsma, Jarek Nieplocha, Edoardo Apra, R. J. Harrison, Adrian T. WongAbstract:NWChem is the software package for Computational Chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. The architecture facilitates rapid development and portability of fully distributed applications modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.
Tjerk P Straatsma - One of the best experts on this subject based on the ideXlab platform.
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NWChem: scalable parallel Computational Chemistry
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011Co-Authors: H.j.j. Van Dam, Eric J. Bylaska, Tjerk P Straatsma, W. A. De Jong, Niranjan Govind, Karol Kowalski, Marat ValievAbstract:NWChem is a general purpose Computational Chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient Computational Chemistry code with high parallel scalability. NWChem is a modern, open source, Computational Chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This codemore » design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in Computational Chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose Computational Chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.« less
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Advances in Scalable Computational Chemistry: NWChem
Annual Reports in Computational Chemistry, 2011Co-Authors: Tjerk P Straatsma, Eric J. Bylaska, H.j.j. Van Dam, W. A. De Jong, N. Govind, K. Kowalski, M. ValievAbstract:Abstract NWChem is the highly scalable Computational Chemistry software package developed by the Molecular Sciences Software group for the Environmental Molecular Sciences Laboratory. The software provides a wide range of capabilities for quantum mechanical and classical mechanical modeling and simulation of chemical and biological systems. The software infrastructure has been designed to facilitate the rapid development and integration of new application modules with a convenient mechanism to enable large-scale computations that rely on a combination of methodologies to be used. Built using the partitioned global address space-based Global Arrays programming model, the design of the software separates the architecture-dependent communication layer from the Computational Chemistry modules. This results in a highly portable code in which only a relatively small part of the code needs to be ported to new computer architectures.
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High performance Computational Chemistry: an overview of NWChem a distributed parallel application
2000Co-Authors: Ricky a. Kendall, Jeffrey a. Nichols, Eric J. Bylaska, David E Bernholdt, Theresa L. Windus, Michel Dupuis, George I. Fann, Jialin Ju, Tjerk P Straatsma, Jarek Nieplocha, Edoardo Apra, R. J. Harrison, Adrian T. WongAbstract:NWChem is the software package for Computational Chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. The architecture facilitates rapid development and portability of fully distributed applications modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.
Peter Murrayrust - One of the best experts on this subject based on the ideXlab platform.
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the semantics of chemical markup language cml for Computational Chemistry compchem
Journal of Cheminformatics, 2012Co-Authors: Weerapong Phadungsukanan, Markus Kraft, Joseph A Townsend, Peter MurrayrustAbstract:This paper introduces a subdomain Chemistry format for storing Computational Chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding Computational Chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum Chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common Computational Chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.
Niranjan Govind - One of the best experts on this subject based on the ideXlab platform.
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NWChem: scalable parallel Computational Chemistry
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011Co-Authors: H.j.j. Van Dam, Eric J. Bylaska, Tjerk P Straatsma, W. A. De Jong, Niranjan Govind, Karol Kowalski, Marat ValievAbstract:NWChem is a general purpose Computational Chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient Computational Chemistry code with high parallel scalability. NWChem is a modern, open source, Computational Chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This codemore » design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in Computational Chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose Computational Chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.« less
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Utilizing high performance computing for Chemistry: parallel Computational Chemistry.
Physical chemistry chemical physics : PCCP, 2010Co-Authors: Wibe A. De Jong, Eric J. Bylaska, Niranjan Govind, Karol Kowalski, Curtis L. Janssen, Thomas J. J. Müller, Ida M. B. Nielsen, Hubertus Van Dam, Valera Veryazov, Roland LindhAbstract:Parallel hardware has become readily available to the Computational Chemistry research community. This perspective will review the current state of parallel Computational Chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum Chemistry methodologies, algorithms, and software development will also be discussed.
Karol Kowalski - One of the best experts on this subject based on the ideXlab platform.
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NWChem: scalable parallel Computational Chemistry
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011Co-Authors: H.j.j. Van Dam, Eric J. Bylaska, Tjerk P Straatsma, W. A. De Jong, Niranjan Govind, Karol Kowalski, Marat ValievAbstract:NWChem is a general purpose Computational Chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient Computational Chemistry code with high parallel scalability. NWChem is a modern, open source, Computational Chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This codemore » design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in Computational Chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose Computational Chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.« less
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Utilizing high performance computing for Chemistry: parallel Computational Chemistry.
Physical chemistry chemical physics : PCCP, 2010Co-Authors: Wibe A. De Jong, Eric J. Bylaska, Niranjan Govind, Karol Kowalski, Curtis L. Janssen, Thomas J. J. Müller, Ida M. B. Nielsen, Hubertus Van Dam, Valera Veryazov, Roland LindhAbstract:Parallel hardware has become readily available to the Computational Chemistry research community. This perspective will review the current state of parallel Computational Chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum Chemistry methodologies, algorithms, and software development will also be discussed.