The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) ...applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. A major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diverse manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos’ abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. The Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries.
•We developed a performance portable programming model (PM) for manycore devices.•Unifying parallel dispatch and data layout is mandatory for performance portability.•The Kokkos C++library implements this PM with pthreads, OpenMP, and CUDA back-ends.•Demonstrate Xeon Phi and NVIDIA GPU performance portability with mini-applications.•Recommend a strategy for legacy application codes to migrate to manycore.
We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to ...reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential 1. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.
As the push towards exascale hardware has increased the diversity of system architectures, performance portability has become a critical aspect for scientific software. We describe the Kokkos ...Performance Portable Programming Model that allows developers to write single source applications for diverse high performance computing architectures. Kokkos provides key abstractions for both the compute and memory hierarchy of modern hardware. We describe the novel abstractions that have been added to Kokkos recently such as hierarchical parallelism, containers, task graphs, and arbitrary-sized atomic operations. We demonstrate the performance of these new features with reproducible benchmarks on CPUs and GPUs.
Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to ...simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.
The manycore revolution in computational hardware can be characterized by increasing thread counts, decreasing memory per thread, and architecture specific performance constraints for memory access ...patterns. High performance computing (HPC) on emerging many core architectures requires codes to exploit every opportunity for thread-level parallelism and satisfy conflicting performance constraints. We developed the Kokkos C++ library to provide scientific and engineering codes with a user accessible many core performance portable programming model. The two foundational abstractions of Kokkos are (1) dispatch work to a many core device for parallel execution and (2) manage multidimensional arrays with polymorphic layouts. The integration of these abstractions enables users' code to satisfy multiple architecture specific memory access pattern performance constraints without having to modify their source code. In this paper we describe the Kokkos abstractions, summarize its application programmer interface (API), and present performance results for a molecular dynamics computational kernel and finite element mini-application.
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