Finding a novel drug is a very long and complex procedure. Using computer simulations, it is possible to accelerate the preliminary phases by performing a virtual screening that filters a large set of drug candidates to a manageable number. This paper presents the implementations and comparative analysis of two GPU-optimised implementations of a virtual screening algorithm targeting novel GPU architectures. This work focuses on the analysis of parallel computation patterns and their mapping onto the target architecture. The first method adopts a traditional approach that spreads the computation for a single molecule across the entire GPU. The second uses a novel batched approach that exploits the parallel architecture of the GPU to evaluate more molecules in parallel. Experimental results showed a different behavior depending on the size of the database to be screened, either reaching a performance plateau sooner or having a more extended initial transient period to achieve a higher throughput (up to 5x), which is more suitable for extreme-scale virtual screening campaigns.

This paper presents a GPU implementation of the graph triangle counting operation based on the set intersection algorithm. The algorithm is implemented in four kernels optimized for different types of graphs in a code delivering performance higher than the current state-of-the-art and without preprocessing the input graph. At runtime, a lightweight heuristic is used to select the kernel to run based on the specific graph taken as input. In contrast to previous works, the presented approach takes advantage of a set intersection operation implemented via bitmaps. Moreover, the simplicity of the approach allows the code to have limited size and engineering complexity.

We present simulations of blood and cancer cell separation in complex microfluidic channels with subcellular resolution, demonstrating unprecedented time to solution, performing at 65.5% of the available 39.4 PetaInstructions/s in the 18, 688 nodes of the Titan supercomputer.

We study the energy used by a production-level regional climate and weather simulation code on a distributed memory system with hybrid CPU-GPU nodes. The code is optimised for both processor architectures, for which we investigate both time and energy to solution. Operational constraints for time to solution can be met with both processor types, although on different numbers of nodes. Energy to solution is a factor 3 lower with GPUs, but strong scaling can be pushed to larger node counts with CPUs to minimize time to solution. Our data shows that an affine relationship exists between energy and node hours consumed by the simulation. We use this property to devise a simple and practical methodology for optimising for energy efficiency that can be applied to other applications, which we demonstrate with the HPCG benchmark. We conclude with a discussion about the relationship to the commonly-used GF/Watt metric.

We present performance results for the simulation of proteins suspensions in crowding conditions obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. Previous versions of MUPHY have been used in the past for the simulation of blood flow through the human coronary arteries and DNA translocation across nanopores. The simulation exhibits excellent scalability up to 18, 000 K20X Nvidia GPUs and achieves almost 20 Petaflops of aggregate sustained performance with a peak performance of 27.5 Petaflops for the most intensive computing component. Those figures demonstrate once again the flexibility of MUPHY in simulating biofluidic phenomena, exploiting at their best the features of the architecture in use. Preliminary results were obtained in the present case on a completely different platform, the IBM Blue Gene/Q. The combination of novel mathematical models, computational algorithms, hardware technology, code tuning and parallelization techniques required to achieve these results are presented.

We present a computational framework for multi-scale simulations of real-life biofluidic problems. The framework allows to simulate suspensions composed by hundreds of millions of bodies interacting with each other and with a surrounding fluid in complex geometries. We apply the methodology to the simulation of blood flow through the human coronary arteries with a spatial resolution comparable with the size of red blood cells, and physiological levels of hematocrit (the red blood cell volume fraction). The simulation exhibits excellent scalability on a cluster of 4000 M2050 Nvidia GPUs and achieves close to 1 Petaflop aggregate performance, which demonstrates the capability to predicting the evolution of biofluidic phenomena of clinical significance. The combination of novel mathematical models, computational algorithms, hardware technology, code tuning and optimization required to achieve these results are presented.

This paper describes the use of CUDA to accelerate the Himeno benchmark on clusters with GPUs. The implementation is designed to optimize memory bandwidth utilization. Our approach achieves over 83% of the theoretical peak bandwidth on a NVIDIA Tesla C1060 GPU and performs at over 50 GFlops. A multi-GPU implementation that utilizes MPI alongside CUDA streams to overlap GPU execution with data transfers allows linear scaling and performs at over 800 GFlops on a cluster with 16 GPUs. The paper presents the optimizations required to achieve this level of performance.

Abstract We describe the porting of the Lattice Boltzmann component of MUPHY, a multi‐physics/scale simulation software, to multiple graphics processing units using the Compute Unified Device Architecture. The novelty of this work is the development ofad hoctechniques for optimizing the indirect addressing that MUPHY uses for efficient simulations of irregular domains. Copyright © 2009 John Wiley & Sons, Ltd.