Landau Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures

The Landau collision integral is an accurate model for the small-angle dominated Coulomb collisions in fusion plasmas. We investigate a high order accurate, fully conservative, finite element discretization of the nonlinear multi-species Landau integral with adaptive mesh refinement using the PETSc library (www.mcs.anl.gov/petsc). We develop algorithms and techniques to efficiently utilize emerging architectures with an approach that minimizes memory usage and movement and is suitable for vector processing. The Landau collision integral is vectorized with Intel AVX-512 intrinsics and the solver sustains as much as 22% of the theoretical peak flop rate of the Second Generation Intel Xeon Phi, Knights Landing, processor

Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory

We present two open-source (BSD) implementations of ellipsoidal harmonic expansions for solving problems of potential theory using separation of variables. Ellipsoidal harmonics are used surprisingly infrequently, considering their substantial value for problems ranging in scale from molecules to the entire solar system. In this article, we suggest two possible reasons for the paucity relative to spherical harmonics. The first is essentially historical---ellipsoidal harmonics developed during the late 19th century and early 20th, when it was found that only the lowest-order harmonics are expressible in closed form. Each higher-order term requires the solution of an eigenvalue problem, and tedious manual computation seems to have discouraged applications and theoretical studies. The second explanation is practical: even with modern computers and accurate eigenvalue algorithms, expansions in ellipsoidal harmonics are significantly more challenging to compute than those in Cartesian or spherical coordinates. The present implementations reduce the "barrier to entry" by providing an easy and free way for the community to begin using ellipsoidal harmonics in actual research. We demonstrate our implementation using the specific and physiologically crucial problem of how charged proteins interact with their environment, and ask: what other analytical tools await re-discovery in an era of inexpensive computation?Comment: 25 pages, 3 figure

Optimizing the Evaluation of Finite Element Matrices

Assembling stiffness matrices represents a significant cost in many finite element computations. We address the question of optimizing the evaluation of these matrices. By finding redundant computations, we are able to significantly reduce the cost of building local stiffness matrices for the Laplace operator and for the trilinear form for Navier-Stokes. For the Laplace operator in two space dimensions, we have developed a heuristic graph algorithm that searches for such redundancies and generates code for computing the local stiffness matrices. Up to cubics, we are able to build the stiffness matrix on any triangle in less than one multiply-add pair per entry. Up to sixth degree, we can do it in less than about two. Preliminary low-degree results for Poisson and Navier-Stokes operators in three dimensions are also promising