Large Scale Parallel Molecular Dynamics Simulations

Hedman, Fredrik; Laaksonen, Aatto

doi:10.1016/s1380-7323(99)80040-5

Cited by 3 publications

(5 citation statements)

References 107 publications

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“…In a first implementation [56,57], we used the libraries FFTW [58] and NFFT [54]. Details of the accuracy and scaling properties can be found in reference papers.…”

Section: Implementation and Resultsmentioning

confidence: 99%

Non-Uniform FFT and Its Applications in Particle Simulations

Wang¹,

Hedman²,

Porcu³

et al. 2014

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“…In a first implementation [56,57], we used the libraries FFTW [58] and NFFT [54]. Details of the accuracy and scaling properties can be found in reference papers.…”

Section: Implementation and Resultsmentioning

confidence: 99%

Non-Uniform FFT and Its Applications in Particle Simulations

Wang¹,

Hedman²,

Porcu³

et al. 2014

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“…For SYCL, while implementation details may diverge, our approach allows the SYCL runtime to directly invoke the PIM library for host-initiated PIM operations. For Fortran code with PIM directive, Flang parses and produces a series of MLIR, which is the mixture of FIR, PIM IR, and ACC IR [30]. Our Flang is based on Flacc to support the existing directive together to satisfy requirement R3.…”

Section: Processing-in-memory (Pim)mentioning

confidence: 99%

Programming Model Extensions for General-Purpose Processing-In-Memory

Hong,

Sommer,

Kim

et al. 2024

ISC High Performance 2024 Research Paper Proceedings (39th International Conference)

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The performance of many applications is limited by the available memory bandwidth. One approach to improve the performance of such memory-bound applications is to move the computation closer to the required data. Processing In Memory (PIM) integrates computational units directly with the memory. To enable PIM technology in widely used programming models, we propose extensions to OpenMP and OpenACC, two examples of directive-based programming models, as well as SYCL. The extensions are designed to be portable across many existing and future parallel computing devices and platforms, making PIM technology widely available.For the extensions, we propose an end-to-end compilation framework based on several steps of abstraction and progressive lowering. To achieve this goal, we formulate a new PIM IR and conduct optimizations tailored to hardware characteristics. By using AMD MI100 GPU with PIM-enabled HBM2 memory, we observe a performance improvement of 1.2-2.1 times for representative examples and a real high-performance computing (HPC) application compared to the same GPU without PIMenabled memory.

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“…After the calculation of structure factor S (n), using the symmetry of S (n) around the origin can reduce the calculations of electrostatic energy . The calculations of electrostatic energy and

\hat{w} true[normaln true]

are also bundled together in a single loop to improve the efficiency in both new ENUF and CU‐ENUF.…”

Section: Acceleration In Reciprocal Spacementioning

confidence: 99%

“…With a theoretical accuracy δ ≪1, we will make the values of eqs. and less than or equal to δ at cutoffs r c, and k c , respectively, which results in the following mathematic relations (16) and (17) . The relations of those parameters can be described as:

erfc (α r_{c}) \approx \exp (- α^{2} r_{c}^{2}) \leq δ \Rightarrow r_{c} \geq \frac{\sqrt{- \ln (δ)}}{α},

\begin{matrix} \exp true(- {(π k_{c} / α L)}^{2} true) \leq δ \\ \Rightarrow k_{c} \geq \frac{α L}{π} \sqrt{- \ln (δ)} \Rightarrow k_{c} \propto L . \end{matrix}

…”

Section: Tests For Accuracy and Performancementioning

confidence: 99%

“…Particularly, the ENUF method, which refers to Ewald summation method based on nonequispaced fast Fourier transform or nonuniform fast Fourier transform (NFFT) technique developed by Laaksonen and coworkers, is an easy‐to‐implement, and efficient method for calculating long‐range electrostatic interactions. The NFFT is a generalization of the FFT, and can be applied to nonequispaced points for Fourier transform.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

et al. 2015

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We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new algorithm is developed for NFFT for the evaluations of electrostatic interaction energies and forces. Both real-space and reciprocal-space computations are further accelerated by using graphical processing units (GPU) with CUDA technology. Especially, the use of CUNFFT (NFFT based on CUDA) very much reduces the reciprocal-space computation. In order to reach the best performance of this method, we propose a procedure for the selection of optimal parameters with controlled accuracies. With the choice of suitable parameters, we show that our method is a good alternative to the standard Ewald method with the same computational precision but a dramatically higher computational efficiency.

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Large Scale Parallel Molecular Dynamics Simulations

Cited by 3 publications

References 107 publications

Non-Uniform FFT and Its Applications in Particle Simulations

Non-Uniform FFT and Its Applications in Particle Simulations

Programming Model Extensions for General-Purpose Processing-In-Memory

Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

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