Accelerating Chemical Shift Prediction of Protein Structures using GPUs

Accurate prediction of the chemical shift of a protein is essential in certain areas of molecular dyanamics research such as drug discovery. This is a compute-intensive problem. Currently, there is not an available application that can predict chemical shift of large protein structures in a realistic amount of time. We took a chemical shift prediction application called PPM_One, and accelerated it using OpenACC to reduce the time taken from 10+ hours on a single core to 2 minutes on NVIDIA V100 GPUs.

Parallelization and Acceleration of Nuclear Reactor Miniapp: Minisweep

Denovo is a production code for nuclear reactor neutronics modeling and is in use by a current DOE INCITE project to model the ITER fusion reactor. Our project investigates the sweep kernel within Denovo that counts for approximately 80-99% of Denovo’s overall computational expenses. We use OpenACC, a high-level, directive-based programming model running on NVIDIA’s next-generation Volta GPU for this work and our preliminary shows promising speedup comparable to CUDA.

AccSeq: A High-Level Parallel NGS tool using Novel Time-Memory Efficient Algorithm

This project explores building a fast whole genome sequence alignment algorithm for both long and short reads. The tool is being evaluated with Saccharomyces Genome Database (SGD) (yeast) and human genome sequences. Stay tuned to learn more.

OpenMP Validation and Verification Testsuite

Sunita’s group builds validation and verification (V&V) testsuites for OpenMP directive-based parallel programming models and focusses on the offloading features. Work on OpenMP testsuite is part of the Exascale Computing Project (ECP) SOLLVE project. The testsuite project is funded by Oak Ridge National Laboratory (ORNL). The goal of this project is to validate and verify implementations of the programming model features in various compilers.

OpenACC Validation and Verification Testsuites

Sunita’s group builds validation and verification testsuite (V&V) for OpenACC directive-based paralell programming models. Work on OpenACC testsuite is supported by OpenACC/NVIDIA. The goal of this project is to validate and verify implementations of the programming model features in various compilers. This testsuite has been integrated into the harness infrastructure of the TITAN and Summitdev systems at Oak Ridge National Lab and is being used for production.

Other Research Projects from CRPL Lab

Please refer to my Computational Research and Programming Lab CRPL website for more projects.