1--- 2orphan: true 3--- 4 5(2025_meeting)= 6 7# 2025 PETSc Annual Users Meeting and Tutorial 8 9## Meeting location 10 11May 20-21, 2025, Davis Hall, University of Buffalo, NY, USA ([105 White Rd, Amherst, NY 14260](https://maps.app.goo.gl/B38RsNe41Zd93rvX7)) 12 13## Meeting times 14 15- Monday, May 19 - Tutorial (tutorials begin at 9am) 16- Tuesday, May 20 - Meeting (begin at 9am) 17- Wednesday, May 21 - Meeting (ends around 5pm) 18 19## Registration 20 21Please [register](https://ti.to/nf-projects/petsc-annual-meeting) to save your seat. 22Fee: \$100, for breaks and lunches; free for students. 23 24## Submit a presentation 25 26[Submit an abstract](https://docs.google.com/forms/d/126KwzajoQvcqU_q7btNsYxFqbe7rJ_vASC-tejZfXDQ) to be included in the schedule. 27We welcome talks from all perspectives, including 28 29- contributions to PETSc 30- use of PETSc in applications or libraries 31- development of libraries and packages [called from PETSc](https://petsc.org/release/install/external_software/) 32- just curious about using PETSc in applications 33 34## Student Travel Support 35 36We have funding to provide travel support for students attending the meeting without their own funding. To apply, check the 37"Student Funding Support" ticket while registering for the meeting. Early registration will increase your chance of obtaining travel support. 38 39## Suggested hotels 40 41- Hotels Near UB North 42 43 - [Motel 6 Amherst, NY](https://www.motel6.com/en/home/property/buffalo-amherst.html) 4400 Maple Rd, Amherst, NY 14226, (716) 834-2231 44 - [Hampton Inn Buffalo - Amherst](https://www.hilton.com/en/hotels/bufcphx-hampton-buffalo-amherst/) 1601 Amherst Manor Dr, Amherst, NY 14221, (716) 559-7010 45 - [Candlewood Suites Buffalo Amherst](https://www.ihg.com/candlewood/hotels/us/en/amherst/bufcw/hoteldetail?cm_mmc=GoogleMaps-_-CW-_-US-_-BUFCW) 20 Flint Rd, Amherst, NY 14226, (716) 688-2100 46 - [DoubleTree by Hilton Hotel Buffalo-Amherst](https://www.hilton.com/en/hotels/buffldt-doubletree-buffalo-amherst/) 10 Flint Rd, Amherst, NY 14226, (716) 689-4414 47 - [Comfort Inn University](https://www.choicehotels.com/new-york/amherst/comfort-inn-hotels/ny293?mc=llgoxxpx) 1 Flint Rd, Amherst, NY 14226, (716) 415-1132 48 - [Fairfield Inn & Suites Buffalo Amherst/University](https://www.marriott.com/en-us/hotels/buffn-fairfield-inn-and-suites-buffalo-amherst-university/overview/?scid=f2ae0541-1279-4f24-b197-a979c79310b0) 3880 Rensch Rd, Amherst, NY 14228, (716) 204-8936 49 - [Staybridge Suites Buffalo-Amherst by IHG](https://www.ihg.com/staybridge/hotels/us/en/amherst/bufrr/hoteldetail?cm_mmc=GoogleMaps-_-SB-_-US-_-BUFRR}) 1290 Sweet Home Rd, Amherst, NY 14228, (716) 276-8750 50 51 52- Hotels in Downtown Buffalo 53 54 - [Holiday In Express & Suites Buffalo Downtown-Medical Ctr by IHG](https://www.ihg.com/holidayinnexpress/hotels/us/en/buffalo/bufms/hoteldetail?cm_mmc=GoogleMaps-_-EX-_-US-_-BUFMS) 601 Main St, Buffalo, NY 14203, (716) 854-5500, Located near a subway station 55 - [Hilton Garden Inn Buffalo Downtown](https://www.hilton.com/en/hotels/bufmsgi-hilton-garden-inn-buffalo-downtown/?SEO_id=GMB-AMER-GI-BUFMSGI&y_source=1_MjA4MTcyMy03MTUtbG9jYXRpb24ud2Vic2l0ZQ%3D%3D) 10 Lafayette Square, Buffalo, NY 14203, (716) 848-1000, Located near a subway station 56 - [Hampton Inn & Suites Buffalo Downtown](https://www.hilton.com/en/hotels/bufdthx-hampton-suites-buffalo-downtown/?SEO_id=GMB-AMER-HX-BUFDTHX&y_source=1_MjA4MzA5Ny03MTUtbG9jYXRpb24ud2Vic2l0ZQ%3D%3D) 220 Delaware Ave, Buffalo, NY 14202, (716) 855-2223, Located near Chippewa St/Nightlife 57 - [Embassy Suites by Hilton Buffalo](https://www.hilton.com/en/hotels/bufeses-embassy-suites-buffalo/?SEO_id=GMB-AMER-ES-BUFESES&y_source=1_MTEwOTkxNC03MTUtbG9jYXRpb24ud2Vic2l0ZQ%3D%3D) 200 Delaware Ave, Buffalo, NY 14202, (716) 842-1000, Located near Chippewa St/Nightlife 58 - [Curtiss Hotel](https://curtisshotel.com/) 210 Franklin St, Buffalo, NY 14202, (716) 954-4900, Located near Chippewa St/Nightlife 59 60## Tentative Agenda 61 62[comment]: # (Intro: Python, Linear/Nonlinear Solver, GPU) 63 64[comment2]: # (Adv: Meshing, SNESVI, Optimization) 65 66### Monday, May 19: Tutorial 67 68| Time | Title | Speaker | 69| -------- | ---------------------------------------------------------------------------------------------------------------------------- | ----------------------- | 70| 9:00 am | Introduction | [Matt Knepley] | 71| 9:15 am | Tutorial I: Introductory PETSc | | 72| 12:00 pm | **Lunch** for tutorial attendees and early arrivees | | 73| 1:30 pm | Emergent flow asymmetries from the metachronal motion of the soft flexible paddles of the gossamer worm | [Alexander Hoover] | 74| 2:00 pm | Tutorial II: Advanced PETSc | | 75| 5:00 pm | End of first day | | 76 77### Tuesday, May 20: Scientific Program 78 79| Time | Title | Speaker | 80| -------- | ---------------------------------------------------------------------------------------------------------------------------- | ----------------------- | 81| 9:00 am | Meeting Introduction | [Matt Knepley] | 82| 9:05 am | A projection method for particle resampling | [Mark Adams] | 83| 9:30 am | Dense Broyden-Fletcher-Goldfarb-Shanno (BFGS) | [Hansol Suh] | 84| 10:00 am | IBAMR: Immersed-Boundary Adaptive Mesh Refinement | [David Wells] | 85| 10:30 am | TaoTerm | [Toby Isaac] | 86| 10:45 am | **Coffee Break** | | 87| 11:00 am | Multiple RHS multigrid for the lattice Dirac equation | [Peter Boyle] | 88| 11:30 am | DMSwarmRT: Ray tracing with PETSc's particle management library DMSwarm | [Joseph Pusztay] | 89| 12:00 pm | Empire AI | [Matt Jones] | 90| 12:15 pm | **Lunch** | | 91| 1:30 pm | Exploring Quantum Phases of Interacting Lattice Models via Exact Diagonalization | [Cheng-Chien Chen] | 92| 2:00 pm | Cardiac Fluid Dynamics | [Boyce Griffith] | 93| 2:30 pm | TBA | [Chris Kees] | 94| 3:00 pm | PetscRegressor | [Richard Mills] | 95| 3:15 pm | **Poster Session and Coffee Break** | | 96| 4:30 pm | **End of Posters** | | 97| 4:45 pm | Leave on bus for dinner at Niagara Falls | | 98 99 100### Wednesday, May 21: Scientific Program 101 102| Time | Title | Speaker | 103| -------- | ---------------------------------------------------------------------------------------------------------------------------- | ----------------------- | 104| 9:00 am | TBA | [Blaise Bourdin] | 105| 9:30 am | Automatic Generation of Matrix-Free Routines for PDE Solvers with Devito via PETSc | [Zoe Leibowitz] | 106| 10:00 am | TBA | [David Salac] | 107| 10:30 am | Making Meshes with DMPlexTransform | [Matt Knepley] | 108| 10:45 am | **Coffee Break** | | 109| 11:00 am | TBA | [Darsh Nathawani] | 110| 11:30 am | TBA | [MOOSE Collective] | 111| 12:00 pm | GitWorkflows | [Satish Balay] | 112| 12:15 pm | **Lunch** | | 113| 1:30 pm | Using PETSc in a Multi-application Environment | [Tim Steinhoff] | 114| 2:00 pm | TBA | [Jack Betteridge] | 115| 2:30 pm | pyop3: A DSL for Unstructured Mesh Stencil Calculations | [Conor Ward] | 116| 3:00 pm | IMEX in PETSc | [Hong Zhang] | 117| 3:15 pm | GPUs in PETSc | [Junchao Zhang] | 118| 3:30 pm | **Coffee Break** | | 119| 3:45 pm | **PETSc Roundtable** | | 120| 4:45 pm | Meeting Closes | | 121 122## List of Abstracts 123 124(alexander-hoover)= 125 126:::{topic} **Emergent flow asymmetries from the metachronal motion of the soft flexible paddles of the gossamer worm** 127**Alexander Hoover** 128 129Cleveland State University 130 131Metachronal waves are ubiquitous in propulsive and fluid transport systems across many different scales and morphologies in the biological world. Gossamer worms, or tomopterids, are a soft-bodied, holopelagic worm that use metachrony with their flexible, gelatinous parapodia to deftly navigate the midwater ocean column that they inhabit. In the following study, we develop a three-dimensional, fluid-structure interaction model, using the IBAMR and libmesh frameworks, of a tomopterid parapodium to explore the emergent metachronal waves formed from the interplay of passive body elasticity, active muscular tension, and hydrodynamic forces. After introducing our model, we examine the effects that varying material properties have on the stroke of an individual parapodium as well as the resulting fluid dynamics. We then explore the temporal dynamics when multiple parapodia are placed sequentially and how differences in the phase can alter the collective kinematics and resulting flow field. Finally, we examine the role of phase differences in a freely-swimming model. 132::: 133 134(mark-adams)= 135 136:::{topic} **A projection method for particle resampling** 137**Mark Adams** 138 139Lawrence Berkeley National Laboratory 140 141Particle discretizations of partial differential equations are advantageous for high-dimensional kinetic models in phase space due to their better scalability than continuum approaches with respect to dimension. Complex processes collectively referred to as particle noise hamper long time simulations with particle methods. One approach to address this problem is particle mesh adaptivity or remapping, known as particle resampling. This talk introduces a resampling method that projects particles to and from a (finite element) function space. The method is simple; using standard sparse linear algebra and finite element techniques, it can adapt to almost any set of new particle locations and preserves all moments up to the order of polynomial represented exactly by the continuum function space. 142 143This work is motivated by the Vlasov-Maxwell-Landau model of magnetized plasmas with up to six dimensions, 3X in physical space and 3V in velocity space, and is developed in the context of a 1X + 1V Vlasov-Poisson model of Landau damping with logically regular particle and continuum phase space grids. Stable long time dynamics are demonstrated up to T=500 and reproducibility artifacts and data with stable dynamics up to T=1000 are publicly available. 144::: 145 146(hansol-suh)= 147 148:::{topic} **Dense Broyden-Fletcher-Goldfarb-Shanno (BFGS)** 149**Hansol Suh** 150 151Argonne National Laboratory 152 153We will present a new dense formulation of BFGS specialize for the Limited Memory-Variable Metric (KSPLMVM) linear solver in PETSc, and illustrate its use for optimization problems. 154::: 155 156(david-wells)= 157 158:::{topic} **IBAMR: Immersed-Boundary Adaptive Mesh Refinement** 159**David Wells** 160 161University of North Carolina, Chapel Hill 162 163IBAMR is a parallel implementation of the immersed boundary method and other relevant numerics, such as Navier-Stokes and multiphase flow solvers. This poster showcases some applications built on IBAMR and describes how they are fundamentally powered by PETSc. 164::: 165 166(joseph-pusztay)= 167 168:::{topic} **DMSwarmRT: Ray tracing with PETSc's particle management library DMSwarm** 169**Joseph Pusztay** 170 171University at Buffalo 172 173In this talk I will present work with DMSwarm, PETSc's parallel particle management library, to construct a general purpose ray trace with applicability to ICF plasma. I will discuss underlying improvements to the DMSwarm API to better support device side computation of swarm operations to facilitate the ray trace, with initial scalability tests and results. Additionally, I will present and discuss light weight time stepping objects for device side computation of systems with large numbers of fields that may be stepped independently. 174::: 175 176(cheng-chien-chen)= 177 178:::{topic} **Exploring Quantum Phases of Interacting Lattice Models via Exact Diagonalization** 179**Cheng-Chien Chen** 180 181University of Alabama at Birmingham 182 183Fermionic particles cannot occupy the same quantum state due to the Pauli exclusion principle. Therefore, solving the quantum many-body Schrödinger equation for electrons on finite-size lattices is equivalent to solving a finite-dimensional eigenvalue problem, where the matrix dimension grows exponentially with the lattice size. Here, I will discuss the exact diagonalization technique for finding the low-energy eigenstates of interacting fermionic models on two-dimensional lattices. These interacting models are shown to host a variety of emergent quantum phases, such as superconductivity and antiferromagnetism. For a sparse matrix with 34 billion basis states, the underlying code based on PETSc/SLEPc achieves a strong scaling performance of 85% linear scaling on more than 100,000 CPUs. The presentation will conclude with a brief discussion of potential future research directions, including ultra-large-scale matrix diagonalization based on matrix-free algorithms and/or quantum circuit simulations. 184::: 185 186(boyce-griffith)= 187 188:::{topic} **Cardiac Fluid Dynamics** 189**Boyce Griffith** 190 191University of North Carolina, Chapel Hill 192 193Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. I will initially focus on models of an in vitro pulse-duplicator system that is commonly used in the development and regulation of prosthetic heart valves. These models enable detailed comparisons between experimental data and computational model predictions but use highly simplified descriptions of cardiac anatomy and physiology. I will also present recent in vitro models, focusing on a new comprehensive model of the human heart. This heart model includes fully three-dimensional descriptions of all major cardiac structures along with biomechanics models that are parameterized using experimental tensile test data obtained exclusively from human tissue specimens. Simulation results demonstrate that the model generates physiological stroke volumes, pressure-volume loops, and valvular pressure-flow relationships, thereby illustrating is its potential for predicting cardiac function in both health and disease. Time permitting, I will end the talk by describing extensions of this model to incorporate a comprehensive description of cardiac electrophysiology and electro-mechanical coupling. 194::: 195 196(zoe-leibowitz)= 197 198:::{topic} **Automatic Generation of Matrix-Free Routines for PDE Solvers with Devito via PETSc** 199**Zoe Leibowitz** 200 201Imperial College, London 202 203Traditional numerical solvers are often optimized for specific hardware architectures, making their adaptation to new computing environments challenging. The rapid evolution of hardware increases the complexity of rewriting and re-optimizing these solvers. By combining domain-specific languages (DSLs) with automated code generation, the level of abstraction is raised, enabling the generation of high-performance code across diverse hardware architectures. Moreover, providing users with a high-level problem specification facilitates the development of complex PDE solvers in a form closer to continuous mathematics, reducing code complexity and maximizing reuse. 204 205Devito, a DSL and compiler for finite-difference solvers, has been extended to integrate iterative solver functionality through an interface with PETSc, enabling the generation of solvers for various computational fluid dynamics (CFD) problems. As an industry-standard framework, Devito automates the generation of highly optimized explicit finite-difference kernels and stencil computations and has been extensively used in large-scale seismic inversion and medical imaging applications. The new developments introduce automatic generation of matrix-free routines in Devito, allowing interaction with PETSc’s suite of solvers. Key enhancements include support for iterative solvers, implicit time-stepping, coupled solvers, and matrix-free preconditioning. These features are fully integrated into Devito’s symbolic API while maintaining compatibility with staggered grids, subdomains, and custom stencils. 206 207This work expands Devito’s capabilities, enabling it to address a broader range of high-performance computing challenges, including incompressible flow problems in CFD. The new framework is demonstrated through benchmark simulations, including the backward-facing step and flow around a cylinder. 208::: 209 210(matt-knepley)= 211 212:::{topic} **Making Meshes with DMPlexTransform** 213**Matt Knepley** 214 215University at Buffalo 216 217Computational meshes, as a way to partition space, form the basis of much of PDE simulation technology, for instance for the finite element and finite volume discretization meth- ods. In complex simulations, we are often driven to modify an input mesh. For example, to refine, coarsen, extrude, change cell types, or filter it. This code can be volumi- nous, error-prone, spread over many special cases, and hard to understand and maintain by subsequent developers. We present a simple, table-driven paradigm for mesh transfor- mation which can execute a large variety of transformations in a performant, parallel manner, along with experiments in the open source library PETSc which can be run by the reader. 218::: 219 220(tim-steinhoff)= 221 222:::{topic} **Using PETSc in a Multi-application Environment** 223**Tim Steinhoff** 224 225Gesellschaft für Anlagen- und Reaktorsicherheit (GRS) gGmbH 226 227In this talk we provide an overview of the use of PETSc in the context of the code family AC<sup>2</sup> which is developed and distributed by GRS. AC<sup>2</sup> consists of multiple codes and is used to simulate the behavior of nuclear reactors during operation, transients, design basis and beyond design basis accidents up to radioactive releases to the environment. Access to PETSc is controlled by the self-developed wrapper NuT (Numerical Toolkit). We present a brief rundown of historical developments introducing NuT and therefore PETSc to handle certain numerical subtasks in AC<sup>2</sup>. This is accompanied by a deeper look into our latest development and the challenges that come with it in order to support the time evolution of nuclide inventories in burnup and decay calculations. 228::: 229 230(conor-ward)= 231 232:::{topic} **pyop3: A DSL for Unstructured Mesh Stencil Calculations** 233**Conor Ward** 234 235Imperial College, London 236 237pyop3 is a new domain-specific language that automates the application of local computational kernels over a mesh, termed 'unstructured mesh stencil calculations’. Such operations are ubiquitous across simulation methos including the finite element method and finite volume method, as well as preconditioners, slope limiters, and more. Written in Python, pyop3 takes advantage of some novel abstractions for describing mesh data (think generalised PetscSection) to describe complex mesh loops in a concise way that is agnostic to the underlying data layout. Having described the computation to be performed, pyop3 then uses just-in-time compilation to generate high-performance C code (CUDA/HIP coming soon) and coordinates its execution in parallel using MPI. 238 239pyop3 is built on top of PETSc, wrapping many of its data types, and the design of the new data layout abstractions are strongly influenced by DMPlex. 240 241This talk will introduce some of the novel abstractions that enable pyop3’s functionality before giving some examples of the sorts of computations that are expressible and the resulting code that is generated. 242::: 243 244## Organizing Committees 245 246### Extramural Committee 247- [Blaise Bourdin](https://math.mcmaster.ca/~bourdinb/) 248- [Danny Finn](https://scholar.google.com/citations?user=l09jI6wAAAAJ&hl=en) 249- [Toby Isaac](https://tisaac.gitlab.io/triquadtethex/) 250- [Lois McInnes](https://wordpress.cels.anl.gov/curfman/) 251- [Louis Moresi](https://www.moresi.info/) 252- [Darsh Nathawani](https://darshnathawani.com/) 253- [Barry Smith](https://barrysmith.github.io/) 254- [Junchao Zhang](https://www.anl.gov/profile/junchao-zhang) 255 256### Local Committee 257- [Margarete Jadamec](https://geovizlab.geology.buffalo.edu/) 258- [Matt Jones](https://www.buffalo.edu/ccr/about-us/people/staff/jones.html) 259- [Matt Knepley](https://cse.buffalo.edu/~knepley/) 260- [Joseph Pusztay](https://www.linkedin.com/in/joseph-pusztay-174183129/) 261- [David Salac](https://engineering.buffalo.edu/mechanical-aerospace/people/faculty/d-salac.html) 262 263## Questions and Meeting Discussion 264 265For questions about the meeting contact <mailto:petsc2025@lists.mcs.anl.gov>. 266Join the discussion about the meeting at [PETSc on Discord](https://discord.gg/Fqm8r6Gcyb), [2025 PETSc Annual Users Meeting channel](https://discord.com/channels/1119324534303109172/1298348560600924200). 267 268## Code of Conduct 269 270All meeting attendees are expected to follow the PETSc/NumFocus Code of Conduct. The local committee will serve as the code of conduct response team, https://numfocus.org/code-of-conduct#response-team. Should any concerns arise during the meeting, please contact any response team member. 271 272## Sponsors 273```{image} https://petsc.gitlab.io/annual-meetings/2025/Center-for-Computational-Research.png 274:width: 400 275``` 276```{image} https://petsc.gitlab.io/annual-meetings/2025/Institute-for-Artificial-Intelligence-and-Data-Science-color.png 277:width: 400 278``` 279
