Parallel Implementation of a PETSc-Based Framework for the General Curvilinear Coastal Ocean Model

The General Curvilinear Coastal Ocean Model (GCCOM) is a 3D curvilinear, structured-mesh, non-hydrostatic, large-eddy simulation model that is capable of running oceanic simulations. GCCOM is an inherently computationally expensive model: it uses an elliptic solver for the dynamic pressure; meter-scale simulations requiring memory footprints on the order of 10 12 cells and terabytes of output data. As a solution for parallel optimization, the Fortran-interfaced Portable–Extensible Toolkit for Scientific Computation (PETSc) library was chosen as a framework to help reduce the complexity of managing the 3D geometry, to improve parallel algorithm design, and to provide a parallelized linear system solver and preconditioner. GCCOM discretizations are based on an Arakawa-C staggered grid, and PETSc DMDA (Data Management for Distributed Arrays) objects were used to provide communication and domain ownership management of the resultant multi-dimensional arrays, while the fully curvilinear Laplacian system for pressure is solved by the PETSc linear solver routines. In this paper, the framework design and architecture are described in detail, and results are presented that demonstrate the multiscale capabilities of the model and the parallel framework to 240 cores over domains of order 10 7 total cells per variable, and the correctness and performance of the multiphysics aspects of the model for a baseline experiment stratified seamount.

Concurrent vs Exclusive Reading in Parallel Decoding of LZ-Compressed Files

Broadcasting a message from one to many processors in a network corresponds to concurrent reading on a random access shared memory parallel machine. Computing the trees of a forest, the level of each node in its tree and the path between two nodes are problems that can easily be solved with concurrent reading in a time logarithmic in the maximum height of a tree. Solving such problems with exclusive reading requires a time logarithmic in the number of nodes, implying message passing between disjoint pairs of processors on a distributed system. Allowing concurrent reading in parallel algorithm design for distributed computing might be advantageous in practice if these problems are faced on shallow trees with some specific constraints. We show an application to LZC-compressed file decoding, whose parallelization employs these computations on such trees for realistic data. On the other hand, zipped files do not have such advantage since they are compressed by the Lempel-Ziv sliding window technique.