Specialize in developing, debugging, and optimizing large complex scientific modeling codes designed to run on High Performance Computing (HPC) platforms. Experience and skills also include visualizing model outputs using a variety of commercial and open source tools and working with other researchers in writing and submitting for publication in scientific peer-reviewed journals. Also skilled in teaching and in presentation of complex scientific topics to highly varied audiences.
NASA Open Science - by NASA Transform to Open Science, 2/2024
AWS Certified Solutions Architect - Associate, 2/2022-2/2025. ID: 34GKJ5C1JEF4QHWE
ORCiD: https://orcid.org/0000-0003-0408-9324
Campus Champion for XSEDE, Extreme Science and Engineering Development Environment
IBM AI Engineering by IBM on Coursera, 10/2020. ID: K3BLMN348SX
Independent Consultant, specializing in developing, debugging, optimizing, and parallelizing large complex scientific modeling codes and designed to run on High Performance Computing (HPC) platforms.
Algorithm development of biogeochemical model CGEM (Coastal Gulf Ecology Model), incorporate CGEM as a bio module for the SCHISM hydrodynamics model. Train and assist other PI/Co-PIs, post-docs, and students to effectively use NSF high performance computing (HPC) resources, including compiling and installation, parallelization, optimization, and code refactoring. NSF computational resources awarded under XSEDE/ACCESS(EES210015) include large distributed systems for hydrodynamics modeling(Expanse, SDSC), GPUs for machine learning(Bridges2, PSC), Ceph storage for model outputs(Open Storage Network), and cloud instances for hosting web applications(Jetstream2).
See:
OyBcSt GitHub Organization – a collection of code and Jupyter Notebooks with sample data and analysis for transparency and reproducibility
OyBcSt Hydrodynamics page – a Jupyter Book website showcasing high resolution model visualizations, an R Shiny app, and GIS products(KMZ)
Assist ORD, Center for Computational Toxicology & Exposure (CCTE), Great Lakes Toxicology & Ecology Division with highly specialized mathematical modeling, high-performance computer coding and optimization skills to develop and improve mathematical models of the Great Lakes, Gulf of Mexico and other coastal systems: Incorporating biogeochemical models into the FVCOM hydrodynamics model, port legacy R scripts and VisIt interactive workflows into Python scripts that may be run in batch mode on HPC resources to create images and animations for large outputs.
See:
NC State's Henry2 HPC cluster is an Intel Xeon based Linux cluster, and compute nodes include a mix of several generations of Intel Xeon processors primarily in dual-socket blade servers, some having attached GPUs.
Support for North Carolina State’s high-performance computing (HPC) cluster:
Provide guidance and instruction in optimal use of the heterogeneous environment, including hardware targeted compiling. Also provide support for installing user maintained software in a shared environment. Create modules for non-trivial software stacks including WRF, UFS, MET, and CMAQ.
Offer hands-on training to HPC users from all backgrounds, including rank beginners and researchers from non-traditional fields. Training materials include video tutorials created in Camtasia and hosted on YouTube. For example, see HPC Terminology and 'Core' Concepts.
Offer consultations in HPC best practices, workflow optimization, code development, debugging, and parallelization. Example projects include: writing scripts or MPI wrappers to bundle serial jobs, porting code or script (e.g., C++, MATLAB) with Windows specific syntax/libraries to work on Linux, modifying existing Fortran analysis codes to subroutines then using f2py to allow the routines to be called from Python, and support for using profiling tools (e.g., ARM Forge, snakeviz).
Offer consultations on using HPC in the classroom, including creating custom HPC training modules and demos that align with the course goals and objectives.
Develop projects for and supervise HPC interns. Projects include writing scripts to assist HPC staff with monitoring utilization, to assist users in checking memory and utilization of running jobs, and to organize 'Software Affinity Groups' (e.g. Bioinformatics Users Group) to facilitate communication between researchers with similar workflows on the HPC.
Connect researchers with external resources such as XSEDE/ACCESS or DOE Leadership Computing Facilities.
Obtain external funding through grants and contracts (NOAA, EPA).
As part of the Environmental Modeling and Visualization (EMVL) team
Participated in the development and performance optimization of environmental and human health models, scientific visualization, data analysis, and applications consulting
Provided demonstrations of EMVL work to EPA scientists, managers, guests, and student groups
Worked with EPA scientists to develop project proposals, project management plans and quality assurance project plans, and maintained transparency and clarity of communication between EMVL and EPA using Wikis, OneDrive, and SharePoint
Assisted EPA scientists, Postdoctoral and Student Fellows, and collaborators to access and use HPC resources
Supported a wide variety of scientific research projects including
Coastal General Ecology Model (CGEM) - Project Lead
Collaborating with EPA and Naval Research Laboratory (NRL) scientists to develop and improve codes that model the physics, chemistry, and biology of the waters of the Gulf of Mexico.
Scientific code development with optimization for HPC
Parallelized two hydrodynamics codes (MPI, hybrid MPI-OpenMP)
Automated calibration, running, post processing, and visualization using R, Python, and VisIt
Generalized CGEM for a generic grid to be used outside of the Gulf of Mexico for generic hydrodynamic inputs including a single cell version CGEM-0D that will run on Linux, Windows, or MacOS
CGEM-0D used to perform parameter sensitivity and identifiability analysis for the bio-geo-chemical model, which has over 200 calibration parameters
Streamline Modeling of Subsurface Contaminants
Developed a FORTRAN program to interpret and interpolate unstructured grid output data from ModFlow and extract data along the calculated streamlines to be used as input to a subsurface contaminant model.
Risk Assessment Modeling
Used R and OpenBugs to perform Bayesian modeling for cancer models, developed R functions and scripts to analyze OpenBugs results, plot distributions, and test for Markov Chain Monte Carlo convergence
Optimization - Project Lead
Used Allinea MAP and Intel VTune to profile and analyze the code to identify bottlenecks and suggest code modifications to decrease run time, also consulted on methods of parallel debugging and error visualization.
As a post-doctoral Fellow at EPA, focused on these three projects:
Bayesian Markov Chain Monte Carlo Physiologically Based Pharmacokinetic (PBPK) modeling: Adapted the Methanol Monkey PK model in acslX into a hierarchical Bayesian PK model to characterize variability in the enzyme kinetics and background methanol levels of monkeys. Developed an MCSim version to optimize performance and run on HPC.
IRIS assessment of Methanol: Support for the Methanol IRIS assessment including literature search and analysis of scientific studies, preparation of responses to peer review charges, using Benchmark Dose Software Modeling (BMDS) to model dose-response, and contributing to the final editing of the IRIS assessment.
Training Materials Support: Worked with EPA scientists and contractors to develop Risk Assessment Training Experience (RATE). Assisted in code testing of BMDS and Categorical Regression (CatReg) software and facilitating a BMDS training course at the Society of Risk Analysis.
AMRMG – a Parallel AMR Nonlinear Multigrid Solver: Developed a parallel nonlinear multigrid solver with adaptive mesh refinement. AMRMG is used to provide the initial data for the relativity group at NASA/GSFC and has made possible one of the first successful evolutions of a binary black hole merger.
Distorted Black Holes using the Puncture Method: Used AMRMG to create a new class of initial data for Numerical Relativity. The sets may represent conditions immediately following a binary black hole merger.
Investigating the Constraints with Spectral Methods: Developed a spectral methods code to investigate and remedy the inherent instability problems in the ADM 3+1 Einstein evolution equations. The stabilization technique is purely mathematical, and can be applied to any system of equations.
Level Set Method Apparent Horizon Finder: Developed a robust and generic apparent horizon finder for analytic or numerically generated (from AMRMG) spacetimes.
Field line tracing routine for ParM3D: Developed a field line tracing program for general toroidal geometry as a diagnostic tool for a parallel MHD code using finite elements on unstructured meshes. (Technical Report), (Seminar)
ORBIT MPI: Implemented an MPI-based parallelization of ORBIT, a guiding center drift orbit integrator. Improves the performance of the code to scale linearly on parallel machines. (Technical Report)
Dynamical instability in polytrope stars: Developed scripts and automated visualizations for exploration of a vast parameter space of initial equilibrium models of polytrope stars.
Bar mode instability simulation support: Updated legacy FORTRAN code, verified routines, ran code in batches on supercomputers, managed data, and produced publication grade visualizations.
Documentation of ADM code: Produced a user’s manual for an extensive FORTRAN numerical relativity evolution code in LaTeX, including verification and documentation of analytical formulas.
Ph.D. Physics (Dissertation in Numerical Relativity), North Carolina State University, Raleigh, NC (2008)
Graduate Certificate in Environmental Assessment, North Carolina State University, Raleigh, NC (2012)
B.S. Physics, Drexel University, Philadelphia, PA (2001)
Liu Z, Lehrter J, Dzwonkowski B, Lowe LL and Coogan J. Using dissolved oxygen variance to investigate the influence of nonextreme wind events on hypoxia in Mobile Bay, a shallow stratified estuary. Front. Mar. Sci. 9:989017, 2002-11-01.
Brandon M. Jarvis, James J. Pauer, Wilson Melendez, Yongshan Wan, John C. Lehrter, Lisa L. Lowe, and Cody W. Simmons. Inter-model comparison of simulated Gulf of Mexico hypoxia in response to reduced nutrient loads: Effects of phytoplankton and organic matter parameterization. Environmental Modelling & Software, 2022-03.
Wang, F., Tian, D., Lowe, L., Kalin, L., & Lehrter, J. Deep learning for daily precipitation and temperature downscaling. Water Resources Research, 57, e2020WR029308: 2021.
Brandon M. Jarvis, Richard M. Greene, Yongshan Wan, John C. Lehrter, Lisa L. Lowe, and Dong S. Ko. Contiguous Low Oxygen Waters between the Continental Shelf Hypoxia Zone and Nearshore Coastal Waters of Louisiana, USA: Interpreting 30 Years of Profiling Data and Three-Dimensional Ecosystem Modeling. Environmental Science and Technology, 2021-03-08.
James J. Pauer, Wilson Melendez, Timothy J. Feist, John C. Lehrter, Brenda Rashleigh, Lisa L. Lowe, Richard M. Green. The impact of alternative nutrient kinetics and computational grid size on model predicted primary production and hypoxic area in the northern Gulf of Mexico. Environmental Modelling & Software, Volume 126, 2020, 104661.
Brandon M. Jarvis, John C. Lehrter, Lisa L. Lowe, James D. Hagy, Yongshan Wan, Michael C. Murrell, Dong S. Ko, Bradley Penta, and Richard W. Gould Jr. Modeling Spatiotemporal Patterns of Ecosystem Metabolism and Organic Carbon Dynamics Affecting Hypoxia on the Louisiana Continental Shelf. JGR Oceans, Volume 125, Issue 4: 2020.
M. Beck, J. Lehrter, L. Lowe, and B. Jarvis. Parameter sensitivity and identifiability for a biogeochemical model of hypoxia in the northern Gulf of Mexico. Ecological Modelling. Elsevier Science BV, Amsterdam, Netherlands, 363:17-30, 2017.
J. Lehrter, D. S. Ko, L. L. Lowe, and B. Penta. Predicted effects of climate change on northern Gulf of Mexico hypoxia. Modeling Coastal Hypoxia: Numerical Simulations of Patterns, Controls and Effects of Dissolved Oxygen Dynamics. Springer, 2016.
J. David Brown and Lisa L. Lowe, Modifying the Einstein Equations off the Constraint Hypersurface. Physical Review, D74:104023, 2006.
J. David Brown and Lisa L. Lowe, Multigrid Elliptic Equation Solver with Adaptive Mesh Refinement. Journal of Computational Physics, 209:582-598, 2005.
J. David Brown and Lisa L. Lowe. Distorted Black Hole Initial Data Using the Puncture Method. Physical Review, D70:124014, 2004.
Joan M. Centrella, Kimberly C. B. New, Lisa L. Lowe, and J. David Brown. Dynamical Rotational Instability at Low T/W. Astrophysical Journal Letters:550:L193-L196, 2001.
Tang, X Z, Fu, G Y, Jardin, S C, Lowe, L L, Park, W, & Strauss, H R. Resistive Magnetohydrodynamics Simulation of Fusion Plasmas. United States. 2001.
Lowe, Lisa L. Orbitmpi Documentation. United States. 2000.