Edis Jakupovic wins two departmental prizes | About | Beckstein Lab

Undergraduate student Edis Jakupovic was awarded two prizes in the Department of Physics.

John and Richard Jacob Award for Undergraduate Research

He won the John and Richard Jacob Award for Undergraduate Research for his research on MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package that he presented in the 2021 Undergraduate Research Symposium (where you can watch a video of his presentation).

Winners of the awards for undergraduate research in the Department of Physics in 2021.

He summarized his project so: MDAnalysis is a Python library for the analysis of molecular dynamics simulations. As datafiles are now typically terabytes in size, file I/O has become a bottleneck in the workflow of analyzing simulation trajectories. We have implemented an HDF5-based file format trajectory reader into MDAnalysis that can perform parallel MPI IO and benchmarked it on various national high-performance computing environments. Although speed-ups on the order of 20x for 48 cores are attainable, scaling up to achieve higher parallel data ingestion rates remains challenging. We developed several algorithmic optimizations in our analysis workflows that lead to improvements in IO times of up to 91x on 112 cores.

2021 Chair’s Distinguished Senior Award

For his overall outstanding academic performance he was awarded one of the 2021 Chair’s Distinguished Senior Awards. The Chair of the Department of Physics, Prof. Patricia Rankin awarded the prize in the 2021 virtual award ceremony.

2021 Chair's Distinguished Senior Award (Department of Physics): Chase Hanson, Edis Jakupovic, Lillian Otteson, Tal Sneh. Presented by Chair Prof. Patricia Rankin.