MATCHPlus

I am new to ACCESS. I have a little bit of past experience running code on NCSA's Blue Waters. As a self-taught programmer, it would be interesting to learn from an experienced mentor. 

Here's an overview of my project:

Anxiety detection is topic that is actively studied but struggles to generalize and perform outside of controlled lab environments. I propose to critically analyze state of the art detection methods to quantitatively quantify failure modes of existing applied machine learning models and introduce methods to robustify real-world challenges. The aim is to start the study by performing sensitivity analysis of existing best-performing models, then testing existing hypothesis of real-world failure of these models. We predict that this will lead us to understand more deeply why models fail and use explainability to design better in-lab experimental protocols and machine learning models that can perform better in real-world scenarios. Findings will dictate future directions that may include improving personalized health detection, careful design of experimental protocols that empower transfer learning to expand on existing reach of anxiety detection models, use explainability techniques to inform better sensing methods and hardware, and other interesting future directions.

Sea levels are rising (3.7 mm/yr and increasing!)! The primary contributor to rising sea levels is enhanced polar ice discharge due to climate change. However, their dynamic response to climate change remains a fundamental uncertainty in future projections. Computational cost limits the simulation time on which models can run to narrow the uncertainty in future sea level rise predictions.  The project's overarching goal is to leverage GPU hardware capabilities to significantly alleviate the computational cost and narrow the uncertainty in future sea level rise predictions. 

[Plan A] The PI is investigating numerical techniques to predict ice-sheet flow for large-to-continental glaciers on GPUs. Suppose a successful technique has been identified, implemented in MATLAB, and verified prior to the start of this project. In that case, the objective will be to port the code to CUDA C and investigate techniques to justify the GPU implementation in the price and power consumption to performance metric compared to a "standard" CPU implementation.

[Plan B] The PI developed a preliminary GPU implementation to predict ice-sheet flow for regional-scale glaciers on GPUs. The GPU ice velocity predictions agreed (~ 1% discrepancy) with a "standard" CPU implementation for the chosen glacier model configurations and input data. The GPU implementation was justified in the price and power consumption to performance metrics. However, the profiling results from the preliminary GPU implementation indicated non-optimal global memory access patterns reported in the LITEX and L2 cache. Furthermore, we observed significant drops in effective memory throughput with increased spatial resolution or degrees of freedom (DoFs). This project will aim to investigate techniques to reduce mesh non-localities and drop in effective memory throughput with an increase in spatial resolution. 

My ongoing project is focused on using species trait value (as data matrices) and its corresponding phylogenetic relationship (as a distance matrix) to reconstruct the evolutionary history of the smoke-induced seed germination trait. The results of this project are expected to increase the predictability of which untested species could benefit from smoke treatment, which could promote germination success of native species in ecological restoration. This computational resources allocated for this project pull from the high-memory partition of our Ivy cluster of HPCC (Centos 8, Slurm 20.11, 1.5 TB memory/node, 20 core /node, 4 node). However, given that I have over 1300 species to analyze, using the maximum amount of resources to speed up the data analysis is a challenge for two reasons: (1) the ancestral state reconstruction (the evolutionary history of plant traits) needs to use the Markov Chain Monte Carlo (MCMC) in Bayesian statistics, which runs more than 10 million steps and, according to experienced evolutionary biologists, could take a traditional single core simulation up 6 months to run; and (2) my data contain over 1300 native species, with about 500 polymorphic points (phylogenetic uncertainty), which would need a large scale of random simulation to give statistical strength. For instance, if I use 100 simulations for each 500 uncertainty points, I would have 50,000 simulated trees. Based on my previous experience with simulations, I could design codes to parallel analyze 50,000 simulated trees but even with this parallelization the long run MCMC will still require 50000 cores to run for up to 6 months. Given this computational and evolutionary research challenge, my current work is focused on discovering a suitable parallelization methods for the MCMC steps. I hope to have some computational experts to discuss my project.