Comprehensive Evaluation of OpenCL-based Convolutional Neural Network Accelerators in Xilinx and Altera FPGAs

Deep learning has significantly advanced the state of the art in artificial intelligence, gaining wide popularity from both industry and academia. Special interest is around Convolutional Neural Networks (CNN), which take inspiration from the hierarchical structure of the visual cortex, to form deep layers of convolutional operations, along with fully connected classifiers. Hardware implementations of these deep CNN architectures are challenged with memory bottlenecks that require many convolution and fully-connected layers demanding large amount of communication for parallel computation. Multi-core CPU based solutions have demonstrated their inadequacy for this problem due to the memory wall and low parallelism. Many-core GPU architectures show superior performance but they consume high power and also have memory constraints due to inconsistencies between cache and main memory. FPGA design solutions are also actively being explored, which allow implementing the memory hierarchy using embedded BlockRAM. This boosts the parallel use of shared memory elements between multiple processing units, avoiding data replicability and inconsistencies. This makes FPGAs potentially powerful solutions for real-time classification of CNNs. Both Altera and Xilinx have adopted OpenCL co-design framework from GPU for FPGA designs as a pseudo-automatic development solution. In this paper, a comprehensive evaluation and comparison of Altera and Xilinx OpenCL frameworks for a 5-layer deep CNN is presented. Hardware resources, temporal performance and the OpenCL architecture for CNNs are discussed. Xilinx demonstrates faster synthesis, better FPGA resource utilization and more compact boards. Altera provides multi-platforms tools, mature design community and better execution times

High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols

Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications