A Design Framework for Mapping Vectorized Synchronous Dataflow Graphs onto CPU-GPU Platforms

Watershed analysis, as a fundamental component of digital terrain analysis, is based on the Digital Elevation Model (DEM), which is a grid (raster) model of the Earth surface and topography. Watershed analysis consists of computationally and data intensive computing algorithms that need to be implemented by leveraging parallel and high-performance computing methods and techniques. In this paper, the Multiple Flow Direction (MFD) algorithm for watershed analysis is implemented and evaluated on multi-core Central Processing Units (CPU) and many-core Graphics Processing Units (GPU), which provides significant improvements in performance and energy usage. The implementation is based on NVIDIA CUDA (Compute Unified Device Architecture) implementation for GPU, as well as on OpenACC (Open ACCelerators), a parallel programming model, and a standard for parallel computing. Both phases of the MFD algorithm (i) iterative DEM preprocessing and (ii) iterative MFD algorithm, are parallelized and run over multi-core CPU and GPU. The evaluation of the proposed solutions is performed with respect to the execution time, energy consumption, and programming effort for algorithm parallelization for different sizes of input data. An experimental evaluation has shown not only the advantage of using OpenACC programming over CUDA programming in implementing the watershed analysis on a GPU in terms of performance, energy consumption, and programming effort, but also significant benefits in implementing it on the multi-core CPU.

Although the High Efficiency Video Coding (HEVC) standard significantly improves the coding efficiency of video compression, it is unacceptable even in offline applications to spend several hours compressing 10 s of high-definition video. In this paper, we propose using a multicore central processing unit (CPU) and an off-the-shelf graphics processing unit (GPU) with 3072 streaming processors (SPs) for HEVC fast encoding, so that the speed optimization does not result in loss of coding efficiency. There are two key technical contributions in this paper. First, we propose an algorithm that is both parallel and fast for the GPU, which can utilize 3072 SPs in parallel to estimate the motion vector (MV) of every prediction unit (PU) in every combination of the coding unit (CU) and PU partitions. Furthermore, the proposed GPU algorithm can avoid coding efficiency loss caused by the lack of a MV predictor (MVP). Second, we propose a fast algorithm for the CPU, which can fully utilize the results from the GPU to significantly reduce the number of possible CU and PU partitions without any coding efficiency loss. Our experimental results show that compared with the reference software, we can encode high-resolution video that consumes 1.9% of the CPU time and 1.0% of the GPU time, with only a 1.4% rate increase.

The random forest ensemble learning with the Graphics Processing Unit (GPU) version of prefix scan method is presented. The efficiency of the implementation of the random forest algorithm depends critically on the scan (prefix sum) algorithm. The prefix scan is used in the depth-first implementation of optimal split point computation. Described are different implementations of the prefix scan algorithms. The speeds of the algorithms depend on three factors: the algorithm itself, which could be improved, the programming skills, and the compiler. In parallel environments, things are even more complicated and depend on the programmer´s knowledge of the Central Processing Unit (CPU) or the GPU architecture. An efficient parallel scan algorithm that avoids bank conflicts is crucial for the prefix scan implementation. In our tests, multicore CPU and GPU implementation based on NVIDIA´s CUDA is compared.

Particle-mesh interpolations are fundamental operations for particle-in-cell codes, as implemented in vortex methods, plasma dynamics and electrostatics simulations. In these simulations, the mesh is used to solve the field equations and the gradients of the fields are used in order to advance the particles. The time integration of particle trajectories is performed through an extensive resampling of the flow field at the particle locations. The computational performance of this resampling turns out to be limited by the memory bandwidth of the underlying computer architecture. We investigate how mesh-particle interpolation can be efficiently performed on graphics processing units (GPUs) and multicore central processing units (CPUs), and we present two implementation techniques. The single-precision results for the multicore CPU implementation show an acceleration of 45-70×, depending on system size, and an acceleration of 85-155× for the GPU implementation over an efficient single-threaded C++ implementation. In double precision, we observe a performance improvement of 30-40× for the multicore CPU implementation and 20-45× for the GPU implementation. With respect to the 16-threaded standard C++ implementation, the present CPU technique leads to a performance increase of roughly 2.8-3.7× in single precision and 1.7-2.4× in double precision, whereas the GPU technique leads to an improvement of 9× in single precision and 2.2-2.8× in double precision.

Abstract. The advent of heterogeneous supercomputers with multi-core central processing units (CPUs) and graphics processing units (GPUs) requires geoscientific codes to be adapted to these new architectures. Here, we describe the porting of Meso-NH version 5.5 community weather research code to GPUs named MESONH-v55-OpenACC with guaranteed bit reproducibility thanks to its own MPPDB_CHECK library. This porting includes the use of OpenACC directives, specific memory management, communications optimization, development of a geometric multigrid (MG) solver and creation of an in-house preprocessor. Performance on the AMD MI250X GPU Adastra platform shows up to 6.0× speedup (4.6× on the NVIDIA A100 Leonardo platform), and achieves a gain of a factor of 2.3 in energy efficiency compared to AMD Genoa CPU Adastra platform using the same configuration with 64 nodes. The code is even 17.8× faster by halving the precision and quadrupling the nodes with a gain in energy efficiency of a factor of 1.3. First scientific simulations of three representative storms using 128 GPUs nodes of Adastra show successful cascade of scales for horizontal grid spacing down to 100 m and grid size up to 2.1 billion points. For one of these storms, Meso-NH is also successfully coupled to the WAVEWATCH III wave model via the OASIS3-MCT coupler without any extra computational cost. This GPU porting paves the way for Meso-NH to be used on future European exascale machines.

SummaryMany e‐business or social network servers have been constructed on cloud. On such open environments, private data of massive users have to be protected by encrypting, such as using Advanced Encryption Standard (AES), and furthermore, this process must be finished in a short time for users' better experience. This gives huge pressure on cloud servers, especially common servers, such as web servers. We urgently need an inexpensive and highly efficient method to relieve cloud servers' pressure. Fortunately, many cores of a graphics processing unit (GPU) can undertake this hard mission because of stronger computing power and lower price. The GPU environments can be virtualized on demand by cloud through the vCUDA technology. Of course, for those clouds not equipped with a GPU, a central processing unit (CPU) can still work as multithreads in parallel. Thus, in a cloud, AES can be parallelized using many cores of a GPU or multicores of a CPU with high efficiency and low cost. For typical cloud applications, such as web services, there are massive users and each one has short plaintext. If we simply parallelize AES in such an application, we cannot obtain better performance because of the GPU's extra data transferring cost. Thus, we coalesce the massive users' data and cut these data into same‐length slices for improving the performance of parallel AES as much as possible. So we design six parallel AES algorithms using GPU parallelism or CPU parallelism, which differ in parallel scope and whether data are coalesced or cut to slices. Specifically, they are coalescent and sliced GPU (GCS), coalescent and unsliced GPU, uncoalescent GPU, coalescent and sliced CPU, coalescent and unsliced CPU, and uncoalescent CPU. Moreover, we implement them on two representative platforms and evaluate their performance. Through comparing their performance, GCS has the best performance among these algorithms. In a cloud with Nvidia GPUs, GCS is a more powerful algorithm for massive users' data encrypting, relatively. Copyright © 2015 John Wiley & Sons, Ltd.

Efficient methods for implementation of multi-level nonrigid mass-preserving image registration on GPUs and multi-threaded CPUs

This paper presents an implementation of the FDTD- compatible Green's function on a heterogeneous parallel processing system. The developed implementation simultaneously utilizes computational power of the central processing unit (CPU) and the graphics processing unit (GPU) to the computational tasks best suited for each architecture. Recently, closed-form expression for this discrete Green's function (DGF) was derived, which facilitates its applications in the FDTD simulations of radiation and scattering problems. Unfortunately, implementation of the new DGF formula in software requires a multiple precision arithmetic and may cause long runtimes. Therefore, an acceleration of the DGF computations on a CPU-GPU heterogeneous parallel processing system was developed using the multiple precision arithmetic and the OpenMP and CUDA parallel programming interfaces. The method avoids drawbacks of the CPU- and GPU-only accelerated implementations of the DGF, i.e., long runtime on the CPU and signiflcant overhead of the GPU initialization respectively for long and short length of the DGF waveform. As a result, the sevenfold speedup was obtained relative to the reference DGF implementation on a multicore CPU thus applicability of the DGF in FDTD simulations was signiflcantly improved.

We have implemented the Martini force field within Lawrence Livermore National Laboratory's molecular dynamics program, ddcMD. The program is extended to a heterogeneous programming model so that it can exploit graphics processing unit (GPU) accelerators. In addition to the Martini force field being ported to the GPU, the entire integration step, including thermostat, barostat, and constraint solver, is ported as well, which speeds up the simulations to 278-fold using one GPU vs one central processing unit (CPU) core. A benchmark study is performed with several test cases, comparing ddcMD and GROMACS Martini simulations. The average performance of ddcMD for a protein-lipid simulation system of 136k particles achieves 1.04 µs/day on one NVIDIA V100 GPU and aggregates 6.19 µs/day on one Summit node with six GPUs. The GPU implementation in ddcMD offloads all computations to the GPU and only requires one CPU core per simulation to manage the inputs and outputs, freeing up remaining CPU resources on the compute node for alternative tasks often required in complex simulation campaigns. The ddcMD code has been made open source and is available on GitHub at https://github.com/LLNL/ddcMD.

Applications executing on multicore processors can now easily offload computations to many core processors, such as Intel Xeon Phi coprocessors. However, it requires high levels of expertise and effort to tune such offloaded applications to realize high-performance execution. Previous efforts have focused on optimizing the execution of offloaded computations on many core processors. However, we observe that the data transfer overhead between multicore and many core processors, and the limited device memories of many core processors often constrain the performance gains that are possible by offloading computations. In this paper, we present three source-to-source compiler optimizations that can significantly improve the performance of applications that offload computations to many core processors. The first optimization automatically transforms offloaded codes to enable data streaming, which overlaps data transfer between multicore and many core processors with computations on these processors to hide data transfer overhead. This optimization is also designed to minimize the memory usage on many core processors, while achieving the optimal performance. The second compiler optimization re-orders computations to regularize irregular memory accesses. It enables data streaming and factorization on many core processors, even when the memory access patterns in the original source codes are irregular. Finally, our new shared memory mechanism provides efficient support for transferring large pointer-based data structures between hosts and many core processors. Our evaluation shows that the proposed compiler optimizations benefit 9 out of 12 benchmarks. Compared with simply offloading the original parallel implementations of these benchmarks, we can achieve 1.16x-52.21x speedups.

MSA Probs is a parallel algorithm developed to align multiple sequence alignment using a central processing unit (CPU). Whereas the CPU has some limitations, such as the inability to parallelize tasks in the processor (latency-oriented). To overcome these limitations, this paper proposes an improved version of MSA Probs that is compatible with a graphical Processing Unit (GPU). This idea helps in enhancing the performance of our algorithm (MSAprobs). To parallelize the sequential algorithm, Compute Unified Device Architecture (CUDA) or OpenCL is commonly used on GPUs. The NIVIDIA API is used to investigate the GPU's computing power. The results of using CPU only in MSAprobs versus the CPU and GPU are compared using two data sets from the Bali Base and OX Bench. The evaluation of the CPU and GPU is done using Threads 1,2 and 4. The results showed that by combining CPU and GPU, performance is improved and execution time is reduced.

Fast GPU Algorithm for Analyzing Effective Connectivity in Functional Brain Imaging

This study aims to employ both central processing units (CPUs) and graphics processing units (GPUs) to collaboratively generate contour lines from a large-scale digital elevation model (DEM). The performance was improved with regard to three aspects. First, the original DEM data were decomposed and assigned according to the GPU’s limited memory so that large-scale data could be correctly addressed. Second, different types of computational tasks between the CPUs and GPUs were dynamically scheduled to ensure that both accelerators cooperate for performance improvement. Third, parallel processing on GPUs and CPUs was separately optimized for more efficient acceleration. Experimental results indicated that applying the parallel algorithm to data with a volume of 37.81 GB and area of 5,975,625.16 km2 reduced the total execution time from 332.84 min to 8.29 min for an optimal speedup of 40.15. In addition, we investigated the effects of the computational intensity, decomposition granularity, and task scheduling on parallel efficiency and performance improvement. We also discussed its degree of effectiveness, broader application, and the future direction of research in the field of geographic information systems.

Multi-core-CPU and GPU-accelerated radiative transfer models based on the discrete ordinate method

GPU acceleration of MPAS microphysics WSM6 using OpenACC directives: Performance and verification