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Register a new userA Portable Implementation of RANLUX++
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High energy physics has a constant demand for random number generators (RNGs) with high statistical quality. In this paper, we present ROOTs implementation of the RANLUX++ generator. We discuss the choice of relying only on standard C++ for portability reasons. Building on an initial implementation, we describe a set of optimizations to increase generator speed. This allows to reach performance very close to the original assembler version. We test our implementation on an Apple M1 and Nvidia GPUs to demonstrate the advantages of portable code.
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Recently, Dammak and coworkers (H. Dammak, Y. Chalopin, M. Laroche, M. Hayoun, and J.J. Greffet. Quantumthermal bath for molecular dynamics simulation. Phys. Rev. Lett., 103:190601, 2009.) proposed that the quantum statistics of vibrations in condensed systems at low temperature could be simulated by running molecular dynamics simulations in the presence of a colored noise with an appropriate power spectral density. In the present contribution, we show how this method can be implemented in a flexible manner and at a low computational cost by synthesizing the corresponding noise on the fly. The proposed algorithm is tested for a simple harmonic chain as well as for a more realistic model of aluminium crystal. The energy and Debye-Waller factor are shown to be in good agreement with those obtained from harmonic approximations based on the phonon spectrum of the systems. The limitations of the method associated with anharmonic effects are also briefly discussed. Some perspectives for disordered materials and heat transfer are considered.
Empirical Dynamic Modeling (EDM) is a state-of-the-art non-linear time-series analysis framework. Despite its wide applicability, EDM was not scalable to large datasets due to its expensive computational cost. To overcome this obstacle, researchers have attempted and succeeded in accelerating EDM from both algorithmic and implementational aspects. In previous work, we developed a massively parallel implementation of EDM targeting HPC systems (mpEDM). However, mpEDM maintains different backends for different architectures. This design becomes a burden in the increasingly diversifying HPC systems, when porting to new hardware. In this paper, we design and develop a performance-portable implementation of EDM based on the Kokkos performance portability framework (kEDM), which runs on both CPUs and GPUs while based on a single codebase. Furthermore, we optimize individual kernels specifically for EDM computation, and use real-world datasets to demonstrate up to $5.5times$ speedup compared to mpEDM in convergent cross mapping computation.
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number of time-steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). We illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster.
A multiphysics finite volume method (FVM) solver, coupling neutronics and shock physics, is under development at Politecnico di Milano for the analysis of shock imploding fissile materials [1]. The proposed solver can be a useful tool to make preliminary safety assessment of subcritical plutonium experiments [2] and, more in general, to perform criticality safety evaluations in case of strongly energetic events (such as chemical explosions) involving fissile materials [3]. To this aim, a multi-group SP3 neutron transport model is coupled with a hydrodynamic shock physics model [4], suitable to describe the propagation of strong shockwaves in solid materials. The shock physics module implements a dynamic mesh to reproduce material deformations and its governing equations are written in an Arbitrary Lagrangian Eulerian (ALE) formulation to preserve the mesh quality in case of large distortions.
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