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Building a database to rank Standard Performance Evaluation Corporation (SPEC) High Performance Group (HPG’s) results using the work in progress HPC2020 benchmark suite

Monday, Jan 1, 0001

Abstract Performance benchmarks are used to stress test hardware and software of large scale computing systems. A corporation known as SPEC has developed a benchmark suite, SPEC ACCEL, consisting of test codes representative of kernels in large applications. This project ranks the published results from ACCEL based on different criteria. The goal is to prepare a ranking website for the work-in-progress real-world SPEC HPG benchmark suite, HPC2021 that will soon be released (time frame 2020-2021).

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Building an OpenACC Validation and Verification Suite

Monday, Jan 1, 0001

Abstract Heterogeneous computing hasemerged as a promising fit for scientific domains such as molecular dy-namics simulations, bioinformatics, weather prediction. Such a comput-ing paradigm includes x86 processors coupled with GPUs, FPGAs, DSPsor a coprocessor paradigm that takes advantage of all the cores andcaches on a single die such as the Knights Landing. OpenACC, a high-level directive-based parallel programming model has emerged as a pro-gramming paradigm that can tackle the intensity of heterogeneity inarchitectures.

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Building an OpenMP Validation and Verification Suite

Monday, Jan 1, 0001

Abstract Heterogeneous computing hasemerged as a promising fit for scientific domains such as molecular dy-namics simulations, bioinformatics, weather prediction. Such a comput-ing paradigm includes x86 processors coupled with GPUs, FPGAs, DSPsor a coprocessor paradigm that takes advantage of all the cores andcaches on a single die such as the Knights Landing. OpenACC, a high-level directive-based parallel programming model has emerged as a pro-gramming paradigm that can tackle the intensity of heterogeneity inarchitectures.

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Exploring acceleration of PhysiCell

Monday, Jan 1, 0001

Project Abstract: In this paper, we utilize OpenACC, a directive-based programming model to accelerate the diffusion portion PhysiCell, a cross-platform agent-based biosimulatione work that has been adopted in cancer, infectious diseases and other complex biological problems. Using NVIDIA HPC SDK OpenACC 21.3, we demonstrate an almost 40x speedup using managed memory on the state-of-the-art NVIDIA Ampere 100 (A100) GPU compared to a serial AMD EPYC core 7742 for a 360 simulated minutes input dataset.

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Parallelizing NASA parallel benchmarks (NPB) on multiple platforms thus learning parallel programming concepts

Monday, Jan 1, 0001

Project Abstract: Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance (NMR) spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due to the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software.

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