superneuroabm 1.0.0__tar.gz

superneuroabm-1.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Oak Ridge National Laboratory
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

superneuroabm-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: superneuroabm
+Version: 1.0.0
+Summary: A GPU-based multi-agent simulation framework for neuromorphic computing.
+Home-page: https://github.com/ORNL/superneuroabm
+Author: Chathika Gunaratne, Shruti Kulkarni, Ashish Gautam, Xi Zhang, Prasanna Date
+Author-email: gunaratnecs@ornl.gov
+License: BSD-3-Clause
+Project-URL: Source, https://github.com/ORNL/superneuroabm
+Project-URL: Bug Tracker, https://github.com/ORNL/superneuroabm/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: sagesim==0.5.0
+Requires-Dist: pyyaml
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# SuperNeuroABM
+
+**SuperNeuroABM** is a GPU-based multi-agent simulation framework for neuromorphic computing. Built on top of [SAGESim](https://github.com/ORNL/SAGESim), it enables fast and scalable simulation of spiking neural networks on both NVIDIA and AMD GPUs.
+
+## Key Features
+
+- **GPU Acceleration**: Leverages CUDA (NVIDIA) or ROCm (AMD) for high-performance simulation
+- **Scalable**: From single GPU to multi-GPU HPC clusters via MPI
+- **Flexible Neuron Models**: Support for various soma and synapse step functions
+- **STDP Support**: Built-in spike-timing-dependent plasticity mechanisms
+- **Network I/O**: Import/export neural network topologies
+
+## Requirements
+
+- Python 3.11+
+- NVIDIA GPU with CUDA drivers **or** AMD GPU with ROCm 5.7.1+
+- MPI implementation (OpenMPI, MPICH, etc.) for multi-GPU execution
+
+## Installation
+
+Your system might require specific steps to install `mpi4py` and/or `cupy` depending on your hardware. In that case, use your system's recommended instructions to install these dependencies first.
+
+```bash
+pip install superneuroabm
+```
+
+## Quick Start
+
+```python
+from superneuroabm.model import SuperNeuroModel
+
+# Create model
+model = SuperNeuroModel()
+
+# Create neurons
+n1 = model.create_neuron()
+n2 = model.create_neuron()
+
+# Connect with synapse
+model.create_synapse(n1, n2, weight=1.0)
+
+# Setup and run
+model.setup(use_gpu=True)
+model.simulate(ticks=100)
+```
+
+## Unit Tests
+
+To run unit tests:
+
+```bash
+python -m unittest tests.test_synapse_and_soma_models
+```
+
+## Publications
+
+[Date, Prasanna, Chathika Gunaratne, Shruti R. Kulkarni, Robert Patton, Mark Coletti, and Thomas Potok. "SuperNeuro: A fast and scalable simulator for neuromorphic computing." In Proceedings of the 2023 International Conference on Neuromorphic Systems, pp. 1-4. 2023.](https://dl.acm.org/doi/abs/10.1145/3589737.3606000)
+
+## License
+
+BSD-3-Clause License - Oak Ridge National Laboratory

superneuroabm-1.0.0/README.md

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+# SuperNeuroABM
+
+**SuperNeuroABM** is a GPU-based multi-agent simulation framework for neuromorphic computing. Built on top of [SAGESim](https://github.com/ORNL/SAGESim), it enables fast and scalable simulation of spiking neural networks on both NVIDIA and AMD GPUs.
+
+## Key Features
+
+- **GPU Acceleration**: Leverages CUDA (NVIDIA) or ROCm (AMD) for high-performance simulation
+- **Scalable**: From single GPU to multi-GPU HPC clusters via MPI
+- **Flexible Neuron Models**: Support for various soma and synapse step functions
+- **STDP Support**: Built-in spike-timing-dependent plasticity mechanisms
+- **Network I/O**: Import/export neural network topologies
+
+## Requirements
+
+- Python 3.11+
+- NVIDIA GPU with CUDA drivers **or** AMD GPU with ROCm 5.7.1+
+- MPI implementation (OpenMPI, MPICH, etc.) for multi-GPU execution
+
+## Installation
+
+Your system might require specific steps to install `mpi4py` and/or `cupy` depending on your hardware. In that case, use your system's recommended instructions to install these dependencies first.
+
+```bash
+pip install superneuroabm
+```
+
+## Quick Start
+
+```python
+from superneuroabm.model import SuperNeuroModel
+
+# Create model
+model = SuperNeuroModel()
+
+# Create neurons
+n1 = model.create_neuron()
+n2 = model.create_neuron()
+
+# Connect with synapse
+model.create_synapse(n1, n2, weight=1.0)
+
+# Setup and run
+model.setup(use_gpu=True)
+model.simulate(ticks=100)
+```
+
+## Unit Tests
+
+To run unit tests:
+
+```bash
+python -m unittest tests.test_synapse_and_soma_models
+```
+
+## Publications
+
+[Date, Prasanna, Chathika Gunaratne, Shruti R. Kulkarni, Robert Patton, Mark Coletti, and Thomas Potok. "SuperNeuro: A fast and scalable simulator for neuromorphic computing." In Proceedings of the 2023 International Conference on Neuromorphic Systems, pp. 1-4. 2023.](https://dl.acm.org/doi/abs/10.1145/3589737.3606000)
+
+## License
+
+BSD-3-Clause License - Oak Ridge National Laboratory

superneuroabm-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

superneuroabm-1.0.0/setup.py

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+from setuptools import setup, find_packages
+from pathlib import Path
+
+# Read README for long description
+this_directory = Path(__file__).parent
+long_description = (this_directory / "README.md").read_text()
+
+setup(
+    name="superneuroabm",
+    version="1.0.0",
+    author="Chathika Gunaratne, Shruti Kulkarni, Ashish Gautam, Xi Zhang, Prasanna Date",
+    author_email="gunaratnecs@ornl.gov",
+    packages=[
+        "superneuroabm",
+        "superneuroabm.step_functions",
+        "superneuroabm.step_functions.soma",
+        "superneuroabm.step_functions.synapse",
+        "superneuroabm.step_functions.synapse.stdp",
+        "superneuroabm.io",
+    ],
+    package_data={
+        "superneuroabm": ["*.yaml"],
+    },
+    include_package_data=True,
+    url="https://github.com/ORNL/superneuroabm",
+    license="BSD-3-Clause",
+    description="A GPU-based multi-agent simulation framework for neuromorphic computing.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    project_urls={
+        "Source": "https://github.com/ORNL/superneuroabm",
+        "Bug Tracker": "https://github.com/ORNL/superneuroabm/issues",
+    },
+    install_requires=["sagesim==0.5.0", "pyyaml", "networkx", "matplotlib"],
+    python_requires=">=3.11",
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
+        "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    ],
+)
+

superneuroabm-1.0.0/superneuroabm/__init__.py

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+"""
+SuperNeuroABM: A GPU-based multi-agent simulation framework for neuromorphic computing.
+"""

superneuroabm-1.0.0/superneuroabm/component_base_config.yaml

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+soma:
+  lif_soma:
+    config_0:
+      hyperparameters:
+        C: 10e-9  # Membrane capacitance in Farads (10 nF)
+        R: 1e6  # Membrane resistance in Ohms (1 TΩ)
+        vthr: -45  # Spike threshold voltage (mV)
+        tref: 5e-3  # Refractory period (5 ms)
+        vrest: -60  # Resting potential (mV)
+        vreset: -60  # Reset potential after spike (mV)
+        tref_allows_integration: 1  # Whether to allow integration during refractory period
+        I_in: 0  # Input current (40 nA)
+        scaling_factor: 1e-5  # Scaling factor for synaptic current
+      internal_state:
+        v: -60.0  # Initial membrane voltage
+        tcount: 0.0  # Time counter
+        tlast: 0.0  # Last spike time
+  izh_soma:
+    config_0:   #intrinsic bursting
+      hyperparameters:
+        k: 1.2
+        vthr: -45
+        C: 150
+        a: 0.01
+        b: 5
+        vpeak: 50
+        vrest: -75
+        d: 130
+        vreset: -56
+        I_in: 420
+      internal_state:
+        v: -75  # Initial membrane voltage
+        u: 0  # Initial recovery variable
+
+    config_1:       # regular spiking
+      hyperparameters:
+        k: 0.7
+        vthr: -40
+        C: 100
+        a: 0.03
+        b: -2
+        vpeak: 35
+        vrest: -60
+        d: 100
+        vreset: -50
+        I_in: 100
+      internal_state:
+        v: -60  # Initial membrane voltage
+        u: 0  # Initial recovery variable
+
+  lif_soma_adaptive_thr:
+    config_0:
+      hyperparameters:
+        C: 10e-9  # Membrane capacitance in Farads (10 nF)
+        R: 1e6  # Membrane resistance in Ohms (1 TΩ)
+        vthr_initial: -45  # Spike threshold voltage (mV)
+        tref: 5e-3  # Refractory period (5 ms)
+        vrest: -60  # Resting potential (mV)
+        vreset: -60  # Reset potential after spike (mV)
+        tref_allows_integration: 1  # Whether to allow integration during refractory period
+        I_in: 0  # Input current (40 nA)
+        scaling_factor: 1e-5  # Scaling factor for synaptic current
+        delta_thr: 1.0  # Threshold increase after spike (mV)
+        tau_decay_thr: 30e-3  # Time constant for threshold decay (100 ms)
+      internal_state:
+        v: -60.0  # Initial membrane voltage
+        tcount: 0.0  # Time counter
+        tlast: 0.0  # Last spike time
+        vthr: -45.0  # Initial spike threshold voltage
+
+
+synapse:
+  single_exp_synapse:
+    no_learning_config_0:
+      hyperparameters:
+        weight: 14.0  # Synaptic weight (strength)
+        synaptic_delay: 1.0  # Transmission delay (ms)
+        scale: 1.0  # Scaling factor
+        tau_fall: 1e-2  # Decay time constant (1 ms)
+        tau_rise: 0  # Rise time constant (instantaneous)
+      internal_state:
+        I_synapse: 0.0  # Initial synaptic current  
+      learning_hyperparameters: 
+        stdp_type: -1  # No learning
+    exp_pair_wise_stdp_config_0:
+      hyperparameters:
+        weight: 14.0  # Synaptic weight (strength)
+        synaptic_delay: 1.0  # Transmission delay (ms)
+        scale: 1.0  # Scaling factor
+        tau_fall: 1e-2  # Decay time constant (1 ms)
+        tau_rise: 0  # Rise time constant (instantaneous)
+      internal_state:
+        I_synapse: 0.0  # Initial synaptic current
+      learning_hyperparameters:
+        stdp_type: 0.0   # Exp pair-wise STDP
+
+        tau_pre_stdp: 10e-3  # Pre-synaptic STDP time constant (10 ms)
+        tau_post_stdp: 10e-3  # Post-synaptic STDP time constant (10 ms)
+        a_exp_pre: 0.005  # Pre-synaptic STDP learning rate
+        a_exp_post: 0.005  # Post-synaptic STDP learning rate
+        stdp_history_length: 100  # Length of STDP history buffer
+      internal_learning_state:
+        pre_trace: 0 # Pre-synaptic trace
+        post_trace: 0 # Post-synaptic trace
+        dW: 0 # Weight change accumulator
+
+    three_bit_exp_pair_wise_stdp_config_0:
+      hyperparameters:
+        weight: 14.0  # Synaptic weight (strength)
+        synaptic_delay: 1.0  # Transmission delay (ms)
+        scale: 1.0  # Scaling factor
+        tau_fall: 1e-2  # Decay time constant (1 ms)
+        tau_rise: 0  # Rise time constant (instantaneous)
+      internal_state:
+        I_synapse: 0.0  # Initial synaptic current
+      learning_hyperparameters:
+        stdp_type: 1.0   # Exp pair-wise STDP
+        tau_pre_stdp: 10e-3  # Pre-synaptic STDP time constant (10 ms)
+        tau_post_stdp: 10e-3  # Post-synaptic STDP time constant (10 ms)
+        a_exp_pre: 0.005  # Pre-synaptic STDP learning rate
+        a_exp_post: 0.005  # Post-synaptic STDP learning rate
+        stdp_history_length: 100  # Length of STDP history buffer
+        wmin: 0.0  # Minimum synaptic weight
+        wmax: 24.0  # Maximum synaptic weight
+        num_levels: 8  # Number of quantization levels (3 bits)
+      internal_learning_state:
+        pre_trace: 0 # Pre-synaptic trace
+        post_trace: 0 # Post-synaptic trace
+        dW: 0 # Weight change accumulator

superneuroabm-1.0.0/superneuroabm/io/__init__.py

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+"""
+I/O utilities for SuperNeuroABM networks.
+"""