Fast parallel cutoff pair interactions for molecular dynamics on heterogeneous systems

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

Purpose:The calculation time is a trade‐off for improving the accuracy of convolution dose calculation with fine calculation spacing of the KERMA kernel. We investigated to accelerate the convolution calculation using an ideal kernel on the Graphic Processing Units (GPU).Methods:The calculation was performed on the AMD graphics hardware of Dual FirePro D700 and our algorithm was implemented using the Aparapi that convert Java bytecode to OpenCL. The process of dose calculation was separated with the TERMA and KERMA steps. The dose deposited at the coordinate (x, y, z) was determined in the process. In the dose calculation running on the central processing unit (CPU) of Intel Xeon E5, the calculation loops were performed for all calculation points. On the GPU computation, all of the calculation processes for the points were sent to the GPU and the multi‐thread computation was done. In this study, the dose calculation was performed in a water equivalent homogeneous phantom with 1503 voxels (2 mm calculation grid) and the calculation speed on the GPU to that on the CPU and the accuracy of PDD were compared.Results:The calculation time for the GPU and the CPU were 3.3 sec and 4.4 hour, respectively. The calculation speed for the GPU was 4800 times faster than that for the CPU. The PDD curve for the GPU was perfectly matched to that for the CPU.Conclusion:The convolution calculation with the ideal kernel on the GPU was clinically acceptable for time and may be more accurate in an inhomogeneous region. Intensity modulated arc therapy needs dose calculations for different gantry angles at many control points. Thus, it would be more practical that the kernel uses a coarse spacing technique if the calculation is faster while keeping the similar accuracy to a current treatment planning system.

Nowadays graphics processing units (GPUs) have become popular parallel computing platforms known as General-Purpose GPU (GPGPU) computing. GPUs thereby are chosen by some security researchers as cryptographic accelerators to secure massive volumes of transactions. However, their security issues are ignored in spite of their popularity and performance. There are some possible information leakages faced with malicious attacks or even in the normal GPU computing. Our objective is to secure the confidentiality of cryptographic keys in GPU computing environments and provide easy-to-use programming with few constraints. In this paper, we propose a prototype in Linux, a system of GPGPU computing solution empowered by GPU virtualization technology, which keeps encrypted keys in guest machine to protect secret keys from leakage even in the event of full system compromise. With the API interception and redirection of CUDA, applications in Virtual Machines (VMs) can access the GPU device in a transparent way. Besides, we use virtio, a dedicated virtual I/O device, to transfer data between virtual and host machines in high performance. In our current study, we evaluate our prototype with the GPU implementation of ECC. We show that it can protect private keys of GPU cryptographic computation and it also incurs low performance penalty compared with the native environment, therefore demonstrating the prototype is secure and requires reasonable overhead.

Bioinspired methods usually need a high amount of computational resources. For this reason, parallelization is an interesting alternative in order to decrease the execution time and to provide accurate results. In this sense, recently there has been a growing interest in developing parallel algorithms using graphic processing units (GPU) also refered as GPU computation. Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs). As GPUs are available in personal computers, and they are easy to use and manage through several GPU programming languages (CUDA, OpenCL, etc.), graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. This paper reviews the use of GPUs to solve scientific problems, giving an overview of current software systems.

A high-order spectral difference (SD) method has been developed with graphics processing units (GPUs) using compute unified device architecture (CUDA). It solves the three-dimensional Navier-Stokes equations on unstructured hexahedral grids with RungeKutta time integration. The method is efficient since operations are completed in a onedimensional fashion and the equations are solved in differential form, removing explicit surface and volume integral calculations. Additionally, solution and flux reconstructions are completed locally per cell, increasing the parallelization of the implementation. Due to this efficiency, the application of GPU computing is appealing. This paper presents the SD method implementation with GPU CUDA computing and presents accuracy studies with isotropic vortex propagation and Couette flow, verifies the high-order accuracy of the solver with a numerical sensitive aero-acoustic problem, and compares the developed solver and a high-order finite difference solver with a case presented in the 1st International Workshop on High-Order CFD Methods. Finally, the GPU solver is compared to a similar central processing unit (CPU) solver, where speed-ups ranging from 20-40x faster are illustrated.

In addition to the intended use of graphics processing units (GPU) to accelerate computer games, their potential has become apparent for scientific computations in the recent years. Molecular modeling and molecular design are only few examples of numerous research areas that are significantly benefiting from novel developments of hardware and software platforms. For example, the impact of high computational power of GPUs has been demonstrated in molecular dynamics (MD) simulations or quantum chemical (QC) calculations. Thus far, several MD programs have been adapted to GPU computing, including NAMD/VMD, GROMACS, AMBER, etc. In addition, modeling tools intended for molecular design based on receptor-ligand interactions, such as molecular docking or core hopping protocols have recently been updated for GPU environment. The tremendous increase in the computing power facilitated by the integration of GPUs and the availability of GPU-based systems could accelerate material research on nanoscale. The price/performance ratio of GPU-based systems supports the development of custom-made protocols for efficient modeling of biomolecular systems and nanostructures. GPU-related molecular modeling tools will also accelerate the combined quantum chemical/molecular mechanics (QC/MM) methodologies. An overview of the performance of NVIDIA Tesla GPU-based system built for high-performance and high-throughput computing aimed for biomolecular modeling and nanodesign is presented.

We present a novel heterogeneous parallel matrix multiplication algorithm that utilizes both central processing units (CPUs) and graphics processing units (GPUs) for large-scale matrices. Based on Strassen’s method, we represent matrix multiplication work as a set of matrix addition and multiplication tasks among their sub-matrices. Then, we distribute the tasks to CPUs and GPUs while considering the characteristics of the tasks and computing resources to minimize the data communication overhead and fully utilize the available computing power. To handle a large matrix efficiently with limited GPU memory, we also propose a block-based work decomposition method. We then further improve the performance of our method by exploiting the concurrent execution abilities of a heterogeneous parallel computing system. We implemented our method on five different heterogeneous systems and applied it to matrices of various sizes. Our method generally shows higher performance than the prior GPU-based matrix multiplication methods. Moreover, compared with the state-of-the-art GPU matrix multiplication library (i.e., CUBLAS), our method achieved up to 1.97 times higher performance using the same GPUs and CPU cores. In some cases, our method using a low-performance GPU (e.g., GTX 1060, 3 GB) achieved performance comparable to that of CUBLAS using a high-performance GPU (e.g., RTX 2080, 8 GB). Also, our method continually improves performance as we use more computing resources like additional CPU cores and GPUs. We could achieve such high performance because our approach fully utilized the capacities of the given heterogeneous parallel computing systems while employing the Strassen’s method, which has a lower asymptotic complexity. These results demonstrate the efficiency and robustness of our algorithm.

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

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.

Feedback control has become a crucial tool in the research on magnetic confinement of plasmas for achieving controlled nuclear fusion. This thesis presents a novel plasma feedback control system that, for the first time, employs a Graphics Processing Unit (GPU) for microsecond-latency, real-time control computations. This novel application area for GPU computing is opened up by a new system architecture that is optimized for low-latency computations on less than kilobyte sized data samples as they occur in typical plasma control algorithms. In contrast to traditional GPU computing approaches that target complex, high-throughput computations with massive amounts of data, the architecture presented in this thesis uses the GPU as the primary processing unit rather than as an auxiliary of the CPU, and data is transferred from A-D/D-A converters directly into GPU memory using peer-to-peer PCI Express transfers. The described design has been implemented in a new, GPU-based control system for the High-Beta Tokamak – Extended Pulse (HBT-EP) device. The system is built from commodity hardware and uses an NVIDIA GeForce GPU and D-TACQ A-D/D-A converters providing a total of 96 input and 64 output channels. The system is able to run with sampling periods down to 4 μs and latencies down to 8 μs. The GPU provides a total processing power of 1.5 x 1012 floating point operations per second. To illustrate the performance and versatility of both the general architecture and concrete implementation, a new control algorithm has been developed. The algorithm is designed for the control of multiple rotating magnetic perturbations in situations where the plasma equilibrium is not known exactly and features an adaptive system model: instead of requiring the rotation frequencies and growth rates embedded in the system model to be set a priori, the adaptive algorithm derives these parameters from the evolution of the perturbation amplitudes themselves. This results in non-linear control computations with high computational demands, but is handled easily by the GPU based system. Both digital processing latency and an arbitrary multi-pole response of amplifiers and control coils is fully taken into account for the generation of control signals. To separate sensor signals into perturbed and equilibrium components without knowledge of the equilibrium fields, a new separation method based on biorthogonal decomposition is introduced and used to derive a filter that performs the separation in real-time. The control algorithm has been implemented and tested on the new, GPU-based feedback control system of the HBT-EP tokamak. In this instance, the algorithm was set up to control four rotating n = 1 perturbations at different poloidal angles. The perturbations were treated as coupled in frequency but independent in amplitude and phase, so that the system effectively controls a helical n = 1 perturbation with unknown poloidal spectrum. Depending on the plasma's edge safety factor and rotation frequency, the control system is shown to be able to suppress the amplitude of the dominant 8 kHz mode by up to 60% or amplify the saturated amplitude by a factor of up to two. Intermediate feedback phases combine suppression and amplification with a speed up or slow down of the mode rotation frequency. Increasing feedback gain results in the excitation of an additional, slowly rotating 1.4 kHz mode without further effects on the 8 kHz mode. The feedback performance is found to exceed previous results obtained with an FPGA- and Kalman-filter based control system without requiring any tuning of system model parameters. Experimental results are compared with simulations based on a combination of the Boozer surface current model and the Fitzpatrick-Aydemir model. Within the subset of phenomena that can be represented by the model as well as determined experimentally, qualitative agreement is found.

The solution of tridiagonal system of equations using graphic processing units (GPU) is assessed. The parallel-Thomas-algorithm (PTA) is developed and the solution of PTA is compared to two known parallel algorithms, i.e. cyclic-reduction (CR) and parallel-cyclic-reduction (PCR). Lid-driven cavity problem is considered to assess these parallel approaches. This problem is also simulated using the classic Thomas algorithm that runs on a central processing unit (CPU). Runtimes and physical parameters of the mentioned GPU and CPU algorithms are compared. The results show that the speedup of CR, PCR and PTA against the CPU runtime is 4.4x,5.2x and 38.5x, respectively. Furthermore, the effect of coalesced and uncoalesced memory access to GPU global memory is examined for PTA, and a 2x-speedup is achieved for the coalesced memory access. Additionally, the PTA performance in a time dependent problem, the unsteady flow over a square, is assessed and a 9x-speedup is obtained against the CPU.

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.

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.

As computation schemes evolve and many new tools become available to programmers to enhance the performance of their applications, many programmers started to look towards highly parallel platforms such as Graphical Processing Unit (GPU). Offloading computations that can take advantage of the architecture of the GPU is a technique that has proven fruitful in recent years. This technology enhances the speed and responsiveness of applications. Also, as a side effect, it reduces the power requirements for those applications and therefore extends portable devices battery life and helps computing clusters to run more power efficiently. Many performance analysis tools such as LTTng, strace and SystemTap already allow Central Processing Unit (CPU) tracing and help programmers to use CPU resources more efficiently. On the GPU side, different tools such as Nvidia’s Nsight, AMD’s CodeXL, and third party TAU and VampirTrace allow tracing Application Programming Interface (API) calls and OpenCL kernel execution. These tools are useful but are completely separate, and none of them allow a unified CPU-GPU tracing experience. We propose an extension to the existing scalable and highly efficient LTTng tracing platform to allow unified tracing of GPU along with CPU’s full tracing capabilities.