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X-ray crystallography is a powerful method that has significantly contributed to our understanding of the biological function of proteins and other molecules. This method relies on the production of crystals that, however, are usually a bottleneck in the process. For some molecules, no crystallization has been achieved or insufficient crystals were obtained. Some other systems do not crystallize at all, such as nanoparticles which, because of their dimensions, cannot be treated by the usual crystallographic methods. To solve this, whole pair distribution function has been proposed to bridge the gap between Bragg and Debye scattering theories. To execute a fitting, the spectra of several different constructs, composed of millions of particles each, should be computed using a particle-pair or particle-particle (pp) distance algorithm. Using this computation as a test bench for current field-programmable gate array (FPGA) technology, we evaluate how the parallel computation capability of FPGAs can be exploited to reduce the computation time. We present two different solutions to the problem using two state-of-the-art FPGA technologies. In the first one, the main C program uses OmpSs (a high-level programming model developed at the Barcelona Supercomputing Center, that enables task offload to different high-performance computing devices) for task invocation, and kernels are built with OpenCL using reduced data sizes to save transmission time. The second approach uses task and data parallelism to operate on data locally and update data globally in a decoupled task. Benchmarks have been evaluated over an Intel D5005 Programmable Acceleration Card, computing a model of 2 million particles in 81.57 s - 24.5 billion atom pairs per second (bapps)- and over a ZU102 in 115.31 s. In our last test, over an up-to-date Alveo U200 board, the computation lasted for 34.68 s (57.67 bapps). In this study, we analyze the results in relation to the classic terms of speed-up and efficiency and give hints for future improvements focused on reducing the global job time., This work was partially supported by the Spanish Government (AEI) and European Union (FEDER) (projects CTQ2017-88948-P, PID2021-124848OB-I00, RTI2018-095232-B-C21, SEV-2015-0493 and TIN2015-65316-P, grant BES-2016-078046) and by the Generalitat de Catalunya (contracts 2017-SGR-1742, 2017-SGR-1414, 2017-SGR-670 and 2017-SGR-1328).

Nowadays, a new parallel paradigm for energy-efficient heterogeneous hardware infrastructures is required to achieve better performance at a reasonable cost on high-performance computing applications. Under this new paradigm, some application parts are offloaded to specialized accelerators that run faster or are more energy-efficient than CPUs. Field-Programmable Gate Arrays (FPGA) are one of those types of accelerators that are becoming widely available in data centers. This paper proposes OmpSs@cloudFPGA, which includes novel extensions to parallel task-based programming models that enable easy and efficient programming of heterogeneous clusters with FPGAs. The programmer only needs to annotate, with OpenMP-like pragmas, the tasks of the application that should be accelerated in the cluster of FPGAs. Next, the proposed programming model framework automatically extracts parts annotated with High-Level Synthesis (HLS) pragmas and synthesizes them into hardware accelerator cores for FPGAs. Additionally, our extensions include and support two novel features: 1) FPGA-to-FPGA direct communication using a Message Passing Interface (MPI) similar Application Programming Interface (API) with one-to-one and collective communications to alleviate host communication channel bottleneck, and 2) creating and spawning work from inside the FPGAs to their own accelerator cores based on an MPI rank-like identification. These features break the classical host-accelerator model, where the host (typically the CPU) generates all the work and distributes it to each accelerator. We also present an evaluation of OmpSs@cloudFPGA for different parallel strategies of the N-Body application on the IBM cloudFPGA research platform. Results show that for cluster sizes up to 56 FPGAs, the performance scales linearly. To the best of our knowledge, this is the best performance obtained for N-body over FPGA platforms, reaching 344 Gpairs/s with 56 FPGAs. Finally, we compare the performance and power consumption of the proposed approach with the ones obtained by a classical execution on the MareNostrum 4 supercomputer, demonstrating that our FPGA approach reduces power consumption by an order of magnitude. This work has been done in the context of the IBM/BSC Deep Learning Center initiative. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 754337 (EuroEXA), from Spanish Government (PID2019-107255GBC21/AEI/10.13039/501100011033), and from Generalitat de Catalunya (2017-SGR-1414 and 2017-SGR-1328).

This paper presents the new features of the OmpSs@FPGA framework. OmpSs is a data-flow programming model that supports task nesting and dependencies to target asynchronous parallelism and heterogeneity. OmpSs@FPGA is the extension of the programming model addressed specifically to FPGAs. OmpSs environment is built on top of Mercurium source to source compiler and Nanos++ runtime system. To address FPGA specifics Mercurium compiler implements several FPGA related features as local variable caching, wide memory accesses or accelerator replication. In addition, part of the Nanos++ runtime has been ported to hardware. Driven by the compiler this new hardware runtime adds new features to FPGA codes, such as task creation and dependence management, providing both performance increases and ease of programming. To demonstrate these new capabilities, different high performance benchmarks have been evaluated over different FPGA platforms using the OmpSs programming model. The results demonstrate that programs that use the OmpSs programming model achieve very competitive performance with low to moderate porting effort compared to other FPGA implementations. This work has received funding from EuroEXA project (European Union’s Horizon 2020 Research and Innovation Programme, under grant agreement No 754337), from Spanish Government (projects PID2019-107255GB and SEV-2015- 0493, grant BES-2016-078046), and Generalitat de Catalunya (contracts 2017-SGR-1414 and 2017-SGR-1328).

Processor simulators rely on detailed timing models of the processor pipeline to evaluate performance. The diversity in real-world processor designs mandates building flexible simulators that expose parts of the underlying model to the user in the form of configurable parameters. Consequently, the accuracy of modeling a real processor relies on both the accuracy of the pipeline model itself, and the accuracy of adjusting the configuration parameters according to the modeled processor. Unfortunately, processor vendors publicly disclose only a subset of their design decisions, raising the probability of introducing specification inaccuracies when modeling these processors. Inaccurately tuning model parameters deviates the simulated processor from the actual one. In the worst case, using improper parameters may lead to imbalanced pipeline models compromising the simulation output. Therefore, simulation models should be hardware-validated before using them for performance evaluation. As processors increase in complexity and diversity, validating a simulator model against real hardware becomes increasingly more challenging and time-consuming. In this work, we propose a methodology for validating simulation models against real hardware. We create a framework that relies on micro-benchmarks to collect performance statistics on real hardware, and machine learning-based algorithms to fine-tune the unknown parameters based on the accumulated statistics. We overhaul the Sniper simulator to support the ARM AArch64 instruction-set architecture (ISA), and introduce two new timing models for ARM-based in-order and out-of-order cores. Using our proposed simulator validation framework, we tune the in-order and out-of-order models to match the performance of a real-world implementation of the Cortex-A53 and Cortex-A72 cores with an average error of 7% and 15%, respectively, across a set of SPEC CPU2017 benchmarks.