SlideShare a Scribd company logo
1 of 28
Download to read offline
Education & Community
Building (in Astrophysics)
Gabrielle Allen
University of Illinois
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, …
Gravitational Wave Physics
Instruments
Models & Simulation
Theory
Scientific Discovery!
Gmn = 8p Tmn
Colliding black holes & neutron
stars, supernovae collapse,
gamma-ray bursts, big bang, …
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
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, …
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.
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)
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
Example scheduling tree
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
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
Einstein Toolkit Consortium
Over 100 members, 56 groups, 20 countries
Community Building
Distributed & Inclusive
Hayley McPherson, PhD student, U. Melbourne
One new module added – new
code for relativistic cosmology -
-- single, isolated grad student
www.eu-network.org
Sources of Gravitational Radiation
EU Astrophysics
Network Overview
Ed Seidel
Albert Einstein Institute
Principal Network Coordinator
2001
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
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
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
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
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
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
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
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…
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
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
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.
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
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?

More Related Content

What's hot

Calit2-a Persistent UCSD/UCI Framework for Collaboration
Calit2-a Persistent UCSD/UCI Framework for CollaborationCalit2-a Persistent UCSD/UCI Framework for Collaboration
Calit2-a Persistent UCSD/UCI Framework for CollaborationLarry Smarr
 
Using OptIPuter Innovations to Enable LambdaGrid Applications
Using OptIPuter Innovations to Enable LambdaGrid ApplicationsUsing OptIPuter Innovations to Enable LambdaGrid Applications
Using OptIPuter Innovations to Enable LambdaGrid ApplicationsLarry Smarr
 
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...Larry Smarr
 
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...EarthCube
 
Toward A National Big Data Superhighway
Toward A National Big Data SuperhighwayToward A National Big Data Superhighway
Toward A National Big Data SuperhighwayLarry Smarr
 
Why Researchers are Using Advanced Networks
Why Researchers are Using Advanced NetworksWhy Researchers are Using Advanced Networks
Why Researchers are Using Advanced NetworksLarry Smarr
 
Toward a Global Interactive Earth Observing Cyberinfrastructure
Toward a Global Interactive Earth Observing CyberinfrastructureToward a Global Interactive Earth Observing Cyberinfrastructure
Toward a Global Interactive Earth Observing CyberinfrastructureLarry Smarr
 
NCSA and Telepresence Collaboration
NCSA and Telepresence CollaborationNCSA and Telepresence Collaboration
NCSA and Telepresence CollaborationLarry Smarr
 
Open-source tools for generating and analyzing large materials data sets
Open-source tools for generating and analyzing large materials data setsOpen-source tools for generating and analyzing large materials data sets
Open-source tools for generating and analyzing large materials data setsAnubhav Jain
 

What's hot (10)

Calit2-a Persistent UCSD/UCI Framework for Collaboration
Calit2-a Persistent UCSD/UCI Framework for CollaborationCalit2-a Persistent UCSD/UCI Framework for Collaboration
Calit2-a Persistent UCSD/UCI Framework for Collaboration
 
Using OptIPuter Innovations to Enable LambdaGrid Applications
Using OptIPuter Innovations to Enable LambdaGrid ApplicationsUsing OptIPuter Innovations to Enable LambdaGrid Applications
Using OptIPuter Innovations to Enable LambdaGrid Applications
 
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...
The OptiPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Te...
 
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...
Toward Real-Time Analysis of Large Data Volumes for Diffraction Studies by Ma...
 
SC13 Diary
SC13 DiarySC13 Diary
SC13 Diary
 
Toward A National Big Data Superhighway
Toward A National Big Data SuperhighwayToward A National Big Data Superhighway
Toward A National Big Data Superhighway
 
Why Researchers are Using Advanced Networks
Why Researchers are Using Advanced NetworksWhy Researchers are Using Advanced Networks
Why Researchers are Using Advanced Networks
 
Toward a Global Interactive Earth Observing Cyberinfrastructure
Toward a Global Interactive Earth Observing CyberinfrastructureToward a Global Interactive Earth Observing Cyberinfrastructure
Toward a Global Interactive Earth Observing Cyberinfrastructure
 
NCSA and Telepresence Collaboration
NCSA and Telepresence CollaborationNCSA and Telepresence Collaboration
NCSA and Telepresence Collaboration
 
Open-source tools for generating and analyzing large materials data sets
Open-source tools for generating and analyzing large materials data setsOpen-source tools for generating and analyzing large materials data sets
Open-source tools for generating and analyzing large materials data sets
 

Similar to Crops In Silico Workshop, Oxford June 2017

The Einstein Toolkit: A Community Computational Infrastructure for Relativist...
The Einstein Toolkit: A Community Computational Infrastructure for Relativist...The Einstein Toolkit: A Community Computational Infrastructure for Relativist...
The Einstein Toolkit: A Community Computational Infrastructure for Relativist...University of Illinois at Urbana-Champaign
 
Learning Systems for Science
Learning Systems for ScienceLearning Systems for Science
Learning Systems for ScienceIan Foster
 
Strong field science core proposal for uph ill site
Strong field science core proposal for uph ill siteStrong field science core proposal for uph ill site
Strong field science core proposal for uph ill siteahsanrabbani
 
Discovering new functional materials for clean energy and beyond using high-t...
Discovering new functional materials for clean energy and beyond using high-t...Discovering new functional materials for clean energy and beyond using high-t...
Discovering new functional materials for clean energy and beyond using high-t...Anubhav Jain
 
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」PC Cluster Consortium
 
Sharing Economy 2.0 & The Internet of People (IoP) Workshop
Sharing Economy 2.0 & The Internet of People (IoP) WorkshopSharing Economy 2.0 & The Internet of People (IoP) Workshop
Sharing Economy 2.0 & The Internet of People (IoP) WorkshopHristian Daskalov
 
Invited Talk: Early Detection of Research Topics
Invited Talk: Early Detection of Research Topics Invited Talk: Early Detection of Research Topics
Invited Talk: Early Detection of Research Topics Angelo Salatino
 
CHASE-CI: A Distributed Big Data Machine Learning Platform
CHASE-CI: A Distributed Big Data Machine Learning PlatformCHASE-CI: A Distributed Big Data Machine Learning Platform
CHASE-CI: A Distributed Big Data Machine Learning PlatformLarry Smarr
 
201109021 mcguinness ska_meeting
201109021 mcguinness ska_meeting201109021 mcguinness ska_meeting
201109021 mcguinness ska_meetingDeborah McGuinness
 
What Academia Can Learn from Open Source
What Academia Can Learn from Open SourceWhat Academia Can Learn from Open Source
What Academia Can Learn from Open SourceAll Things Open
 
Accelerating Discovery via Science Services
Accelerating Discovery via Science ServicesAccelerating Discovery via Science Services
Accelerating Discovery via Science ServicesIan Foster
 
Grid07 7 Gagliardi
Grid07 7 GagliardiGrid07 7 Gagliardi
Grid07 7 Gagliardiimec.archive
 
ExaLearn Overview - ECP Co-Design Center for Machine Learning
ExaLearn Overview - ECP Co-Design Center for Machine LearningExaLearn Overview - ECP Co-Design Center for Machine Learning
ExaLearn Overview - ECP Co-Design Center for Machine Learninginside-BigData.com
 

Similar to Crops In Silico Workshop, Oxford June 2017 (20)

The Einstein Toolkit: A Community Computational Infrastructure for Relativist...
The Einstein Toolkit: A Community Computational Infrastructure for Relativist...The Einstein Toolkit: A Community Computational Infrastructure for Relativist...
The Einstein Toolkit: A Community Computational Infrastructure for Relativist...
 
Climate Extremes Workshop - Networks and Extremes: Review and Further Studies...
Climate Extremes Workshop - Networks and Extremes: Review and Further Studies...Climate Extremes Workshop - Networks and Extremes: Review and Further Studies...
Climate Extremes Workshop - Networks and Extremes: Review and Further Studies...
 
Learning Systems for Science
Learning Systems for ScienceLearning Systems for Science
Learning Systems for Science
 
Engineering Careers in Astronomy
Engineering Careers in AstronomyEngineering Careers in Astronomy
Engineering Careers in Astronomy
 
Strong field science core proposal for uph ill site
Strong field science core proposal for uph ill siteStrong field science core proposal for uph ill site
Strong field science core proposal for uph ill site
 
Web and Complex Systems Lab @ Kno.e.sis
Web and Complex Systems Lab @ Kno.e.sisWeb and Complex Systems Lab @ Kno.e.sis
Web and Complex Systems Lab @ Kno.e.sis
 
Discovering new functional materials for clean energy and beyond using high-t...
Discovering new functional materials for clean energy and beyond using high-t...Discovering new functional materials for clean energy and beyond using high-t...
Discovering new functional materials for clean energy and beyond using high-t...
 
Engineering Careers in Astronomy
Engineering Careers in AstronomyEngineering Careers in Astronomy
Engineering Careers in Astronomy
 
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」
PCCC22:筑波大学計算科学研究センター テーマ2「学際計算科学による最新の研究成果」
 
Sharing Economy 2.0 & The Internet of People (IoP) Workshop
Sharing Economy 2.0 & The Internet of People (IoP) WorkshopSharing Economy 2.0 & The Internet of People (IoP) Workshop
Sharing Economy 2.0 & The Internet of People (IoP) Workshop
 
Invited Talk: Early Detection of Research Topics
Invited Talk: Early Detection of Research Topics Invited Talk: Early Detection of Research Topics
Invited Talk: Early Detection of Research Topics
 
CHASE-CI: A Distributed Big Data Machine Learning Platform
CHASE-CI: A Distributed Big Data Machine Learning PlatformCHASE-CI: A Distributed Big Data Machine Learning Platform
CHASE-CI: A Distributed Big Data Machine Learning Platform
 
201109021 mcguinness ska_meeting
201109021 mcguinness ska_meeting201109021 mcguinness ska_meeting
201109021 mcguinness ska_meeting
 
What Academia Can Learn from Open Source
What Academia Can Learn from Open SourceWhat Academia Can Learn from Open Source
What Academia Can Learn from Open Source
 
Collins seattle-2014-final
Collins seattle-2014-finalCollins seattle-2014-final
Collins seattle-2014-final
 
CLIM: Transition Workshop - Extremes and Networks: a review of activities -...
CLIM: Transition Workshop - Extremes and  Networks: a  review of activities -...CLIM: Transition Workshop - Extremes and  Networks: a  review of activities -...
CLIM: Transition Workshop - Extremes and Networks: a review of activities -...
 
Cyberistructure
CyberistructureCyberistructure
Cyberistructure
 
Accelerating Discovery via Science Services
Accelerating Discovery via Science ServicesAccelerating Discovery via Science Services
Accelerating Discovery via Science Services
 
Grid07 7 Gagliardi
Grid07 7 GagliardiGrid07 7 Gagliardi
Grid07 7 Gagliardi
 
ExaLearn Overview - ECP Co-Design Center for Machine Learning
ExaLearn Overview - ECP Co-Design Center for Machine LearningExaLearn Overview - ECP Co-Design Center for Machine Learning
ExaLearn Overview - ECP Co-Design Center for Machine Learning
 

More from University of Illinois at Urbana-Champaign (6)

Computational Tools for Multimessenger Astronomy in the Gravitational Wave Era
Computational Tools for Multimessenger Astronomy in the Gravitational Wave EraComputational Tools for Multimessenger Astronomy in the Gravitational Wave Era
Computational Tools for Multimessenger Astronomy in the Gravitational Wave Era
 
Component Specification in the Cactus Framework: The Cactus Configuration Lan...
Component Specification in the Cactus Framework: The Cactus Configuration Lan...Component Specification in the Cactus Framework: The Cactus Configuration Lan...
Component Specification in the Cactus Framework: The Cactus Configuration Lan...
 
Esi web2.0 may2010
Esi web2.0 may2010Esi web2.0 may2010
Esi web2.0 may2010
 
Ci days notre_dame_april2010
Ci days notre_dame_april2010Ci days notre_dame_april2010
Ci days notre_dame_april2010
 
Panel at Internet2 Spring Meeting, April 2010
Panel at Internet2 Spring Meeting,  April 2010Panel at Internet2 Spring Meeting,  April 2010
Panel at Internet2 Spring Meeting, April 2010
 
Cluster Computing Web2 Sept2009
Cluster Computing Web2 Sept2009Cluster Computing Web2 Sept2009
Cluster Computing Web2 Sept2009
 

Recently uploaded

Environmental Acoustics- Speech interference level, acoustics calibrator.pptx
Environmental Acoustics- Speech interference level, acoustics calibrator.pptxEnvironmental Acoustics- Speech interference level, acoustics calibrator.pptx
Environmental Acoustics- Speech interference level, acoustics calibrator.pptxpriyankatabhane
 
BACTERIAL SECRETION SYSTEM by Dr. Chayanika Das
BACTERIAL SECRETION SYSTEM by Dr. Chayanika DasBACTERIAL SECRETION SYSTEM by Dr. Chayanika Das
BACTERIAL SECRETION SYSTEM by Dr. Chayanika DasChayanika Das
 
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...Chayanika Das
 
Timeless Cosmology: Towards a Geometric Origin of Cosmological Correlations
Timeless Cosmology: Towards a Geometric Origin of Cosmological CorrelationsTimeless Cosmology: Towards a Geometric Origin of Cosmological Correlations
Timeless Cosmology: Towards a Geometric Origin of Cosmological CorrelationsDanielBaumann11
 
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptx
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptxPharmaceutical warehouse audit using eAuditor Audits & Inspections .pptx
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptxeAuditor Audits & Inspections
 
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdf
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdfCDS Fundamentals of digital communication system UNIT 1 AND 2.pdf
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdfshubhangisonawane6
 
DERMATOMYCOSIS Epidermophyton KKR.pptx
DERMATOMYCOSIS Epidermophyton   KKR.pptxDERMATOMYCOSIS Epidermophyton   KKR.pptx
DERMATOMYCOSIS Epidermophyton KKR.pptxKARTHIK REDDY C A
 
Food_safety_Management_pptx.pptx in microbiology
Food_safety_Management_pptx.pptx in microbiologyFood_safety_Management_pptx.pptx in microbiology
Food_safety_Management_pptx.pptx in microbiologyHemantThakare8
 
Fungal Sex Hormones SIRENIN ANTHERIDIOL.
Fungal Sex Hormones SIRENIN ANTHERIDIOL.Fungal Sex Hormones SIRENIN ANTHERIDIOL.
Fungal Sex Hormones SIRENIN ANTHERIDIOL.KARTHIK REDDY C A
 
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learning
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep LearningCombining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learning
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learningvschiavoni
 
FBI Profiling - Forensic Psychology.pptx
FBI Profiling - Forensic Psychology.pptxFBI Profiling - Forensic Psychology.pptx
FBI Profiling - Forensic Psychology.pptxPayal Shrivastava
 
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...Speed Breeding in Vegetable Crops- innovative approach for present era of cro...
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...jana861314
 
DETECTION OF MUTATION BY CLB METHOD.pptx
DETECTION OF MUTATION BY CLB METHOD.pptxDETECTION OF MUTATION BY CLB METHOD.pptx
DETECTION OF MUTATION BY CLB METHOD.pptx201bo007
 
SANDAL SPIKE MYCOPLASMAL DISEASE K R ppt
SANDAL SPIKE MYCOPLASMAL DISEASE K R pptSANDAL SPIKE MYCOPLASMAL DISEASE K R ppt
SANDAL SPIKE MYCOPLASMAL DISEASE K R pptKARTHIK REDDY C A
 
Potato spindle tuber disease VIRIOID DISEASE
Potato spindle tuber disease  VIRIOID DISEASEPotato spindle tuber disease  VIRIOID DISEASE
Potato spindle tuber disease VIRIOID DISEASEKARTHIK REDDY C A
 
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...Sérgio Sacani
 
Mycoplasma Mycoplasma pneumoniae K R.pptx
Mycoplasma Mycoplasma pneumoniae  K R.pptxMycoplasma Mycoplasma pneumoniae  K R.pptx
Mycoplasma Mycoplasma pneumoniae K R.pptxKARTHIK REDDY C A
 

Recently uploaded (20)

Environmental Acoustics- Speech interference level, acoustics calibrator.pptx
Environmental Acoustics- Speech interference level, acoustics calibrator.pptxEnvironmental Acoustics- Speech interference level, acoustics calibrator.pptx
Environmental Acoustics- Speech interference level, acoustics calibrator.pptx
 
BACTERIAL SECRETION SYSTEM by Dr. Chayanika Das
BACTERIAL SECRETION SYSTEM by Dr. Chayanika DasBACTERIAL SECRETION SYSTEM by Dr. Chayanika Das
BACTERIAL SECRETION SYSTEM by Dr. Chayanika Das
 
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...
ESSENTIAL FEATURES REQUIRED FOR ESTABLISHING FOUR TYPES OF BIOSAFETY LABORATO...
 
Timeless Cosmology: Towards a Geometric Origin of Cosmological Correlations
Timeless Cosmology: Towards a Geometric Origin of Cosmological CorrelationsTimeless Cosmology: Towards a Geometric Origin of Cosmological Correlations
Timeless Cosmology: Towards a Geometric Origin of Cosmological Correlations
 
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptx
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptxPharmaceutical warehouse audit using eAuditor Audits & Inspections .pptx
Pharmaceutical warehouse audit using eAuditor Audits & Inspections .pptx
 
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdf
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdfCDS Fundamentals of digital communication system UNIT 1 AND 2.pdf
CDS Fundamentals of digital communication system UNIT 1 AND 2.pdf
 
DERMATOMYCOSIS Epidermophyton KKR.pptx
DERMATOMYCOSIS Epidermophyton   KKR.pptxDERMATOMYCOSIS Epidermophyton   KKR.pptx
DERMATOMYCOSIS Epidermophyton KKR.pptx
 
Food_safety_Management_pptx.pptx in microbiology
Food_safety_Management_pptx.pptx in microbiologyFood_safety_Management_pptx.pptx in microbiology
Food_safety_Management_pptx.pptx in microbiology
 
Fungal Sex Hormones SIRENIN ANTHERIDIOL.
Fungal Sex Hormones SIRENIN ANTHERIDIOL.Fungal Sex Hormones SIRENIN ANTHERIDIOL.
Fungal Sex Hormones SIRENIN ANTHERIDIOL.
 
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learning
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep LearningCombining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learning
Combining Asynchronous Task Parallelism and Intel SGX for Secure Deep Learning
 
Bioenergetics and the role of ATP to drive the beats of life.
Bioenergetics and the role of ATP to drive the beats of life.Bioenergetics and the role of ATP to drive the beats of life.
Bioenergetics and the role of ATP to drive the beats of life.
 
Battery Reasearch Reagents from TCI Chemicals
Battery Reasearch Reagents from TCI ChemicalsBattery Reasearch Reagents from TCI Chemicals
Battery Reasearch Reagents from TCI Chemicals
 
FBI Profiling - Forensic Psychology.pptx
FBI Profiling - Forensic Psychology.pptxFBI Profiling - Forensic Psychology.pptx
FBI Profiling - Forensic Psychology.pptx
 
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...Speed Breeding in Vegetable Crops- innovative approach for present era of cro...
Speed Breeding in Vegetable Crops- innovative approach for present era of cro...
 
DETECTION OF MUTATION BY CLB METHOD.pptx
DETECTION OF MUTATION BY CLB METHOD.pptxDETECTION OF MUTATION BY CLB METHOD.pptx
DETECTION OF MUTATION BY CLB METHOD.pptx
 
SANDAL SPIKE MYCOPLASMAL DISEASE K R ppt
SANDAL SPIKE MYCOPLASMAL DISEASE K R pptSANDAL SPIKE MYCOPLASMAL DISEASE K R ppt
SANDAL SPIKE MYCOPLASMAL DISEASE K R ppt
 
Potato spindle tuber disease VIRIOID DISEASE
Potato spindle tuber disease  VIRIOID DISEASEPotato spindle tuber disease  VIRIOID DISEASE
Potato spindle tuber disease VIRIOID DISEASE
 
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...
Observation of Gravitational Waves from the Coalescence of a 2.5–4.5 M⊙ Compa...
 
Mycoplasma Mycoplasma pneumoniae K R.pptx
Mycoplasma Mycoplasma pneumoniae  K R.pptxMycoplasma Mycoplasma pneumoniae  K R.pptx
Mycoplasma Mycoplasma pneumoniae K R.pptx
 
TISSUE TYPING .pptx
TISSUE TYPING                       .pptxTISSUE TYPING                       .pptx
TISSUE TYPING .pptx
 

Crops In Silico Workshop, Oxford June 2017

  • 1. Education & Community Building (in Astrophysics) Gabrielle Allen University of Illinois
  • 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. 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. 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. 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. 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. 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. 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
  • 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. 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. Einstein Toolkit Consortium Over 100 members, 56 groups, 20 countries
  • 14. Distributed & Inclusive Hayley McPherson, PhD student, U. Melbourne One new module added – new code for relativistic cosmology - -- single, isolated grad student
  • 15. www.eu-network.org Sources of Gravitational Radiation EU Astrophysics Network Overview Ed Seidel Albert Einstein Institute Principal Network Coordinator 2001
  • 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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?