Using Performance Analysis Tools to Speed Up Your Codes and Workflows

Presenters: John Stone (Theoretical and Computational Biophysics Group) and Galen Arnold (NCSA), University of Illinois

Tuesday, June 1, 2021



Sample Lorenz Code slides:

Python Programming video:


The profiling and performance analysis webinar will address application performance from theoretical principles (Amdahl’s law) to real world applications of performance tools and tuning scenarios. Traditional compiled languages (C/C++/Fortran) as well as Python will be used with both CPU and GPU platforms as hardware implementations.


Galen Arnold: As a system engineer with NCSA, Galen enjoys helping people get the most out of HPC systems such as: Blue Waters and XSEDE systems with accelerators. He’s part of the Blue Waters applications support team. He has a good working knowledge of most things unix/linux/hpc/networking and has a knack for debugging code. He believes k&r-c is the one true language but reluctantly admits the superior numerical performance of fortran codes.

John Stone: Mr. Stone is a Senior Research Programmer with the Theoretical and Computational Biophysics Group and NIH Center for Macromolecular Modeling and Bioinformatics. Stone is the lead developer of VMD, a high performance tool for preparation, analysis, and visualization of biomolecular simulations used by over 100,000 researchers all over the world. Our research papers describing VMD and its algorithms have been cited by more than 33,000 peer-reviewed research papers, both by users of VMD itself and by researchers developing related software and algorithms. Mr. Stone’s research interests include molecular visualization, GPU computing, parallel computing, ray tracing, haptics, virtual environments, and immersive visualization. Mr. Stone is a frequent presenter and mentor in HPC and exascale computing training workshops and related “Hackathon” events that aim to give computational scientists both the knowledge of theory and the practical experience they need to successfully develop high performance scientific software for next-generation parallel computing systems. Mr. Stone was inducted as an NVIDIA CUDA Fellow in 2010. In 2015 Mr. Stone joined the Khronos Group Advisory Panel for the Vulkan Graphics API. In 2017, 2018, and 2019 Mr. Stone was awarded as an IBM Champion for Power, for innovative thought leadership in the technical community. In 2020, Mr. Stone joined the Khronos working group for ANARI, a new analytic rendering standard for high-fidelity scientific and technical visualization. Mr. Stone and coathors won the ACM Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research at Supercomputing 2020. He also provides consulting services for projects involving computer graphics, GPU computing, and high performance computing. See also: John Stone