Massive Parallelization of Massive Sample-size Survival Analysis

Large-scale observational health databases are increasingly popular for conducting comparative effectiveness and safety studies of medical products. However, increasing number of patients poses computational challenges when fitting survival regression models in such studies. In this paper, we use graphics processing units (GPUs) to parallelize the computational bottlenecks of massive sample-size survival analyses. Specifically, we develop and apply time- and memory-efficient single-pass parallel scan algorithms for Cox proportional hazards models and forward-backward parallel scan algorithms for Fine-Gray models for analysis with and without a competing risk using a cyclic coordinate descent optimization approach We demonstrate that GPUs accelerate the computation of fitting these complex models in large databases by orders-of-magnitude as compared to traditional multi-core CPU parallelism. Our implementation enables efficient large-scale observational studies involving millions of patients and thousands of patient characteristics

A Study of High Performance Multiple Precision Arithmetic on Graphics Processing Units

Multiple precision (MP) arithmetic is a core building block of a wide variety of algorithms in computational mathematics and computer science. In mathematics MP is used in computational number theory, geometric computation, experimental mathematics, and in some random matrix problems. In computer science, MP arithmetic is primarily used in cryptographic algorithms: securing communications, digital signatures, and code breaking. In most of these application areas, the factor that limits performance is the MP arithmetic. The focus of our research is to build and analyze highly optimized libraries that allow the MP operations to be offloaded from the CPU to the GPU. Our goal is to achieve an order of magnitude improvement over the CPU in three key metrics: operations per second per socket, operations per watt, and operation per second per dollar. What we find is that the SIMD design and balance of compute, cache, and bandwidth resources on the GPU is quite different from the CPU, so libraries such as GMP cannot simply be ported to the GPU. New approaches and algorithms are required to achieve high performance and high utilization of GPU resources. Further, we find that low-level ISA differences between GPU generations means that an approach that works well on one generation might not run well on the next. Here we report on our progress towards MP arithmetic libraries on the GPU in four areas: (1) large integer addition, subtraction, and multiplication; (2) high performance modular multiplication and modular exponentiation (the key operations for cryptographic algorithms) across generations of GPUs; (3) high precision floating point addition, subtraction, multiplication, division, and square root; (4) parallel short division, which we prove is asymptotically optimal on EREW and CREW PRAMs

GPU上での展開に適した可逆データ圧縮方式に関する研究

広島大学(Hiroshima University)博士(工学)Doctor of Engineeringdoctora