We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed memory computers. As a result, the new version can easily handle larger molecules or situations with higher accuracy requirements. To demonstrate the updated code, we applied the new version to a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles, and were able to reduce the time-to-solution from 10 hours reported in the previous release on a shared memory computer to less than 30 seconds on a Cray XC30 cluster using 12, 288 cores.Programming language: C++ Supplementary material: Journal reference of previous version: AEGB v2 0 Does the new version supersede the previous version?: Yes Reasons for the new version: Memory requirement and time-to-solution for large molecules of interest exceed the capacity of shared memory computers. Summary of revisions: The revision extends the AFMPB to operate on distributed memory computers using the DASHMM [1, 2] library. Nature of problem: Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Solution method: The linearized Poisson-Boltzmann equation is reformulated as a boundary integral equation and is subsequently discretized using the node-patch scheme. The resulting linear system is solved using GMRES. Within each iteration, the matrix-vector multiplication is accelerated using the DASHMM library on distributed memory computers.
We present version 1.2.0 of DASHMM, a general library implementing hierarchical multipole methods using the asynchronous multi-tasking HPX-5 runtime system. Compared with the previous release [10], this new version: (1) enables execution in both shared and distributed memory architectures; (2) extends DASHMM's infrastructure to support advanced multipole methods [18]; and (3) provides built-in implementations of both the Yukawa [15] potential and Helmholtz [16] potential in the low frequency regime. These additions have not impacted the user interface, which remains simple and extensible.
Methods to solve the relativistic hydrodynamic equations are a key computational kernel in a large number of astrophysics simulations and are crucial to understanding the electromagnetic signals that originate from the merger of astrophysical compact objects. Because of the many physical length scales present when simulating such mergers, these methods must be highly adaptive and capable of automatically resolving numerous localized features and instabilities that emerge throughout the computational domain across many temporal scales. While this has been historically accomplished with adaptive mesh refinement (AMR) based methods, alternatives based on wavelet bases and the wavelet transformation have recently achieved significant success in adaptive representation for advanced engineering applications. This work presents a new method for the integration of the relativistic hydrodynamic equations using iterated interpolating wavelets and introduces a highly adaptive implementation for multidimensional simulation. The wavelet coefficients provide a direct measure of the local approximation error for the solution and place collocation points that naturally adapt to the fluid flow while providing good conservation of fluid quantities. The resulting implementation, oahu, is applied to a series of demanding one-and two-dimensional problems which explore high Lorentz factor outflows and the formation of several instabilities, including the Kelvin-Helmholtz instability and the Rayleigh-Taylor instability.
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