Comparative analysis of software optimization methods in context of branch predication on GPUs

General Purpose computing for Graphical Processing Units (GPGPU) technology is a powerful tool for offloading parallel data processing tasks to Graphical Processing Units (GPUs). This technology finds its use in variety of domains – from science and commerce to hobbyists. GPU-run general-purpose programs will inevitably run into performance issues stemming from code branch predication. Code predication is a GPU feature that makes both conditional branches execute, masking the results of incorrect branch. This leads to considerable performance losses for GPU programs that have large amounts of code hidden away behind conditional operators. This paper focuses on the analysis of existing approaches to improving software performance in the context of relieving the aforementioned performance loss. Description of said approaches is provided, along with their upsides, downsides and extents of their applicability and whether they address the outlined problem. Covered approaches include: optimizing compilers, JIT-compilation, branch predictor, speculative execution, adaptive optimization, run-time algorithm specialization, profile-guided optimization. It is shown that the aforementioned methods are mostly catered to CPU-specific issues and are generally not applicable, as far as branch-predication performance loss is concerned. Lastly, we outline the need for a separate performance improving approach, addressing specifics of branch predication and GPGPU workflow.

Opal: An open source ray-tracing propagation simulator for electromagnetic characterization

Accurate characterization and simulation of electromagnetic propagation can be obtained by ray-tracing methods, which are based on a high frequency approximation to the Maxwell equations and describe the propagating field as a set of propagating rays, reflecting, diffracting and scattering over environment elements. However, this approach has been usually too computationally costly to be used in large and dynamic scenarios, but this situation is changing thanks the increasing availability of efficient ray-tracing libraries for graphical processing units. In this paper we present Opal, an electromagnetic propagation simulation tool implemented with ray-tracing on graphical processing units, which is part of the Veneris framework. Opal can be used as a stand-alone ray-tracing simulator, but its main strength lies in its integration with the game engine, which allows to generate customized 3D environments quickly and intuitively. We describe its most relevant features and provide implementation details, highlighting the different simulation types it supports and its extension possibilites. We provide application examples and validate the simulation on demanding scenarios, such as tunnels, where we compare the results with theoretical solutions and further discuss the tradeoffs between the simulation types and its performance.

Quantum Chemistry for Molecules at Extreme Pressure on Graphical Processing Units: Implementation of Extreme Pressure Polarizable Continuum Model

Pressure plays essential roles in chemistry by altering structures and controlling chemical reactions. The extreme-pressure polarizable continuum model (XP-PCM) is an emerging method with an efficient quantum mechanical description of small and medium-size molecules at high pressure (on the order of GPa). However, its application to large molecular systems was previously hampered by CPU computation bottleneck: the Pauli repulsion potential unique to XP-PCM requires the evaluation of a large number of electric field integrals, resulting in significant computational overhead compared to the gas-phase or standard-pressure polarizable continuum model calculations. Here, we exploit advances in Graphical Processing Units (GPUs) to accelerate the XP-PCM integral evaluations. This enables high-pressure quantum chemistry simulation of proteins that used to be computationally intractable. We benchmarked the performance using 18 small proteins in aqueous solutions. Using a single GPU, our method evaluates the XP-PCM free energy of a protein with over 500 atoms and 4000 basis functions within half an hour. The time taken by the XP-PCM-integral evaluation is typically 1\% of the time taken for a gas-phase density functional theory (DFT) on the same system. The overall XP-PCM calculations require less computational effort than that for their gas-phase counterpart due to the improved convergence of self-consistent field iterations. Therefore, the description of the high-pressure effects with our GPU accelerated XP-PCM is feasible for any molecule tractable for gas-phase DFT calculation. We have also validated the accuracy of our method on small molecules whose properties under high pressure are known from experiments or previous theoretical studies.