Publications

Clausen, Jonathan C.; Brunini, Victor B.; Forster, Christopher J.; Noble, David R.; Trott, Christian R.; Hammond, Simon D.; Hoemmen, Mark F.; Lin, Paul L.

Abstract not provided.

Trott, Christian R.; Shipman, Galen S.; Lopez, Graham L.

Abstract not provided.

Thompson, Aidan P.; Trott, Christian R.

Within the EXAALT project, the SNAP [1] approach is being used to develop high accuracy potentials for use in large-scale long-time molecular dynamics simulations of materials behavior. In particular, we have developed a new SNAP potential that is suitable for describing the interplay between helium atoms and vacancies in high-temperature tungsten[2]. This model is now being used to study plasma-surface interactions in nuclear fusion reactors for energy production. The high-accuracy of SNAP potentials comes at the price of increased computational cost per atom and increased computational complexity. The increased cost is mitigated by improvements in strong scaling that can be achieved using advanced algorithms [3].

Trott, Christian R.

Abstract not provided.

Caday, Peter C.; Hoemmen, Mark F.; Hollman, David S.; Liber, Nevin L.; Lo, Li-Ta L.; Lopez, Graham L.; Luszczek, Piotr L.; Knepper, Sarah K.; Trott, Christian R.

Abstract not provided.

Foiles, Stephen M.; Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.

Abstract not provided.

International Journal of High Performance Computing Applications

Levy, Scott; Ferreira, Kurt; Bridges, Patrick G.; Thompson, Aidan P.; Trott, Christian R.

Building the next-generation of extreme-scale distributed systems will require overcoming several challenges related to system resilience. As the number of processors in these systems grow, the failure rate increases proportionally. One of the most common sources of failure in large-scale systems is memory. In this paper, we propose a novel runtime for transparently exploiting memory content similarity to improve system resilience by reducing the rate at which memory errors lead to node failure. We evaluate the viability of this approach by examining memory snapshots collected from eight high-performance computing (HPC) applications and two important HPC operating systems. Based on the characteristics of the similarity uncovered, we conclude that our proposed approach shows promise for addressing system resilience in large-scale systems.

Ferreira, Kurt; Thompson, Aidan P.; Trott, Christian R.; Levy, Scott L.

Abstract not provided.

Rajamanickam, Sivasankaran R.; Bradley, Andrew M.; Deveci, Mehmet D.; Kim, Kyungjoo K.; Trott, Christian R.

Abstract not provided.

Cook, Jeanine C.; Edwards, Harold C.; Dinge, Dennis D.; Glass, Micheal W.; Hammond, Simon D.; Hoekstra, Robert J.; Lin, Paul L.; Rajan, Mahesh R.; Trott, Christian R.; Vaughan, Courtenay T.

Abstract not provided.

Hammond, Simon D.; Trott, Christian R.; Lin, Paul L.; Vaughan, Courtenay T.; Cook, Jeanine C.; Dinge, Dennis D.; Pase, Douglas M.; Benner, R.E.; Hoekstra, Robert J.

Abstract not provided.

Trott, Christian R.; Hammond, Simon D.; Dinge, Dennis D.; Lin, Paul L.; Vaughan, Courtenay T.; Cook, Jeanine C.; Rajan, Mahesh R.; Edwards, Harold C.; Hoekstra, Robert J.

For the FY15 ASC L2 Trilab Codesign milestone Sandia National Laboratories performed two main studies. The first study investigated three topics (performance, cross-platform portability and programmer productivity) when using OpenMP directives and the RAJA and Kokkos programming models available from LLNL and SNL respectively. The focus of this first study was the LULESH mini-application developed and maintained by LLNL. In the coming sections of the report the reader will find performance comparisons (and a demonstration of portability) for a variety of mini-application implementations produced during this study with varying levels of optimization. Of note is that the implementations utilized including optimizations across a number of programming models to help ensure claims that Kokkos can provide native-class application performance are valid. The second study performed during FY15 is a performance assessment of the MiniAero mini-application developed by Sandia. This mini-application was developed by the SIERRA Thermal-Fluid team at Sandia for the purposes of learning the Kokkos programming model and so is available in only a single implementation. For this report we studied its performance and scaling on a number of machines with the intent of providing insight into potential performance issues that may be experienced when similar algorithms are deployed on the forthcoming Trinity ASC ATS platform.

Edwards, Harold C.; Trott, Christian R.

This report outlines the research, development, and support requirements for the Advanced Simulation and Computing (ASC ) Advanced Technology, Development, and Mitigation (ATDM) Performance Portability (a.k.a., Kokkos) project for 2015 - 2019 . The research and development (R&D) goal for Kokkos (v2) has been to create and demonstrate a thread - parallel programming model a nd standard C++ library - based implementation that enables performance portability across diverse manycore architectures such as multicore CPU, Intel Xeon Phi, and NVIDIA Kepler GPU. This R&D goal has been achieved for algorithms that use data parallel pat terns including parallel - for, parallel - reduce, and parallel - scan. Current R&D is focusing on hierarchical parallel patterns such as a directed acyclic graph (DAG) of asynchronous tasks where each task contain s nested data parallel algorithms. This five y ear plan includes R&D required to f ully and performance portably exploit thread parallelism across current and anticipated next generation platforms (NGP). The Kokkos library is being evaluated by many projects exploring algorithm s and code design for NGP. Some production libraries and applications such as Trilinos and LAMMPS have already committed to Kokkos as their foundation for manycore parallelism an d performance portability. These five year requirements includes support required for current and antic ipated ASC projects to be effective and productive in their use of Kokkos on NGP. The greatest risk to the success of Kokkos and ASC projects relying upon Kokkos is a lack of staffing resources to support Kokkos to the degree needed by these ASC projects. This support includes up - to - date tutorials, documentation, multi - platform (hardware and software stack) testing, minor feature enhancements, thread - scalable algorithm consulting, and managing collaborative R&D.

Thompson, Aidan P.; Schultz, Peter A.; Crozier, Paul C.; Moore, Stan G.; Swiler, Laura P.; Stephens, John A.; Trott, Christian R.; Foiles, Stephen M.; Tucker, Garritt J.

This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (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 on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients 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. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers and advanced processor ar- chitectures. Finally, we briefly describe the MSM method for efficient calculation of electrostatic interactions on massively parallel computers.

Thompson, Aidan P.; Schultz, Peter A.; Swiler, Laura P.; Trott, Christian R.; Tucker, Garritt T.; Foiles, Stephen M.

Abstract not provided.

Phipps, Eric T.; Pawlowski, Roger P.; Trott, Christian R.

Abstract not provided.

Trott, Christian R.

Abstract not provided.

Rajamanickam, Sivasankaran R.; Berger-Vergiat, Luc B.; Dang, Vinh Q.; Ellingwood, Nathan D.; Kim, Kyungjoo K.; McLendon, William C.; Trott, Christian R.; Wilke, Jeremiah J.

Abstract not provided.

Trott, Christian R.; Hammond, Simon D.

Abstract not provided.

Hammond, Simon D.; Trott, Christian R.; Vaughan, Courtenay T.; Dinge, Dennis D.; Lin, Paul L.; Pase, Douglas M.; Benner, R.E.; Cook, Jeanine C.; Hoekstra, Robert J.

Abstract not provided.

Wilke, Jeremiah J.; Trott, Christian R.; Edwards, Harold C.; Glass, Micheal W.; Clay, Robert L.

Abstract not provided.

Trott, Christian R.

Abstract not provided.

Trott, Christian R.

Abstract not provided.

Trott, Christian R.

Abstract not provided.

Pawlowski, Roger P.; Phillips, Edward G.; Shadid, John N.; Lin, Paul L.; Cyr, Eric C.; Conde, Sidafa C.; Bettencourt, Matthew T.; Phipps, Eric T.; Trott, Christian R.

Abstract not provided.