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GTC ON-DEMAND

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Abstract:
The chemical shift of a protein structure offers a lot of information about the physical properties of the protein. Being able to accurately predict this shift is essential in drug discovery and in some other areas of molecular dynamics research. But because chemical shift prediction algorithms are so computationally intensive, no application can predict chemical shift of large protein structures in a realistic amount of time. We explored this problem by taking an algorithm called PPM_One and ported it to NVIDIA V100 GPUs using the directive-based programming model, OpenACC. When testing several different protein structures of datasets ranging from 1M to 11M atoms we observed ~45X average speedup between the datasets and a maximum of a 61X speedup. We'll discuss techniques to overcome programmatic challenges and highlight the scientific advances enabled by the model OpenACC.
The chemical shift of a protein structure offers a lot of information about the physical properties of the protein. Being able to accurately predict this shift is essential in drug discovery and in some other areas of molecular dynamics research. But because chemical shift prediction algorithms are so computationally intensive, no application can predict chemical shift of large protein structures in a realistic amount of time. We explored this problem by taking an algorithm called PPM_One and ported it to NVIDIA V100 GPUs using the directive-based programming model, OpenACC. When testing several different protein structures of datasets ranging from 1M to 11M atoms we observed ~45X average speedup between the datasets and a maximum of a 61X speedup. We'll discuss techniques to overcome programmatic challenges and highlight the scientific advances enabled by the model OpenACC.  Back
 
Topics:
Computational Biology & Chemistry
Type:
Talk
Event:
GTC Silicon Valley
Year:
2019
Session ID:
S9277
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Abstract:
We'll discuss the Max Planck/University of Chicago Radiative MHD code (MURaM), the primary model for simulating the sun's upper convection zone, its surface, and the corona. Accelerating MURaM allows physicists to interpret high-resolution solar observations. We'll describe the programmatic challenges and optimization techniques we employed while using the OpenACC programming model to accelerate MURaM on GPUs and multicore architectures. We will also examine what we learned and how it could be broadly applied on atmospheric applications that demonstrate radiation-transport methods.
We'll discuss the Max Planck/University of Chicago Radiative MHD code (MURaM), the primary model for simulating the sun's upper convection zone, its surface, and the corona. Accelerating MURaM allows physicists to interpret high-resolution solar observations. We'll describe the programmatic challenges and optimization techniques we employed while using the OpenACC programming model to accelerate MURaM on GPUs and multicore architectures. We will also examine what we learned and how it could be broadly applied on atmospheric applications that demonstrate radiation-transport methods.  Back
 
Topics:
Climate, Weather & Ocean Modeling, Programming Languages
Type:
Talk
Event:
GTC Silicon Valley
Year:
2019
Session ID:
S9288
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