software for agent based social simulation (((((( with raster inputs ... · i 2012 – europar:...
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Software for agent based social simulation((((((((
(hhhhhhhhhwith raster inputs indistributed HPC environments
Sergiy Gogolenko
Oct 11, WSSP’17
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HPCsoftware · platforms
GSSscientific evidence to supportpolicy-making · public action · civic society
pilots:grean growthhealth habits
urban planning
⊕ → LESSONS
GG bridge. Photo from c©pixabay.com
Deliver a stack of HPC compliant software for GSS usersI creating realistic synthetic populationsI network reconstruction (creating synthetic social networks, etc)I parallel and distributed multi-agent systems simulation (for GSS only)I analytics: basic data and graph analytics, sensitivity analysis, parameter sweep, etcI other related software2/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((
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Agent-based modeling and simulation
Annual Workshops on HPC ForumsI 2012 – EuroPar: Workshop on Parallel and Distributed Agent-Based Simulations
(PADABS)I 2016 – IPDPS: IEEE Workshop on Parallel and Distributed Processing for
Computational Social Systems (ParSocial)
ABMS in a Nutshell
I bottom-up approachI individual-based simulation→ tendency
I componentsI agents: discrete autonomous entityI environment: GIS, relationships, etcI actions and interactions Environment
Agent1attributesrules of b.
Agentiattributesrules of b.
Agentnattributesrules of b.
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Agent-based modeling and simulation
Annual Workshops on HPC ForumsI 2012 – EuroPar: Workshop on Parallel and Distributed Agent-Based Simulations
(PADABS)I 2016 – IPDPS: IEEE Workshop on Parallel and Distributed Processing for
Computational Social Systems (ParSocial)
ABMS in a Nutshell
I bottom-up approachI individual-based simulation→ tendency
I componentsI agents: discrete autonomous entityI environment: GIS, relationships, etcI actions and interactions Environment
Agent1attributesrules of b.
Agentiattributesrules of b.
Agentnattributesrules of b.
3/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 1. Agents
“molecular dynamics society”
real society is heterogeneous
The Simpsons : Treehouse of Horror XIII (Season 27) [from c©fxx.com]
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MAS in GSS : Lesson 1. Agents
“molecular dynamics society”
real society is heterogeneous
The Simpsons : Treehouse of Horror XIII (Season 27) [from c©fxx.com]
4/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 1. Agents
I heterogeneous
I serializable(introspection)
I I/OI data exchangeI checkpointing
I mobile
The Simpsons c©[from c©fxx.com]
5/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 1. Agents
I heterogeneous
I serializable(introspection)
I I/OI data exchangeI checkpointing
I mobile
The Simpsons c©[from c©fxx.com]
5/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 1. Agents
I heterogeneousI serializable
(introspection)I I/OI data exchangeI checkpointing
I mobile
The Simpsons c©[from c©fxx.com]
5/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 2. Environment
Border fence Tijuana-San Diego. Photo from c©wikimedia.org
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MAS in GSS : Lesson 2. Environment
obstacles imposed by nature
Border fence Tijuana-San Diego. Photo from c©wikimedia.org
6/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 2. Environment
obstacles imposed by nature
urbanization
Border fence Tijuana-San Diego. Photo from c©wikimedia.org
6/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 2. Environment
obstacles imposed by nature
urbanization
other concerns
Border fence Tijuana-San Diego. Photo from c©wikimedia.org
6/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 2. Environment
Earth at Night. Photo by NASA c©wikimedia.org
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MAS in GSS : Lesson 2. Environment
sparse 2D
Earth at Night. Photo by NASA c©wikimedia.org
7/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 3. Interactions
I short distance (spatialproximity)
I metric: halo (area of interest –AOI)
I halo size: agent typeindependent
I BC: von Neumann, Moore,periodic
ha��ZZe ll o
c©The Walt Disney Company [img from youtube.com]
I long distance (socialrelationships)
I undirected graphsI dynamic (evolving)I might be weighted
I might need several graphs
Social Network Tree by c©pixabay.com
8/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 3. Interactions
I short distance (spatialproximity)
I metric: halo (area of interest –AOI)
I halo size: agent typeindependent
I BC: von Neumann, Moore,periodic
ha��ZZe ll o
c©The Walt Disney Company [img from youtube.com]
I long distance (socialrelationships)
I undirected graphsI dynamic (evolving)I might be weighted
I might need several graphs
Social Network Tree by c©pixabay.com
8/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 3. Interactions
I short distance (spatialproximity)
I metric: halo (area of interest –AOI)
I halo size: agent typeindependent
I BC: von Neumann, Moore,periodic
ha��ZZe ll o
c©The Walt Disney Company [img from youtube.com]
I long distance (socialrelationships)
I undirected graphsI dynamic (evolving)I might be weighted
I might need several graphs
Social Network Tree by c©pixabay.com8/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((
((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 3. Interactions
scientific collaboration network ( c©Olivier H. Beauchesne)
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MAS in GSS : Lesson 3. Interactions
social relationships may dominate
scientific collaboration network ( c©Olivier H. Beauchesne)
9/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 4. Users
Technical���XXXtraits background of average GSS modelerI Python and/or RI minimum boilerplatesI spend time on mastering low level parallel APIs (MPI, OpenMP, CUDA,...)
Embeded DSLsI linear algebra
Eigen ...
I CFD
FEniCS ...
10/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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MAS in GSS : Lesson 4. Users
Technical���XXXtraits background of average GSS modelerI Python and/or RI minimum boilerplatesI spend time on mastering low level parallel APIs (MPI, OpenMP, CUDA,...)
Embeded DSLsI linear algebra
Eigen ...
I CFD
FEniCS ...
10/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Formalization
rastersconvey
GIS env. input
Collection of sites:
map : position → struct
raster 1
raster 2
raster 3
sites
(loci of interaction)
are pixel positions spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
never settled
agents
(with soc. nets)
settlesites
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
11/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Basic domain decomposition
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
Computational graph
1. vertex weight: wi = #agentsi
2. SDC-edge weight: wij = wi + wj
3. LDC-edge weight: wij = #linksij
1
3 24
51
→ partitioner (ParMETIS, PT-Scotch, etc)
12/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Basic domain decomposition
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
Computational graph1. vertex weight: wi = #agentsi
2. SDC-edge weight: wij = wi + wj
3. LDC-edge weight: wij = #linksij
1
3 2
451
→ partitioner (ParMETIS, PT-Scotch, etc)
12/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Basic domain decomposition
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
Computational graph1. vertex weight: wi = #agentsi
2. SDC-edge weight: wij = wi + wj
3. LDC-edge weight: wij = #linksij
1
3 24
5
1
→ partitioner (ParMETIS, PT-Scotch, etc)
12/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Basic domain decomposition
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
Computational graph1. vertex weight: wi = #agentsi
2. SDC-edge weight: wij = wi + wj
3. LDC-edge weight: wij = #linksij
1
3 24
51
→ partitioner (ParMETIS, PT-Scotch, etc)
12/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Basic domain decomposition
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
Computational graph1. vertex weight: wi = #agentsi
2. SDC-edge weight: wij = wi + wj
3. LDC-edge weight: wij = #linksij
1
3 24
51
→ partitioner (ParMETIS, PT-Scotch, etc)
12/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Model : Workaround
But what if rasters have very high resolution?
Issue with mapping of sites to processesI need it for agent move operation
Inverse of Spain at Night from c©wikimedia.orgc©wikimedia.org
Computational graph-coarsening
I uniform meshI bound min chunk width: w ≥ 2 · haloI disadvantages: disbalanced weights,
highly skewed degree distributionI multi-scale mesh
I quad-tree(like in Barnes-Hut algorithm)
I vector GIS informationI (local) administrative units ≡ unstr. tree
13/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Workaround
But what if rasters have very high resolution?Issue with mapping of sites to processes
I need it for agent move operation
Inverse of Spain at Night from c©wikimedia.org
c©wikimedia.org
Computational graph-coarsening
I uniform meshI bound min chunk width: w ≥ 2 · haloI disadvantages: disbalanced weights,
highly skewed degree distributionI multi-scale mesh
I quad-tree(like in Barnes-Hut algorithm)
I vector GIS informationI (local) administrative units ≡ unstr. tree
13/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Workaround
But what if rasters have very high resolution?Issue with mapping of sites to processes
I need it for agent move operation
Inverse of Spain at Night from c©wikimedia.org
c©wikimedia.org
Computational graph-coarseningI uniform mesh
I bound min chunk width: w ≥ 2 · haloI disadvantages: disbalanced weights,
highly skewed degree distribution
I multi-scale meshI quad-tree
(like in Barnes-Hut algorithm)I vector GIS information
I (local) administrative units ≡ unstr. tree
13/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Workaround
But what if rasters have very high resolution?Issue with mapping of sites to processes
I need it for agent move operation
Inverse of Spain at Night from c©wikimedia.org
c©wikimedia.org
Computational graph-coarseningI uniform mesh
I bound min chunk width: w ≥ 2 · haloI disadvantages: disbalanced weights,
highly skewed degree distributionI multi-scale mesh
I quad-tree(like in Barnes-Hut algorithm)
I vector GIS informationI (local) administrative units ≡ unstr. tree
13/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Model : Workaround
But what if rasters have very high resolution?Issue with mapping of sites to processes
I need it for agent move operation
Inverse of Spain at Night from c©wikimedia.org
c©wikimedia.org
Computational graph-coarseningI uniform mesh
I bound min chunk width: w ≥ 2 · haloI disadvantages: disbalanced weights,
highly skewed degree distributionI multi-scale mesh
I quad-tree(like in Barnes-Hut algorithm)
I vector GIS informationI (local) administrative units ≡ unstr. tree
13/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Software : ABMS Frameworks
parallel12.5%
acceptable
37.5%
50%
I 24 popular frameworksI 3 have parallel facilities (only RepastHPC in C++)
... rather pessimistic paper(seems like RepastHPC is the only choice)
14/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Software : Distributed ABMS Frameworks for HPC
C/C++60%
Java40%
I 10 open source ABMS frameworks for HPCI some in Jave
I D-MASON, Jade, MACE3J, SWAGESI 6 out of 10 in C/C++ (Charm++)
I recent: RepastHPC, FlameHPC, Pandoraoldies: EcoLab, PDES-MAS, ABM++
I beyon the paper scope: EpiSemdemics, FluTE, ...
... we need another tool though!
15/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Software : Distributed ABMS Frameworks for HPC
C/C++60%
Java40%
I 10 open source ABMS frameworks for HPCI some in Jave
I D-MASON, Jade, MACE3J, SWAGESI 6 out of 10 in C/C++ (Charm++)
I recent: RepastHPC, FlameHPC, Pandoraoldies: EcoLab, PDES-MAS, ABM++
I beyon the paper scope: EpiSemdemics, FluTE, ...
... we need another tool though!
15/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Distributed ABMS Frameworks for HPC
C/C++60%
Java40%
I 10 open source ABMS frameworks for HPCI some in Jave
I D-MASON, Jade, MACE3J, SWAGESI 6 out of 10 in C/C++ (Charm++)
I recent: RepastHPC, FlameHPC, Pandoraoldies: EcoLab, PDES-MAS, ABM++
I beyon the paper scope: EpiSemdemics, FluTE, ...
... we need another tool though!
15/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
Munch, Edvard. The Scream c©wikimedia.org
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
What?Yet another ABMS framework?
Maybe we can reuse something from existing...Munch, Edvard. The Scream c©wikimedia.org;
16/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)
I social relationshipsI evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)I social relationships
I evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)
I social relationshipsI evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)I social relationships
I evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)I social relationships
I evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)I social relationships
I evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Building blocks (Primitives)
Processes
proc 00
proc 01proc 10
proc 11proc 20
proc 21
spatialgraph
v 0v 1
v 2
v 3
v 4 v 5
social
graphs (nets)
I agents (& synthetic population)I type introspectionI heterogeneous container
(fast heterogeneous hash table)I social relationships
I evolving undirected graphsI with and without edge weights
I spatial informationI map: position→ pixel info
I distribution (domain decomposition)I graph coarsening support
I map: position→ coarse pieceI graph partitionerI communication layer
I I/O and checkpointingI serialization in HPC compliant format
(HDF5, NetCDF)I GIS support
17/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Pandora & RepastHPC
Pandora HPC
I
I version: 1I commits: 630; Jun 17, 2016I since 2013
I
I version: 2.2.0I commits: 249; last Sep 30, 2016I since 2008
18/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
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Software : Environment Representation
Pandora RepastHPC
social relationships representationevolving social graphs +edge weights +multiplicity +implementation native (ptrs)
spatial component representationformat std::map of dense matri-
cesgrid projector + vector ofdense matrices (val layers)
boundary conditions von Neumann von Neumann, MooreGIS support rasters with GDAL -
19/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Domain Decomposition
“naı̈ve” uniform rectangular mesh
proc00
proc01
proc10
proc11
proc20
proc21
a
aRepastHPC allows to own partitioners written from scratch if one uses network projectors only (e.g., see chiSIM
project by N.Collier et al.)
20/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Container for Agents
std::map (world)links
idagent →
links
idagent →
links
idagent →
links
idagent →
links
idagent →
links∅
ProblemsI std::map: O(ln n)
, non-contiguous
I std::unordered map?
Can we do better?
I Sure! (e.g., google::dense hash map)see, e.g., tessil benchmark of major hash maps
std::unordered map (shared context)
c©http://codecapsule.com
21/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Container for Agents
std::map (world)links
idagent →
links
idagent →
links
idagent →
links
idagent →
links
idagent →
links∅
ProblemsI std::map: O(ln n), non-contiguousI std::unordered map: non-contiguous
Can we do better?
I Sure! (e.g., google::dense hash map)see, e.g., tessil benchmark of major hash maps
std::unordered map (shared context)
c©http://codecapsule.com
21/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Container for Agents
std::map (world)links
idagent →
links
idagent →
links
idagent →
links
idagent →
links
idagent →
links∅
ProblemsI std::map: O(ln n), non-contiguousI std::unordered map: non-contiguous
Can we do better?I Sure! (e.g., google::dense hash map)
see, e.g., tessil benchmark of major hash maps
std::unordered map (shared context)
c©http://codecapsule.com
21/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Agent Types and Introspection
Compile-time introspection substitutesPandora
I code generation (+ some boilerplates)I error-prone pseudo-parsing with Python
RepastHPC
I boilerplatesI Package pattern
Do some work at run-time
Why? Can we do better?I compile-time introspection was a headache in C++ up to C++14 standard
I Boost::HANA (by Louis Dionne)→ improved Boost::FusionI Apache Thrift (and its Facebook brench)
I since C++17 we can convert POD-struct→std::tuple non-intrusively withoutmacro and external tooling (A. Polukhin. CppCon, 2016)
I since C++20 reflection might be part of standard
22/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Agent Types and Introspection
Compile-time introspection substitutesPandora
I code generation (+ some boilerplates)I error-prone pseudo-parsing with Python
RepastHPC
I boilerplatesI Package pattern
Do some work at run-time
Why? Can we do better?I compile-time introspection was a headache in C++ up to C++14 standard
I Boost::HANA (by Louis Dionne)→ improved Boost::FusionI Apache Thrift (and its Facebook brench)
I since C++17 we can convert POD-struct→std::tuple non-intrusively withoutmacro and external tooling (A. Polukhin. CppCon, 2016)
I since C++20 reflection might be part of standard
22/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Software : Agent Types and Introspection
Compile-time introspection substitutesPandora
I code generation (+ some boilerplates)I error-prone pseudo-parsing with Python
RepastHPC
I boilerplatesI Package pattern
Do some work at run-time
Why? Can we do better?I compile-time introspection was a headache in C++ up to C++14 standard
I Boost::HANA (by Louis Dionne)→ improved Boost::FusionI Apache Thrift (and its Facebook brench)
I since C++17 we can convert POD-struct→std::tuple non-intrusively withoutmacro and external tooling (A. Polukhin. CppCon, 2016)
I since C++20 reflection might be part of standard
22/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
No more destruction!Brullov, Karl. The Last Day of Pompeii c©wikimedia.org
23/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Let’s construct...
What do we have?I RepastHPC is a good tool
for years 2008-2013I ... though we can do a way better with modern C++ (since C++14) and third-parties
I compile-time introspection, lambdas + std::function, std::tuple, ...
I recently we started to work on a new frameworkI prepare “state-of-the-art” HPC compliant primitives for GSS usersI strive both user-friendliness (EDSL like API) and performance
I advances in this development... modest so farI prototype with run-time heterogeneity mechanicms and introspectionI use SNAP graph library for dealing with social relationshipsI graph coarsening with uniform meshesI HDF5 I/O format and its implementation (Rafal Lichwala, PSNC)
What do we plan and work on?I shift to extensive use of compile-time: templates, introspection, tuples, CRT, etcI more third parties: hash tables, graph librariesI graph coarsening with multi-scale meshes
24/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Let’s construct...
What do we have?I RepastHPC is a good tool for years 2008-2013I ... though we can do a way better with modern C++ (since C++14) and third-parties
I compile-time introspection, lambdas + std::function, std::tuple, ...
I recently we started to work on a new frameworkI prepare “state-of-the-art” HPC compliant primitives for GSS usersI strive both user-friendliness (EDSL like API) and performance
I advances in this development... modest so farI prototype with run-time heterogeneity mechanicms and introspectionI use SNAP graph library for dealing with social relationshipsI graph coarsening with uniform meshesI HDF5 I/O format and its implementation (Rafal Lichwala, PSNC)
What do we plan and work on?I shift to extensive use of compile-time: templates, introspection, tuples, CRT, etcI more third parties: hash tables, graph librariesI graph coarsening with multi-scale meshes
24/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Let’s construct...
What do we have?I RepastHPC is a good tool for years 2008-2013I ... though we can do a way better with modern C++ (since C++14) and third-parties
I compile-time introspection, lambdas + std::function, std::tuple, ...
I recently we started to work on a new frameworkI prepare “state-of-the-art” HPC compliant primitives for GSS usersI strive both user-friendliness (EDSL like API) and performance
I advances in this development... modest so farI prototype with run-time heterogeneity mechanicms and introspectionI use SNAP graph library for dealing with social relationshipsI graph coarsening with uniform meshesI HDF5 I/O format and its implementation (Rafal Lichwala, PSNC)
What do we plan and work on?I shift to extensive use of compile-time: templates, introspection, tuples, CRT, etcI more third parties: hash tables, graph librariesI graph coarsening with multi-scale meshes
24/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Let’s construct...
What do we have?I RepastHPC is a good tool for years 2008-2013I ... though we can do a way better with modern C++ (since C++14) and third-parties
I compile-time introspection, lambdas + std::function, std::tuple, ...
I recently we started to work on a new frameworkI prepare “state-of-the-art” HPC compliant primitives for GSS usersI strive both user-friendliness (EDSL like API) and performance
I advances in this development... modest so farI prototype with run-time heterogeneity mechanicms and introspectionI use SNAP graph library for dealing with social relationshipsI graph coarsening with uniform meshesI HDF5 I/O format and its implementation (Rafal Lichwala, PSNC)
What do we plan and work on?I shift to extensive use of compile-time: templates, introspection, tuples, CRT, etcI more third parties: hash tables, graph librariesI graph coarsening with multi-scale meshes
24/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Let’s construct...
What do we have?I RepastHPC is a good tool for years 2008-2013I ... though we can do a way better with modern C++ (since C++14) and third-parties
I compile-time introspection, lambdas + std::function, std::tuple, ...
I recently we started to work on a new frameworkI prepare “state-of-the-art” HPC compliant primitives for GSS usersI strive both user-friendliness (EDSL like API) and performance
I advances in this development... modest so farI prototype with run-time heterogeneity mechanicms and introspectionI use SNAP graph library for dealing with social relationshipsI graph coarsening with uniform meshesI HDF5 I/O format and its implementation (Rafal Lichwala, PSNC)
What do we plan and work on?I shift to extensive use of compile-time: templates, introspection, tuples, CRT, etcI more third parties: hash tables, graph librariesI graph coarsening with multi-scale meshes
24/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Thank you for
your patience!
26/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::
::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::
Don’t blame me only! Don’t cheer me only!
Michael Gienger Ralf Schneider Bastian Koller
26/26 :: Sergiy Gogolenko :: Software for agent based social simulation(((((hhhhhwith raster inputs in distributed HPC environments :: Oct 11, WSSP’17 ::