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Crops In Silico Workshop, Oxford June 2017

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Talk for the plant science community on how the numerical relativity built a community around shared software.

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Crops In Silico Workshop, Oxford June 2017

  1. 1. Education & Community Building (in Astrophysics) Gabrielle Allen University of Illinois
  2. 2. Gravitational Wave Physics Instruments (LIGO) Models & Simulation Theory Scientific Discovery! Gmn = 8p Tmn Colliding black holes & neutron stars, supernovae collapse, gamma-ray bursts, big bang, …
  3. 3. Gravitational Wave Physics Instruments Models & Simulation Theory Scientific Discovery! Gmn = 8p Tmn Colliding black holes & neutron stars, supernovae collapse, gamma-ray bursts, big bang, …
  4. 4. Complex Problems • Multiscale, multiphysics, data- driven • E.g. To model neutron stars need general relativity, magneto-hydrodyamics, neutrino & radiation transport, complex equations of state, chemical reactions all integrated together • Need simple but effective interfaces that can be implemented in software Schnetter et al, PetaScale Computing: Algorithms and Applications, 2007
  5. 5. Cactus Framework (1997 - ) www.CactusCode.org • Open source component framework for HPC • Modular system with high level abstractions – Components (“thorns”) defined by parameters, variables, methods – Cactus “flesh” glues components together – Cactus Computational Toolkit: general thorns • Multiple application areas develop toolkits – Numerical relativity, CFD, coastal science, petroleum, quantum gravity, cosmology, …
  6. 6. Key Features  Cactus framework provides scheduling, application APIs for parallel operations  Driver thorn provides load balancing, parallelization  Application thorns deal only with local part of parallel mesh  Different thorns (with same interface) can be used to provide the same functionality, easily swapped.
  7. 7. Thorn (Components) • Configuration files (CCL files) define interface of thorns with the Flesh and other thorns – Implementation name and inheritance relations – Variables – Runtime parameters – Scheduled methods and storage, synchronization – Any configuration details • Public (global) and private (internal)
  8. 8. Cactus Thorns 8 Core “Flesh” Plug-In “Thorns” (components) driver input/output interpolation Elliptic solvers coordinates boundary conditions black holes equations of state remote steering wave evolvers multigrid parameters grid variables error handling scheduling extensible APIs make system ANSI C Coastal science Your Physics !! Quantum gravity Maxwells equations Neutron stars
  9. 9. Example scheduling tree
  10. 10. Building a Computational Numerical Relativity Community • Cactus came from the relativity community (USA GC) • European project with 10 sites developed community open code base • Each group had different expertise • Cactus allowed developing shared interfaces/standards • Easy to add a component, share components • Supports both collaboration and competition EU Network for Gravitational Wave Sources: 2001
  11. 11. Today: Einstein Toolkit • Software – Around 200 Cactus components – 3100 files, 1M LOC – Tools for analysis and visualization • Shared interfaces, tests, variables • Einstein Toolkit Consortium – Einstein Toolkit Maintainers and Members – Development plan with 6 month release schedule – Weekly open call, planning/bug fixes • Examples and tutorials – Complete production codes for black holes, neutron stars, cosmology, gravitational waves • Community support: active mail list and ticket system http://www.einsteintoolkit.o rg
  12. 12. Einstein Toolkit Consortium Over 100 members, 56 groups, 20 countries
  13. 13. Community Building
  14. 14. Distributed & Inclusive Hayley McPherson, PhD student, U. Melbourne One new module added – new code for relativistic cosmology - -- single, isolated grad student
  15. 15. www.eu-network.org Sources of Gravitational Radiation EU Astrophysics Network Overview Ed Seidel Albert Einstein Institute Principal Network Coordinator 2001
  16. 16. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Scientific and technological reasons for carrying out research in our field  Exploring Einstein’s General Relativity Want to develop theoretical lab to probe this fundamental theory  Fundamental theory of Physics (Gravity)  Among most complex equations of physics  Predict black holes, gravity waves, want much more  Exciting new field: Gravitational Wave Astronomy  LIGO, VIRGO, GEO, LISA, … ~ $1 Billion worldwide!  Fundamentally new information about Universe  A last major test of Einstein’s theory: do GWs exist? A century later, both of these developments happening at the same time: very exciting coincidence!  But, the community needed to carry out theoretical work is lacking… Not enough people or training
  17. 17. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation This EU Network Astrophysics 10 EU Institutions, 3 years, €1.5M Continue these problems Entire Community becoming Grid enabled  NSF Black Hole Grand Challenge  8 US Institutions, 5 years, $4M  Solve problem of colliding black holes (try…) NASA Neutron Star Grand Challenge 5 US Institutions, 3years, $1.4M Solve problem of colliding neutron stars (try…) NSF ASC Project 5 US Institutions, 3 years, $2.2M Develop “Collaboratory ” EU GridLab 10 EU Institutions, 3 years, €5M Develop Grid Tech For these projects Grand Challenge Collaboratories Building Communities to Solve These Problems
  18. 18. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Network research objectives  The formation of a close alliance among the different expert groups to solve urgent problems required for GWA, too large and complex for any single group.  The development & training of a young community of researchers for this emerging research area of GWA.  The development of a community simulation code for relativistic astrophysics  The application of these numerical and approximation tools to a set of core astrophysics problems  Good focus problems for training a community
  19. 19. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Theoretical Tools Einstein Eqs Pert. theory Post-Newtonian TheoryEnablers Focus Physics Areas Outreach /Collab GridLab ZIB/Garching LBL/NCSA/ANL NCSA/WashU Cactus Community NSF KDI Computational Tools Cactus Grid Viz KDI 3D BH Collisions Other (strange stars, Core collapse, etc) 3D NS processes and mergers World General View of Network
  20. 20. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Our Team 7 Focus areas, links created, strengthened by Network Valencia Ports SOTON Meudon Jena Palma Trieste AUTH Rome WashU Potsdam Jena Cactus Dev/Training CS Efforts Worldwide PotsdamPorts SOTON Valencia Rome Trieste AUTH BH Data/Evolutions Potsdam Nonlinear GR Hydro And Applications Valencia Trieste Meudon Potsdam Characteristic Codes SOTON Meudon Palma Rome AUTH Jena SOTON Ports Palma Stellar Pert Theory Valencia Jena AUTH Palma Perturbative Time Evolutions Valencia JenaJena Post-Newtonian Schemes Ports Palma Rome Valencia
  21. 21. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Project View: Code Leverage NS Studies Meudon BBH Meudon BNS Hydra Projects extremely Collaborative Build on each other Share Modules or Build them together Cactus an important collaborative technology EE’s MOL Horizon Finders Wave Extractors Lazarus Elliptics Parallel I/O Gauges AMR EE’s MOL Horizon Finders Wave Extractors Lazarus Elliptics Parallel I/O Gauges AMR EE’s Community Workshop this spring/fall improves EE’s, all simulations Vacuum BH Studies
  22. 22. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Developing a Community: People Leverage  Actual Network funding rather small  10-12 positions (some positions converted to 2 for shorter times) – 6-7 postdocs, 4-5 predocs  Very Strong Leverage! 6:1 ratio of paid/volunteer effort  10 coordinators  65 others officially working on the project at least part-time  Other sites in Europe joining in – Is it possible to get additional funding to help them?  Other projects in US and EU adding value  Attending this meeting  ~65!!  This project has seeded a much larger effort  Now  Even more later
  23. 23. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Community Code: Advantages  Sharing of Expertise: No single group can do  Sharing of Code among projects  Infrastructure  BH routines apply directly to NS work, etc…  But free to keep routines in group as long as desired  Better Code  Open source encourages people to be more careful in coding!  Encourages documentation  Encourages deeper thinking about how it interfaces to another code  More trusted code, results  When code becomes open, and people can run it for themselves, they will begin to believe the results  Improvements propagate quickly though community  Not well accepted yet, but we are starting a good trend…
  24. 24. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation Work Plan Cactus Nonlinear BH simulations Hydrodynamics Post-Newtonian theory Stellar perturbation theory Perturbative time evolutions Characteristic Methods Training complete, AMR tested 12 months 24 months 36 months Remote/distributed Simulations, input from projects below Addressing Efficacy Of Characteristic Hydro Full community Code release, with documentation Merger simulations with studies of waves Continually refined as techniques developed Completed binary NS Initial Data Module Simulations refined as techniques developed Accretion Code PN GW, reaction expressions Post-N.Hydro Code, Post-N Initial Data Module Simulations continue Pert Eqs. for rotating NS, nonlinear results Modes computed, valuable input to num. simulations Close limit module, time evolution for rotating NSs Perturbative evolutions, Input to num. simulations Time
  25. 25. Ed Seidel Albert Einstein Institute www.eu-network.org Sources of Gravitational Radiation The training programme  Feedback on talks, practice talks, etc  Review Talk topics selected by YR’s  Schools planned  Training sessions, extensive online tutorials  High performance computing,  Cactus (our code framework)  Visualization tools,  Code maintenance systems (CVS), etc  Developing “soft skills”  Collaboration/Communication built in to this project  Helping to prepare talks, documentation  YRs have to ask first questions at meetings
  26. 26. Lessons • Define simple test problems within the context of the motivating challenge problems. • Strong and persistent coordination for both technical and strategic goals. • Focus around interfaces (of different types), science domain interfaces were critical. • Focus on students (a 20 year activity), organize & track exchanges, summer schools/training. • Partner with computer scientists, look for opportunities to share code/tools with other domains. • Advisory committee to help keep all on track.
  27. 27. Crops in Silico Single Plant Weather Climate Crops Gene Regulatory Photosynthesis Field Region EarthPlantLeafCellMolecule Lengthscale Timescale Decades Year Week Hydrology Capillary Fluid Flow Soil Minute ms Roots
  28. 28. Model Interfaces • What is the set of challenge science problems? • What are the key abstract models needed to solve these? • What are the core input and output variables as well as parameters for each abstract model? • What models/tools do we already have to build from?

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