Alistair Rendell

Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi

Publisher: American Chemical Society (ACS)

Date: 24-02-2014

DOI: 10.1021/CT4010596

Abstract: Increasingly, modern computer systems comprise a multicore general-purpose processor augmented with a number of special purpose devices or accelerators connected via an external interface such as a PCI bus. The NVIDIA Kepler Graphical Processing Unit (GPU) and the Intel Phi are two ex les of such accelerators. Accelerators offer peak performances that can be well above those of the host processor. How to exploit this heterogeneous environment for legacy application codes is not, however, straightforward. This paper considers how matrix operations in typical quantum chemical calculations can be migrated to the GPU and Phi systems. Double precision general matrix multiply operations are endemic in electronic structure calculations, especially methods that include electron correlation, such as density functional theory, second order perturbation theory, and coupled cluster theory. The use of approaches that automatically determine whether to use the host or an accelerator, based on problem size, is explored, with computations that are occurring on the accelerator and/or the host. For data-transfers over PCI-e, the GPU provides the best overall performance for data sizes up to 4096 MB with consistent upload and download rates between 5-5.6 GB/s and 5.4-6.3 GB/s, respectively. The GPU outperforms the Phi for both square and nonsquare matrix multiplications.

Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10

Publisher: Wiley

Date: 11-09-2014

DOI: 10.1002/JCC.23720

Abstract: Use of the modern parallel programming language X10 for computing long-range Coulomb and exchange interactions is presented. By using X10, a partitioned global address space language with support for task parallelism and the explicit representation of data locality, the resolution of the Ewald operator can be parallelized in a straightforward manner including use of both intranode and internode parallelism. We evaluate four different schemes for dynamic load balancing of integral calculation using X10's work stealing runtime, and report performance results for long-range HF energy calculation of large molecule/high quality basis running on up to 1024 cores of a high performance cluster machine.

Reinforcement learning for automated performance tuning: Initial evaluation for sparse matrix format selection

Publisher: IEEE

Date: 09-2008

DOI: 10.1109/CLUSTR.2008.4663802

PGAS-FMM: Implementing a distributed fast multipole method using the X10 programming language

Publisher: Wiley

Date: 17-05-2014

DOI: 10.1002/CPE.3039

Generating optimal CUDA sparse matrix–vector product implementations for evolving GPU hardware

Publisher: Wiley

Date: 17-04-2011

DOI: 10.1002/CPE.1732

First Principles Study of Gallium Atom Adsorption on the α-Al₂O₃(0001) Surface

Publisher: American Chemical Society (ACS)

Date: 26-04-2006

DOI: 10.1021/JP057391U

Abstract: The adsorption of Ga atoms in low coverage on the Al-terminated alpha-Al(2)O(3)(0001) surface has been studied theoretically by using first principles periodic boundary condition (PBC) calculations within the framework of the generalized gradient approximation (GGA). Eight possible adsorption sites are investigated, but only two are found to correspond to stationary points. Both of these locations are characterized as hollow sites, with three surrounding surface O atoms and an Al atom in the center located deeper within the Al(2)O(3) slab. The slight difference in the stability of these two sites is due to a difference in the chemical interactions between the Ga atom and the surface O atoms. Strong interactions between the Highest Occupied Molecular Orbital (HOMO) of the Ga atom and the surface state of the Al(2)O(3) surface are observed. This interaction promotes charge transfer from the Ga to the surface Al atoms, which in turn causes the surface Al atoms to move up from the surface.

Effective Use of Dynamic Page Migration on NUMA Platforms: The Gaussian Chemistry Code on the SunFire X4600M2 System

Publisher: IEEE

Date: 2009

DOI: 10.1109/I-SPAN.2009.127

Placing Rigorous Bounds on Numerical Errors in Hartree–Fock Energy Computations

Publisher: American Chemical Society (ACS)

Date: 13-05-2011

DOI: 10.1021/CT200026T

Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound

Publisher: SAGE Publications

Date: 29-04-2015

DOI: 10.1177/1094342015581024

Abstract: Model-based treatment planning and exposimetry for high-intensity focused ultrasound requires the numerical simulation of nonlinear ultrasound propagation through heterogeneous and absorbing media. This is a computationally demanding problem due to the large distances travelled by the ultrasound waves relative to the wavelength of the highest frequency harmonic. Here, the k-space pseudospectral method is used to solve a set of coupled partial differential equations equivalent to a generalised Westervelt equation. The model is implemented in C++ and parallelised using the message passing interface (MPI) for solving large-scale problems on distributed clusters. The domain is partitioned using a 1D slab decomposition, and global communication is performed using a sparse communication pattern. Operations in the spatial frequency domain are performed in transposed space to reduce the communication burden imposed by the 3D fast Fourier transform. The performance of the model is evaluated using grid sizes up to 4096×2048×2048 grid points, distributed over a cluster using up to 1024 compute cores. Given the global nature of the gradient calculation, the model shows good strong scaling behaviour, with a speed-up of 1.7x whenever the number of cores is doubled. This means large-scale simulations can be distributed across high numbers of cores on a cluster to minimise execution times with a relatively small overhead. The efficacy of the model is demonstrated by simulating the ultrasound beam pattern for a high-intensity focused ultrasound sonication of the kidney.

Electronic Effects in Biomolecular Simulations:  Investigation of the KcsA Potassium Ion Channel

Publisher: American Chemical Society (ACS)

Date: 14-08-2004

DOI: 10.1021/JP0487298

Energy-Efficient Computational Chemistry: Comparison of x86 and ARM Systems

Publisher: American Chemical Society (ACS)

Date: 09-10-2015

DOI: 10.1021/ACS.JCTC.5B00713

Abstract: The computational efficiency and energy-to-solution of several applications using the GAMESS quantum chemistry suite of codes is evaluated for 32-bit and 64-bit ARM-based computers, and compared to an x86 machine. The x86 system completes all benchmark computations more quickly than either ARM system and is the best choice to minimize time to solution. The ARM64 and ARM32 computational performances are similar to each other for Hartree-Fock and density functional theory energy calculations. However, for memory-intensive second-order perturbation theory energy and gradient computations the lower ARM32 read/write memory bandwidth results in computation times as much as 86% longer than on the ARM64 system. The ARM32 system is more energy efficient than the x86 and ARM64 CPUs for all benchmarked methods, while the ARM64 CPU is more energy efficient than the x86 CPU for some core counts and molecular sizes.

The design of MPI based distributed shared memory systems to support OpenMP on clusters

Publisher: IEEE

Date: 2007

DOI: 10.1109/CLUSTR.2007.4629236

Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase

Publisher: American Chemical Society (ACS)

Date: 31-08-2002

DOI: 10.1021/JP021070Q

Implementation of 3D FFTs Across Multiple GPUs in Shared Memory Environments

Publisher: IEEE

Date: 12-2012

DOI: 10.1109/PDCAT.2012.79

Programming the Adapteva Epiphany 64-Core Network-on-Chip Coprocessor

Publisher: IEEE

Date: 05-2014

DOI: 10.1109/IPDPSW.2014.112

Ga Cleaning of Al₂O₃ Substrate:  Low Coverage Adsorption of Ga on a Hydrogen-Contaminated α-Al₂O₃(0001) Surface

Publisher: American Chemical Society (ACS)

Date: 02-02-2007

DOI: 10.1021/JP063931R

Modelling the Performance of the Gaussian Chemistry Code on x86 Architectures

Publisher: Springer Berlin Heidelberg

Date: 2008

DOI: 10.1007/978-3-540-79409-7_4

Modelling the Runtime of the Gaussian Computational Chemistry Application and Assessing the Impacts of Microarchitectural Variations

Publisher: Elsevier BV

Date: 2011

DOI: 10.1016/J.PROCS.2011.04.030

First principles study of gallium‐cleaning for hydrogen‐contaminated α‐Al₂O₃(0001) surfaces

Publisher: Wiley

Date: 05-02-2013

DOI: 10.1002/JCC.23236

Abstract: The use of gallium for cleaning hydrogen-contaminated Al2O3 surfaces is explored by performing first principles density functional calculations of gallium adsorption on a hydrogen-contaminated Al-terminated α-Al2O3(0001) surface. Both physisorbed and chemisorbed H-contaminated α-Al2O3(0001) surfaces with one monolayer (ML) gallium coverage are investigated. The thermodynamics of gallium cleaning are considered for a variety of different asymptotic products, and are found to be favorable in all cases. Physisorbed H atoms have very weak interactions with the Al2O3 surface and can be removed easily by the Ga ML. Chemisorbed H atoms form stronger interactions with the surface Al atoms. Bonding energy analysis and departure simulations indicate, however, that chemisorbed H atoms can be effectively removed by the Ga ML.

Non-threaded and Threaded Approaches to MultiRail Communication with uDAPL

Publisher: IEEE

Date: 10-2009

DOI: 10.1109/NPC.2009.10

Modelling The Bacterial Photosynthetic Reaction Center. Vi. Use Of Density-Functional Theory To Determine The Nature Of The Vibronic Coupling Between The Four Lowest-Energy Electronic States Of The Special-Pair Radical Cation

Publisher: AIP Publishing

Date: 24-07-2003

DOI: 10.1063/1.1569910

Abstract: It is now over ten years since the first FTIR spectra were recorded of the radical cation of the special-pair, a dimer of bacteriochlorophyll molecules that forms the primary electron donor responsible for primary charge separation in bacterial photosynthesis. While spectra of this type promise to reveal much concerning the role of the special pair electron donor in photosynthesis, attempts to model and interpret them have been limited by poor knowledge of the vibrationally specific aspects of the electron–phonon coupling and have thus been restricted to crude model calculations only. We develop techniques through which density-functional theory can be employed to evaluate most of the unknown properties. This includes symmetric-mode displacements, antisymmetric-mode vibronic coupling constants, and interstate electronic couplings evaluated for interactions between the four lowest-energy states of the special-pair cation radical: the ground state, the primary hole-transfer state, and states involving these two combined with SHOMO to HOMO transitions. Geometry optimizations are performed for all four states of the dimer while vibrational analyses are obtained for the first two vibronic coupling constants are extracted from analysis of stolen infrared transition moments using Herzberg–Teller theory. Quantitatively, these results are employed in the subsequent paper in this series to simulate the observed spectra. Qualitatively, these results indicate that: (1) vibronic coupling occurs through a large number of antisymmetric modes of the dimer rather than through a small number of strongly active modes, (2) the role of symmetric vibrational motions of the dimer is only minor, (3) that the active symmetric modes are significant in number and low in frequency, (4) that vibronic coupling between the hole-transfer state and the SHOMO to HOMO state is relatively weak and influences spectra only near resonance, and (5) that the calculated electronic couplings are qualitatively realistic and may provide an explanation for the much weaker coupling observed in chlorophyll-containing reaction centers.

The Potassium Ion Channel:  Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential

Publisher: American Chemical Society (ACS)

Date: 15-11-2001

DOI: 10.1021/JP013069H

Comparison of linear‐scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

Publisher: Wiley

Date: 13-08-2002

DOI: 10.1002/JCC.10122

Abstract: QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further ided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.

Automatically generated Coulomb fitting basis sets: Design and accuracy for systems containing H to Kr

Publisher: AIP Publishing

Date: 15-08-2007

DOI: 10.1063/1.2752807

Abstract: For intermediate sized chemical systems the use of an auxiliary basis set (ABS) to fit the charge density provides a useful means of accelerating the performance of various quantum chemical methods. As a consequence much effort has been devoted to the design of various ABSs. This paper explores a fundamentally new approach where the ABS is created dynamically based on the specific orbital basis set (OBS) being used. The new approach includes a parameter that is used to coalesce candidate fitting functions together but which can also be used to provide some coarse grain control over the number of functions in the ABS. The accuracy of the new automatically generated ABS (auto-ABS) is systemically studied for a variety of small systems containing the elements H–Kr. Errors in the Coulomb energy computed using auto-ABS and with a variety of OBSs are shown to be small compared to errors in the Hartree-Fock energy due to incompleteness in the OBS. In contrast to fixed size ABSs, the use of auto-ABS is shown to lead to smaller errors as the size (quality) of the OBS is expanded. The performance of auto-ABS is also compared with the use of the recently proposed universal fitting sets [Weigend, Phys. Chem. Chem. Phys. 8, 1057 (2006)] for 180 compounds containing atoms from H to Kr.

Runtime sparse matrix format selection

Publisher: Elsevier BV

Date: 05-2010

DOI: 10.1016/J.PROCS.2010.04.016

Deterministic global optimization in ab-initio quantum chemistry

Publisher: Springer Science and Business Media LLC

Date: 14-02-2012

DOI: 10.1007/S10898-012-9868-5

Validity of current force fields for simulations on boron nitride nanotubes

Publisher: Institution of Engineering and Technology (IET)

Date: 2010

DOI: 10.1049/MNL.2009.0112

Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method

Publisher: Acoustical Society of America (ASA)

Date: 06-2012

DOI: 10.1121/1.4712021

Abstract: The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required per wavelength for accurate simulations. The model is based on coupled first-order acoustic equations valid for nonlinear wave propagation in heterogeneous media with power law absorption. These are derived from the equations of fluid mechanics and include a pressure-density relation that incorporates the effects of nonlinearity, power law absorption, and medium heterogeneities. The additional terms accounting for convective nonlinearity and power law absorption are expressed as spatial gradients making them efficient to numerically encode. The governing equations are then discretized using a k-space pseudospectral technique in which the spatial gradients are computed using the Fourier-collocation method. This increases the accuracy of the gradient calculation and thus relaxes the requirement for dense computational grids compared to conventional finite difference methods. The accuracy and utility of the developed model is demonstrated via several numerical experiments, including the 3D simulation of the beam pattern from a clinical ultrasound probe.

Resolutions of the Coulomb operator: VII. Evaluation of long-range Coulomb and exchange matrices

Publisher: American Chemical Society (ACS)

Date: 16-01-2013

DOI: 10.1021/CT301110Y

Abstract: Use of the resolution of Ewald operator method for computing long-range Coulomb and exchange interactions is presented. We show that the accuracy of this method can be controlled by a single parameter in a manner similar to that used by conventional algorithms that compute two-electron integrals. Significant performance advantages over conventional algorithms are observed, particularly for high quality basis sets and globular systems. The approach is directly applicable to hybrid density functional theory.

Programming the Adapteva Epiphany 64-core network-on-chip coprocessor

Publisher: SAGE Publications

Date: 27-08-2015

DOI: 10.1177/1094342015599238

Abstract: Energy efficiency is the primary impediment in the path to exascale computing. Consequently, the high-performance computing community is increasingly interested in low-power high-performance embedded systems as building blocks for large-scale high-performance systems. The Adapteva Epiphany architecture integrates low-power RISC cores on a 2D mesh network and promises up to 70 GFLOPS/Watt of theoretical performance. However, with just 32 KB of memory per eCore for storing both data and code, programming the Epiphany system presents significant challenges. In this paper we evaluate the performance of a 64-core Epiphany system with a variety of basic compute and communication micro-benchmarks. Further, we implemented two well known application kernels, 5-point star-shaped heat stencil with a peak performance of 65.2 GFLOPS and matrix multiplication with 65.3 GFLOPS in single precision across 64 Epiphany cores. We discuss strategies for implementing high-performance computing application kernels on such memory constrained low-power devices and compare the Epiphany with competing low-power systems. With future Epiphany revisions expected to house thousands of cores on a single chip, understanding the merits of such an architecture is of prime importance to the exascale initiative.

University Of Sydney

Location: Australia

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Durham University

Location: United Kingdom of Great Britain and Northern Ireland

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Flinders University

Location: Australia

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Discovery Projects - Grant ID: DP0987773

Start Date: 10-2009

End Date: 06-2015

Amount: $360,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0558228

Start Date: 2005

End Date: 12-2008

Amount: $233,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0989872

Start Date: 10-2009

End Date: 12-2013

Amount: $229,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0774896

Start Date: 09-2007

End Date: 12-2011

Amount: $240,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0347178

Start Date: 03-2003

End Date: 12-2005

Amount: $498,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP110200410

Start Date: 07-2011

End Date: 06-2016

Amount: $446,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0669726

Start Date: 06-2007

End Date: 06-2012

Amount: $250,000.00

Funder: Australian Research Council

Special Research Initiatives - Grant ID: SR0354636

Start Date: 2004

End Date: 12-2004

Amount: $30,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP100100588

Start Date: 03-2010

End Date: 12-2014

Amount: $805,000.00

Funder: Australian Research Council