sagesim 0.1.0__tar.gz

sagesim-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Oak Ridge National Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

sagesim-0.1.0/PKG-INFO

@@ -0,0 +1,77 @@
+Metadata-Version: 2.2
+Name: sagesim
+Version: 0.1.0
+Summary: Scalable Agent-based GPU Enabled Simulator.
+Author-email: Chathika Gunaratne <chathikagunaratne@gmail.com>
+Maintainer-email: Chathika Gunaratne <chathikagunaratne@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024 Oak Ridge National Laboratory
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Repository, https://github.com/ornl/sagesim.git
+Keywords: agent-based,hpc,gpu
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: awkward==2.7.4
+Requires-Dist: cupy_cuda12x==13.3.0
+Requires-Dist: mpi4py==4.0.3
+Requires-Dist: networkx==3.4.2
+Requires-Dist: numpy==2.2.3
+Requires-Dist: ragged==0.2.0
+Requires-Dist: setuptools==75.8.0
+
+# SAGESim
+
+Scalable Agent-based GPU Enabled Simulator
+
+# Requirements
+
+ - Python 3.7+
+ - `conda create -n sagesimenv python=3.9`
+ - `conda activate sagesimenv`
+ - Install CUDA toolkit
+ - - https://developer.nvidia.com/cuda-toolkit
+ - - https://rocm.docs.amd.com/projects/install-on-linux/en/docs-6.0.2/
+ - - [Install using Anaconda](`conda install -c anaconda cudatoolkit`)
+ - install mpi4py (Recommend using conda): https://mpi4py.readthedocs.io/en/stable/install.html#using-conda
+ - [Follow the instructions here to install CuPy](https://docs.cupy.dev/en/stable/install.html)
+ - `pip install -r requirements.txt`
+ 
+# Run Example
+
+ - `git clone https://code.ornl.gov/sagesim/sagesim`
+ - `export PYTHONPATH=/path/to/clone_repo`
+ - `cd /path/to/clone_repo/examples/sir`
+ - `mpiexec -n 4 python run.py`
+
+
+# There are some unfortunate quirks to using CuPyx `jit.rawkernel`:
+ - nan checked by inequality to self. Unfortunate limitation of cupyx.
+ - Dicts and objects are unsupported.
+ - *args and **kwargs are unsupported.
+ - nested functions are unsupported.
+ - Be sure to use `cupy` data types and array routines in favor of `numpy`: [https://docs.cupy.dev/en/stable/reference/routines.html]
+ - `for` loops must use range iterator only. No 'for each' style loops.
+ - `return` does not seem to work well either
+ - `break` and `continue` are unsupported!
+ - Cannot reassign variables within `if` or `for` statements. Must be assigned at top level of function or new variable declared under subscope.
+ -  `-1` indexing does not necessarily work as expected, as it will access the last element of the memory block of the array instead of the logical array. Use `len(my_array) - 1` instead

sagesim-0.1.0/README.md

@@ -0,0 +1,36 @@
+# SAGESim
+
+Scalable Agent-based GPU Enabled Simulator
+
+# Requirements
+
+ - Python 3.7+
+ - `conda create -n sagesimenv python=3.9`
+ - `conda activate sagesimenv`
+ - Install CUDA toolkit
+ - - https://developer.nvidia.com/cuda-toolkit
+ - - https://rocm.docs.amd.com/projects/install-on-linux/en/docs-6.0.2/
+ - - [Install using Anaconda](`conda install -c anaconda cudatoolkit`)
+ - install mpi4py (Recommend using conda): https://mpi4py.readthedocs.io/en/stable/install.html#using-conda
+ - [Follow the instructions here to install CuPy](https://docs.cupy.dev/en/stable/install.html)
+ - `pip install -r requirements.txt`
+ 
+# Run Example
+
+ - `git clone https://code.ornl.gov/sagesim/sagesim`
+ - `export PYTHONPATH=/path/to/clone_repo`
+ - `cd /path/to/clone_repo/examples/sir`
+ - `mpiexec -n 4 python run.py`
+
+
+# There are some unfortunate quirks to using CuPyx `jit.rawkernel`:
+ - nan checked by inequality to self. Unfortunate limitation of cupyx.
+ - Dicts and objects are unsupported.
+ - *args and **kwargs are unsupported.
+ - nested functions are unsupported.
+ - Be sure to use `cupy` data types and array routines in favor of `numpy`: [https://docs.cupy.dev/en/stable/reference/routines.html]
+ - `for` loops must use range iterator only. No 'for each' style loops.
+ - `return` does not seem to work well either
+ - `break` and `continue` are unsupported!
+ - Cannot reassign variables within `if` or `for` statements. Must be assigned at top level of function or new variable declared under subscope.
+ -  `-1` indexing does not necessarily work as expected, as it will access the last element of the memory block of the array instead of the logical array. Use `len(my_array) - 1` instead

sagesim-0.1.0/examples/sir/run.py

@@ -0,0 +1,120 @@
+from time import time
+import argparse
+from sir_model import SIRModel
+from state import SIRState
+from mpi4py import MPI
+
+from random import sample
+
+import networkx as nx
+
+comm = MPI.COMM_WORLD
+num_workers = comm.Get_size()
+worker = comm.Get_rank()
+
+
+def generate_small_world_network(n, k, p):
+    """
+    Generate a small world network using the Watts-Strogatz model.
+
+    Parameters:
+    - n (int): The number of nodes in the network.
+    - k (int): Each node is connected to its k nearest neighbors in a ring topology.
+    - p (float): The probability of rewiring each edge.
+
+    Returns:
+    - networkx.Graph: The generated small world network.
+    """
+    return nx.watts_strogatz_graph(n, k, p)
+
+
+def test_network():
+    network = nx.Graph()
+    network.add_nodes_from(range(8))
+    network.add_edges_from(
+        [(0, 1), (0, 4), (2, 3), (3, 4), (4, 5), (4, 7), (6, 5), (7, 6)]
+    )
+
+    for n in network.nodes:
+        if n == 0:
+            model.create_agent(SIRState.INFECTED.value)
+        else:
+            model.create_agent(SIRState.SUSCEPTIBLE.value)
+
+    for edge in network.edges:
+        model.connect_agents(edge[0], edge[1])
+        print(edge[0], "->", edge[1])
+    return model
+
+
+def generate_small_world_of_agents(
+    model, num_agents: int, num_init_connections: int, num_infected: int
+) -> SIRModel:
+    network = generate_small_world_network(num_agents, num_init_connections, 0.2)
+    for n in network.nodes:
+        model.create_agent(SIRState.SUSCEPTIBLE.value)
+
+    for n in sample(sorted(network.nodes), num_infected):
+        model.set_agent_property_value(n, "state", SIRState.INFECTED.value)
+
+    for edge in network.edges:
+        model.connect_agents(edge[0], edge[1])
+    return model
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--num_agents",
+        type=int,
+    )
+    parser.add_argument(
+        "--percent_init_connections",
+        type=float,
+    )
+    parser.add_argument(
+        "--num_nodes",
+        type=int,
+    )
+    args = parser.parse_args()
+
+    model = SIRModel()
+    model.setup(use_gpu=True)
+    num_agents = args.num_agents
+    num_init_connections = int(args.percent_init_connections * num_agents)
+    num_nodes = args.num_nodes
+
+    model_creation_start = time()
+    model = generate_small_world_of_agents(
+        model, num_agents, num_init_connections, int(0.1 * num_agents)
+    )  # test_network()  #
+    model_creation_end = time()
+    model_creation_duration = model_creation_end - model_creation_start
+    """print(
+        [
+            SIRState(model.get_agent_property_value(agent_id, property_name="state"))
+            for agent_id in range(n_agents)
+        ]
+    )"""
+
+    simulate_start = time()
+    model.simulate(10, sync_workers_every_n_ticks=2)
+    simulate_end = time()
+    simulate_duration = simulate_end - simulate_start
+
+    if worker == 0:
+        with open("execution_times.csv", "a") as f:
+            f.write(
+                f"{num_agents}, {num_init_connections}, {num_nodes}, {num_workers}, {model_creation_duration}, {simulate_duration}\n"
+            )
+
+    if worker == 0:
+        print(
+            [
+                SIRState(
+                    model.get_agent_property_value(agent_id, property_name="state")
+                )
+                for agent_id in range(num_agents)
+            ]
+        )

sagesim-0.1.0/examples/sir/sir_breed.py

@@ -0,0 +1,42 @@
+from random import random
+
+from sagesim.breed import Breed
+from state import SIRState
+from cupyx import jit
+
+global INFECTED
+INFECTED = SIRState.INFECTED.value
+global SUSCEPTIBLE
+SUSCEPTIBLE = SIRState.SUSCEPTIBLE.value
+
+
+class SIRBreed(Breed):
+
+    def __init__(self) -> None:
+        name = "SIR"
+        super().__init__(name)
+        self.register_property("state", SIRState.SUSCEPTIBLE.value)
+        self.register_step_func(step_func)
+
+
+def step_func(id, id2index, globals, breeds, locations, states):
+    # agent_index = step_func_helper_get_agent_index(id, id2index)
+    # nan checked by inequality to self. Unfortunate limitation of cupyx
+    if (id == id) and (id2index[int(id)] == id2index[int(id)]):
+        agent_index = int(id2index[int(id)])
+
+        neighbors = locations[agent_index]  # network location is defined by neighbors
+        rand = random()  # 0.1#step_func_helper_get_random_float(rng_states, id)
+
+        p_infection = globals[1]
+
+        for i in range(len(neighbors)):
+            neighbor_id = neighbors[i]
+            # neighbor_index = step_func_helper_get_agent_index(neighbor_id, id2index)
+            if (neighbor_id == neighbor_id) and (
+                id2index[int(neighbor_id)] == id2index[int(neighbor_id)]
+            ):
+                neighbor_index = int(id2index[int(neighbor_id)])
+                neighbor_state = states[neighbor_index]
+                if neighbor_state == 2 and rand < p_infection:
+                    states[agent_index] = 2

sagesim-0.1.0/examples/sir/sir_model.py

@@ -0,0 +1,22 @@
+from sagesim.model import Model
+from sagesim.space import NetworkSpace
+from sir_breed import SIRBreed
+from state import SIRState
+
+
+class SIRModel(Model):
+
+    def __init__(self, p_infection=0.5) -> None:
+        space = NetworkSpace()
+        super().__init__(space)
+        self._sir_breed = SIRBreed()
+        self.register_breed(breed=self._sir_breed)
+        self.register_global_property("p_infection", p_infection)
+
+    def create_agent(self, state):
+        agent_id = self.create_agent_of_breed(self._sir_breed, state=state)
+        self.get_space().add_agent(agent_id)
+        return agent_id
+
+    def connect_agents(self, agent_0, agent_1):
+        self.get_space().connect_agents(agent_0, agent_1)

sagesim-0.1.0/examples/sir/state.py

@@ -0,0 +1,7 @@
+from enum import Enum
+
+
+class SIRState(Enum):
+    SUSCEPTIBLE = 1
+    INFECTED = 2
+    RECOVERED = 3

sagesim-0.1.0/examples/sir/step_func_code.py

@@ -0,0 +1,66 @@
+
+    
+from random import random
+    
+from cupyx import jit
+    
+
+
+
+import cupy as cp
+import math
+
+@jit.rawkernel(device='cuda')
+def step_func(id, id2index, globals, breeds, locations, states):
+    # agent_index = step_func_helper_get_agent_index(id, id2index)
+    # nan checked by inequality to self. Unfortunate limitation of cupyx
+    if (id == id) and (id2index[int(id)] == id2index[int(id)]):
+        agent_index = int(id2index[int(id)])
+
+        neighbors = locations[agent_index]  # network location is defined by neighbors
+        rand = random()  # 0.1#step_func_helper_get_random_float(rng_states, id)
+
+        p_infection = globals[1]
+
+        for i in range(len(neighbors)):
+            neighbor_id = neighbors[i]
+            # neighbor_index = step_func_helper_get_agent_index(neighbor_id, id2index)
+            if (neighbor_id == neighbor_id) and (
+                id2index[int(neighbor_id)] == id2index[int(neighbor_id)]
+            ):
+                neighbor_index = int(id2index[int(neighbor_id)])
+                neighbor_state = states[neighbor_index]
+                if neighbor_state == 2 and rand < p_infection:
+                    states[agent_index] = 2
+
+    
+
+@jit.rawkernel()
+def stepfunc(
+    device_global_data_vector,
+    a0,a1,a2,
+    sync_workers_every_n_ticks,
+    agent_ids,
+    agents_index_in_subcontext,
+    ):
+        thread_id = jit.blockIdx.x * jit.blockDim.x + jit.threadIdx.x
+        #g = cuda.cg.this_grid()
+        agent_id = thread_id        
+        if agent_id < agent_ids.shape[0]:
+            breed_id = a0[agent_id]                
+            for tick in range(sync_workers_every_n_ticks):
+                
+            
+                if breed_id == 0:
+                    step_func(
+                        agent_id,
+                        agents_index_in_subcontext,
+                        device_global_data_vector,
+                        a0,a1,a2,
+                    )
+            #cuda.syncthreads()
+
+                            
+                if thread_id == 0:
+                    device_global_data_vector[0] += 1
+    

sagesim-0.1.0/pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools >= 75.8.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sagesim"
+version = "0.1.0"
+dependencies = [
+    "awkward==2.7.4",
+    "cupy_cuda12x==13.3.0",
+    "mpi4py==4.0.3",
+    "networkx==3.4.2",
+    "numpy==2.2.3",
+    "ragged==0.2.0",
+    "setuptools==75.8.0",
+]
+requires-python = ">=3.11"
+authors = [
+  {name = "Chathika Gunaratne", email = "chathikagunaratne@gmail.com"}
+]
+maintainers = [
+  {name = "Chathika Gunaratne", email = "chathikagunaratne@gmail.com"}
+]
+
+description = "Scalable Agent-based GPU Enabled Simulator."
+
+readme = "README.md"
+license = {file = "LICENSE", type = "text/plain"}
+
+keywords = ["agent-based", "hpc", "gpu"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[project.urls]
+Repository = "https://github.com/ornl/sagesim.git"