Pervasive Parallel And Distributed Computing In A Liberal Arts College Curriculum

We present a model for incorporating parallel and distributed computing (PDC) throughout an undergraduate CS curriculum. Our curriculum is designed to introduce students early to parallel and distributed computing topics and to expose students to these topics repeatedly in the context of a wide variety of CS courses. The key to our approach is the development of a required intermediate-level course that serves as a introduction to computer systems and parallel computing. It serves as a requirement for every CS major and minor and is a prerequisite to upper-level courses that expand on parallel and distributed computing topics in different contexts. With the addition of this new course, we are able to easily make room in upper-level courses to add and expand parallel and distributed computing topics. The goal of our curricular design is to ensure that every graduating CS major has exposure to parallel and distributed computing, with both a breadth and depth of coverage. Our curriculum is particularly designed for the constraints of a small liberal arts college, however, much of its ideas and its design are applicable to any undergraduate CS curriculum

Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

Air pollution modelling using a graphics processing unit with CUDA

The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture - has been developed by NVIDIA to utilize this performance in general purpose computations. Here we show for the first time a possible application of GPU for environmental studies serving as a basement for decision making strategies. A stochastic Lagrangian particle model has been developed on CUDA to estimate the transport and the transformation of the radionuclides from a single point source during an accidental release. Our results show that parallel implementation achieves typical acceleration values in the order of 80-120 times compared to CPU using a single-threaded implementation on a 2.33 GHz desktop computer. Only very small differences have been found between the results obtained from GPU and CPU simulations, which are comparable with the effect of stochastic transport phenomena in atmosphere. The relatively high speedup with no additional costs to maintain this parallel architecture could result in a wide usage of GPU for diversified environmental applications in the near future.Comment: 5 figure

Investigating Single Precision Floating General Matrix Multiply in Heterogeneous Hardware

The fundamental operation of matrix multiplication is ubiquitous across a myriad of disciplines. Yet, the identification of new optimizations for matrix multiplication remains relevant for emerging hardware architectures and heterogeneous systems. Frameworks such as OpenCL enable computation orchestration on existing systems, and its availability using the Intel High Level Synthesis compiler allows users to architect new designs for reconfigurable hardware using C/C++. Using the HARPv2 as a vehicle for exploration, we investigate the utility of several of the most notable matrix multiplication optimizations to better understand the performance portability of OpenCL and the implications for such optimizations on this and future heterogeneous architectures. Our results give targeted insights into the applicability of best practices that were for existing architectures when used on emerging heterogeneous systems

LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft

High Performance Computing for DNA Sequence Alignment and Assembly

Recent advances in DNA sequencing technology have dramatically increased the scale and scope of DNA sequencing. These data are used for a wide variety of important biological analyzes, including genome sequencing, comparative genomics, transcriptome analysis, and personalized medicine but are complicated by the volume and complexity of the data involved. Given the massive size of these datasets, computational biology must draw on the advances of high performance computing. Two fundamental computations in computational biology are read alignment and genome assembly. Read alignment maps short DNA sequences to a reference genome to discover conserved and polymorphic regions of the genome. Genome assembly computes the sequence of a genome from many short DNA sequences. Both computations benefit from recent advances in high performance computing to efficiently process the huge datasets involved, including using highly parallel graphics processing units (GPUs) as high performance desktop processors, and using the MapReduce framework coupled with cloud computing to parallelize computation to large compute grids. This dissertation demonstrates how these technologies can be used to accelerate these computations by orders of magnitude, and have the potential to make otherwise infeasible computations practical

Parallel cloth simulation using OpenMp and CUDA

The widespread availability of parallel computing architectures has lead to research regarding algorithms and techniques that best exploit available parallelism. In addition to the CPU parallelism available; the GPU has emerged as a parallel computational device. The goal of this study was to explore the combined use of CPU and GPU parallelism by developing a hybrid parallel CPU/GPU cloth simulation application. In order to evaluate the benefits of the hybrid approach, the application was first developed in sequential CPU form, followed by a parallel CPU form. The application uses Backward Euler implicit time integration to solve the differential equations of motion associated with the physical system. The Conjugate Gradient (CG) algorithm is used to determine the solution vector for the system of equations formed by the Backward Euler approach. The matrix/vector, vector/vector, and vector/scalar operations required by CG are handled by calls to BLAS level 1 and level 2 functions. In the sequential CPU and parallel CPU versions, the Intel Math Kernel Library implementation of BLAS is used. In the hybrid parallel CPU/GPU version, the Nvidia CUDA based BLAS implementation (CUBLAS) is used. In the parallel CPU and hybrid implementations, OpenMP directives are used to parallelize the force application loop that traverses the list of forces acting on the system. Runtimes were collected for each version of the application while simulating cloth meshes with particle resolutions of 20x20, 40x40, and 60x60. The performance of each version was compared at each mesh resolution. The level of performance degradation experienced when transitioning to the larger mesh sizes was also determined. The hybrid parallel CPU/GPU implementation yielded the highest frame rate for the 40x40 and 60x60 meshes. The parallel CPU implementation yielded the highest frame rate for the 20x20 mesh. The performance of the hybrid parallel CPU/GPU implementation degraded the least as it transitioned to the two larger mesh sizes. The results of this study will potentially lead to further research regarding the use of GPUs to perform the matrix/vector operations associated with the CG algorithm under more complex cloth simulation scenarios