SPEC ACCEL Benchmark Description

314.omriq

Sam S. Stone, John A. Stratton

Ported to OpenACC by Mathew Colgrove

Medicine

One of the original Parboil benchmarks, MRI-Q, calculates equation 3 in the GPU-based MRI reconstruction paper by Stone et al., and is based on the implementation used to publish their work. An MRI image reconstruction is a conversion from sampled radio responses to magnetic field gradients. Sample “coordinates” are in the space of magnetic field gradients or k-space. The Q matrix in MRI image reconstruction is a precomputable value based on the sampling trajectory, the plan of how points in k-space will be sampled. The algorithm examines a large set of input representing the intended MRI scanning trajectory and the points that will be sampled. Each element of the Q matrix is computed by a summation of contributions from all trajectory sample points. Each contribution involves a three-element vector dot product of the input and output 3-D location, and a few trigonometric operations. The output Q elements are complex numbers, but the inputs are multi-element vectors. An output element (and its corresponding input denoting its 3-D location) is assigned to a single thread. To make sure the thread-private data structures exhibit good coalescing, a structure-of-arrays layout was chosen for the complex values and physical positions of a thread’s output. The shared input data set, however, is cached using GPU constant memory or some other high-bandwidth resource, and elects an array-of-structures implementation to keep each structure in a single cache line. When limited-capacity constant memory is employed, the data is tiled such that one tile is put in constant memory before each kernel invocation, which accumulates that tile’s contributions into the output. MRI-Q is a fundamentally compute-bound application, as trigonometric functions are expensive and the regularity of the problem allows for easy management of bandwidth. Therefore, once tiling and data layout remove any artificial bandwidth bottleneck, the most important optimizations were the low-level sequential code optimizations improving the instruction stream efficiency, such as loop unrolling.

314.omriq's input is in one file, containing the number of K-space values, the number of X-space values, and then the list of K-space coordinates, X-space coordinates, and Phi-field complex values for the K-space samples. Each set of coordinates and the complex values are stored as arrays, with each field written contiguously.

314.omriq outputs the resulting Q matrix of complex values in "real, imaginary" format for each line.

*C*

*OpenACC*

Input file is in little-endian binary format.

- [10] S. S. Stone, J. P. Haldar, S. C. Tsao, W. W. Hwu., Z. Liang, and B. P. Sutton. Accelerating advanced MRI reconstructions on GPUs. In International Conference on Computing Frontiers, pages 261–272, 2008.

Last updated: $Date: 2015-03-02 15:15:22 -0500 (Mon, 02 Mar 2015) $