Name | Region | Skills | Interests |
---|---|---|---|
Adrian Del Maestro | Northeast | ||
Anita Schwartz | Campus Champions | ||
Andrew Sherman | ACCESS CSSN, Campus Champions, CAREERS | ||
Chris Carothers | CAREERS | ||
Cody Stevens | Campus Champions | ||
Balamurugan Desinghu | ACCESS CSSN, Campus Champions, CAREERS, Northeast | ||
Daniel Howard | RMACC, Campus Champions, ACCESS CSSN | ||
Edwin Posada | Campus Champions | ||
Gaurav Khanna | Campus Champions, CAREERS, Northeast | ||
Craig Gross | Campus Champions | ||
Jacob Pessin | Northeast | ||
Katia Bulekova | ACCESS CSSN, Campus Champions, CAREERS, Northeast | ||
Marina Kraeva | Campus Champions | ||
Thomas Langford | Campus Champions, CAREERS | ||
Lonnie Crosby | Campus Champions | ||
Martin Cuma | RMACC, Campus Champions | ||
Michael Puerrer | Campus Champions, Northeast | ||
Justin Oelgoetz | Campus Champions | ||
Paul Rulis | Campus Champions | ||
Ron Rahaman | Campus Champions | ||
Sean Anderson | Campus Champions | ||
Grant Scott | Great Plains | ||
Xiaoqin Huang | ACCESS CSSN | ||
Shaohao Chen | Northeast | ||
Swabir Silayi | Campus Champions | ||
Seung Woo Son | Northeast | ||
William Lai | ACCESS CSSN |
Title | Date |
---|---|
COMPLECS: Parallel Computing Concepts | 5/02/24 |
Title | Category | Tags | Skill Level |
---|---|---|---|
Advanced Compilers: The Self-Guided Online Course | Learning | optimization, parallelization, training, compiling | Advanced |
Benchmarking with a cross-platform open-source flow solver, PyFR | Tool | finite-element-analysis, benchmarking, parallelization, github, fluid-dynamics, openmpi, c++, cuda, mpi | Intermediate |
Bioinformatics Workflow Management with Nextflow | Docs | cloud-computing, parallelization, data-management, bioinformatics, training | Beginner, Intermediate |
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.
Rensselaer Polytechnic Institute
CAREERS
mentor, steering committee, regional admin
University of Rhode Island
Campus Champions, Northeast
research computing facilitator
University of Rhode Island
Campus Champions, CAREERS, Northeast
mentor, regional facilitator, researcher/educator, research computing facilitator, Affinity Group Leader, steering committee
Old Dominion University
Campus Champions, Northeast, ACCESS CSSN
mentor, research computing facilitator, cssn
University of Missouri-Kansas City
Campus Champions
researcher/educator, research computing facilitator