Parallel Simulation of a Fluid Flow by Means of the SPH Method: OpenMP vs. MPI Comparison

The SPH method for simulating incompressible fluids is presented in this article. The background and principles of the SPH method are explained and its application to incompressible fluids simulations is discussed. The parallel implementation of the SPH simulation with OpenMP and MPI environments are demonstrated. Both models of parallel implementation are analyzed and discussed. The comparison of both models is performed and discussed, as well as their results

Harvesting graphics power for MD simulations

We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPU's is compared to their main processor counterpart. We achieve speedups of up to 80, 40 and 150 fold, respectively. With newest generation of GPU's one can run standard MD simulations at 10^7 flops/$.Comment: 12 pages, 5 figures. Submitted to Mol. Si

MILC Code Performance on High End CPU and GPU Supercomputer Clusters

With recent developments in parallel supercomputing architecture, many core, multi-core, and GPU processors are now commonplace, resulting in more levels of parallelism, memory hierarchy, and programming complexity. It has been necessary to adapt the MILC code to these new processors starting with NVIDIA GPUs, and more recently, the Intel Xeon Phi processors. We report on our efforts to port and optimize our code for the Intel Knights Landing architecture. We consider performance of the MILC code with MPI and OpenMP, and optimizations with QOPQDP and QPhiX. For the latter approach, we concentrate on the staggered conjugate gradient and gauge force. We also consider performance on recent NVIDIA GPUs using the QUDA library

Scalable data clustering using GPUs

The computational demands of multivariate clustering grow rapidly, and therefore processing large data sets, like those found in flow cytometry data, is very time consuming on a single CPU. Fortunately these techniques lend themselves naturally to large scale parallel processing. To address the computational demands, graphics processing units, specifically NVIDIA\u27s CUDA framework and Tesla architecture, were investigated as a low-cost, high performance solution to a number of clustering algorithms. C-means and Expectation Maximization with Gaussian mixture models were implemented using the CUDA framework. The algorithm implementations use a hybrid of CUDA, OpenMP, and MPI to scale to many GPUs on multiple nodes in a high performance computing environment. This framework is envisioned as part of a larger cloud-based workflow service where biologists can apply multiple algorithms and parameter sweeps to their data sets and quickly receive a thorough set of results that can be further analyzed by experts. Improvements over previous GPU-accelerated implementations range from 1.42x to 21x for C-means and 3.72x to 5.65x for the Gaussian mixture model on non-trivial data sets. Using a single NVIDIA GTX 260 speedups are on average 90x for C-means and 74x for Gaussians with flow cytometry files compared to optimized C code running on a single core of a modern Intel CPU. Using the TeraGrid Lincoln high performance cluster at NCSA C-means achieves 42% parallel efficiency and a CPU speedup of 4794x with 128 Tesla C1060 GPUs. The Gaussian mixture model achieves 72% parallel efficiency and a CPU speedup of 6286x

Invasive compute balancing for applications with shared and hybrid parallelization

This is the author manuscript. The final version is available from the publisher via the DOI in this record.Achieving high scalability with dynamically adaptive algorithms in high-performance computing (HPC) is a non-trivial task. The invasive paradigm using compute migration represents an efficient alternative to classical data migration approaches for such algorithms in HPC. We present a core-distribution scheduler which realizes the migration of computational power by distributing the cores depending on the requirements specified by one or more parallel program instances. We validate our approach with different benchmark suites for simulations with artificial workload as well as applications based on dynamically adaptive shallow water simulations, and investigate concurrently executed adaptivity parameter studies on realistic Tsunami simulations. The invasive approach results in significantly faster overall execution times and higher hardware utilization than alternative approaches. A dynamic resource management is therefore mandatory for a more efficient execution of scenarios similar to our simulations, e.g. several Tsunami simulations in urgent computing, to overcome strong scalability challenges in the area of HPC. The optimizations obtained by invasive migration of cores can be generalized to similar classes of algorithms with dynamic resource requirements.This work was supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre ”Invasive Computing” (SFB/TR 89)

Towards Energy Efficiency in Heterogeneous Processors: Findings on Virtual Screening Methods

The integration of the latest breakthroughs in computational modeling and high performance computing (HPC) has leveraged advances in the fields of healthcare and drug discovery, among others. By integrating all these developments together, scientists are creating new exciting personal therapeutic strategies for living longer that were unimaginable not that long ago. However, we are witnessing the biggest revolution in HPC in the last decade. Several graphics processing unit architectures have established their niche in the HPC arena but at the expense of an excessive power and heat. A solution for this important problem is based on heterogeneity. In this paper, we analyze power consumption on heterogeneous systems, benchmarking a bioinformatics kernel within the framework of virtual screening methods. Cores and frequencies are tuned to further improve the performance or energy efficiency on those architectures. Our experimental results show that targeted low‐cost systems are the lowest power consumption platforms, although the most energy efficient platform and the best suited for performance improvement is the Kepler GK110 graphics processing unit from Nvidia by using compute unified device architecture. Finally, the open computing language version of virtual screening shows a remarkable performance penalty compared with its compute unified device architecture counterpart.Ingeniería, Industria y Construcció

Definition of a Method for the Formulation of Problems to be Solved with High Performance Computing

Computational power made available by current technology has been continuously increasing, however today’s problems are larger and more complex and demand even more computational power. Interest in computational problems has also been increasing and is an important research area in computer science. These complex problems are solved with computational models that use an underlying mathematical model and are solved using computer resources, simulation, and are run with High Performance Computing. For such computations, parallel computing has been employed to achieve high performance. This thesis identifies families of problems that can best be solved using modelling and implementation techniques of parallel computing such as message passing and shared memory. Few case studies are considered to show when the shared memory model is suitable and when the message passing model would be suitable. The models of parallel computing are implemented and evaluated using some algorithms and simulations. This thesis mainly focuses on showing the more suitable model of computing for the various scenarios in attaining High Performance Computing

Introduction of shared-memory parallelism in a distributed-memory multifrontal solver

We study the adaptation of a parallel distributed-memory solver towards a shared-memory code, targeting multi-core architectures. The advantage of adapting the code over a new design is to fully benefit from its numerical kernels, range of functionalities and internal features. Although the studied code is a direct solver for sparse systems of linear equations, the approaches described in this paper are general and could be useful to a wide range of applications. We show how existing parallel algorithms can be adapted to an OpenMP environment while, at the same time, also relying on third-party optimized multithreaded libraries. We propose simple approaches to take advantage of NUMA architectures, and original optimizations to limit thread synchronization costs. For each point, the performance gains are analyzed in detail on test problems from various application areas.Dans cet article, nous étudions l'adaptation d'un code parallèle à mémoire distribuée en un code visant les architectures à mémoire partagée de type multi-coeurs. L'intérêt d'adapter un code existant plutôt que d'en concevoir un nouveau est de pouvoir bénéficier directement de toute la richesse de ses fonctionnalités numériques ainsi que de ses caractéristiques internes. Même si le code sur lequel porte l'étude est un solveur direct multifrontale pour systèmes linéaires creux, les algorithmes et techniques discutés sont générales et peuvent s'appliquer à des domaines d'application plus généraux. Nous montrons comment des algorithmes parallèles existant peuvent être adaptés à un environnement OpenMP tout en exploitant au mieux des librairies existantes optimisées. Nous présentons des approches simples pour tirer parti des spécificités des architectures NUMA, ainsi que des optimisations originales permettant de limiter les coûts de synchronisation dans le modèle fork-join que l'on utilise. Pour chacun de ces points, les gains en performance sont analysés sur des cas tests provenant de domaines d'applications variés