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Docking@Home
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molecular-docking
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Instructions to use OpenPeerAI/DockingAtHOME with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Docking@Home
How to use OpenPeerAI/DockingAtHOME with Docking@Home:
# No code snippets available yet for this library. # To use this model, check the repository files and the library's documentation. # Want to help? PRs adding snippets are welcome at: # https://github.com/huggingface/huggingface.js
- Notebooks
- Google Colab
- Kaggle
| """ | |
| cloud_agents.py - Cloud Agents Integration for Intelligent Task Orchestration | |
| This module integrates OpenPeer AI's Cloud Agents for AI-driven task distribution, | |
| resource optimization, and intelligent scheduling of molecular docking workloads. | |
| Authors: OpenPeer AI, Riemann Computing Inc., Bleunomics, Andrew Magdy Kamal | |
| Version: 1.0.0 | |
| Date: 2025 | |
| """ | |
| import os | |
| import json | |
| import asyncio | |
| from typing import Dict, List, Optional, Any | |
| from dataclasses import dataclass, asdict | |
| from datetime import datetime | |
| import logging | |
| try: | |
| from huggingface_hub import InferenceClient | |
| from transformers import AutoTokenizer, AutoModel | |
| except ImportError: | |
| print("Warning: HuggingFace libraries not installed. Install with: pip install transformers huggingface-hub") | |
| # Configure logging | |
| logging.basicConfig(level=logging.INFO) | |
| logger = logging.getLogger(__name__) | |
| class Task: | |
| """Represents a molecular docking task""" | |
| task_id: str | |
| ligand_file: str | |
| receptor_file: str | |
| priority: str = "normal" # low, normal, high, critical | |
| estimated_compute_time: float = 0.0 | |
| required_memory: int = 0 | |
| use_gpu: bool = True | |
| status: str = "pending" | |
| assigned_node: Optional[str] = None | |
| created_at: datetime = None | |
| def __post_init__(self): | |
| if self.created_at is None: | |
| self.created_at = datetime.now() | |
| class ComputeNode: | |
| """Represents a compute node in the distributed system""" | |
| node_id: str | |
| cpu_cores: int | |
| gpu_available: bool | |
| gpu_type: Optional[str] = None | |
| memory_gb: int = 16 | |
| current_load: float = 0.0 | |
| tasks_completed: int = 0 | |
| average_task_time: float = 0.0 | |
| is_active: bool = True | |
| location: Optional[str] = None | |
| class CloudAgentsOrchestrator: | |
| """ | |
| AI-powered orchestration using Cloud Agents for intelligent | |
| task distribution and resource optimization | |
| """ | |
| def __init__(self, config: Optional[Dict] = None): | |
| """ | |
| Initialize Cloud Agents orchestrator | |
| Args: | |
| config: Configuration dictionary | |
| """ | |
| self.config = config or {} | |
| self.hf_token = self.config.get('hf_token', os.getenv('HF_TOKEN')) | |
| self.model_name = self.config.get('model_name', 'OpenPeer AI/Cloud-Agents') | |
| self.tasks: Dict[str, Task] = {} | |
| self.nodes: Dict[str, ComputeNode] = {} | |
| self.task_queue: List[str] = [] | |
| self.client: Optional[InferenceClient] = None | |
| self.is_initialized = False | |
| logger.info("CloudAgentsOrchestrator initialized") | |
| async def initialize(self) -> bool: | |
| """ | |
| Initialize the Cloud Agents system | |
| Returns: | |
| True if initialization successful | |
| """ | |
| try: | |
| logger.info("Initializing Cloud Agents...") | |
| # Initialize HuggingFace Inference Client | |
| if self.hf_token: | |
| self.client = InferenceClient( | |
| model=self.model_name, | |
| token=self.hf_token | |
| ) | |
| logger.info(f"Connected to Cloud Agents model: {self.model_name}") | |
| else: | |
| logger.warning("HuggingFace token not provided. Using local mode.") | |
| self.is_initialized = True | |
| logger.info("Cloud Agents initialized successfully") | |
| return True | |
| except Exception as e: | |
| logger.error(f"Failed to initialize Cloud Agents: {e}") | |
| return False | |
| def register_node(self, node: ComputeNode) -> bool: | |
| """ | |
| Register a compute node with the orchestrator | |
| Args: | |
| node: ComputeNode instance | |
| Returns: | |
| True if registration successful | |
| """ | |
| try: | |
| self.nodes[node.node_id] = node | |
| logger.info(f"Node registered: {node.node_id} (GPU: {node.gpu_available})") | |
| return True | |
| except Exception as e: | |
| logger.error(f"Failed to register node: {e}") | |
| return False | |
| def submit_task(self, task: Task) -> str: | |
| """ | |
| Submit a new docking task | |
| Args: | |
| task: Task instance | |
| Returns: | |
| Task ID | |
| """ | |
| self.tasks[task.task_id] = task | |
| self.task_queue.append(task.task_id) | |
| logger.info(f"Task submitted: {task.task_id} (Priority: {task.priority})") | |
| return task.task_id | |
| async def optimize_task_distribution(self) -> Dict[str, Any]: | |
| """ | |
| Use AI to optimize task distribution across nodes | |
| Returns: | |
| Optimization recommendations | |
| """ | |
| try: | |
| # Prepare context for AI agent | |
| context = { | |
| "total_tasks": len(self.tasks), | |
| "pending_tasks": len(self.task_queue), | |
| "active_nodes": len([n for n in self.nodes.values() if n.is_active]), | |
| "gpu_nodes": len([n for n in self.nodes.values() if n.gpu_available]), | |
| "avg_node_load": sum(n.current_load for n in self.nodes.values()) / max(len(self.nodes), 1) | |
| } | |
| # Use Cloud Agents for intelligent decision making | |
| prompt = self._create_optimization_prompt(context) | |
| if self.client: | |
| # Query Cloud Agents model | |
| response = await self._query_cloud_agents(prompt) | |
| recommendations = self._parse_ai_response(response) | |
| else: | |
| # Fallback to rule-based optimization | |
| recommendations = self._rule_based_optimization() | |
| logger.info(f"Optimization complete: {recommendations}") | |
| return recommendations | |
| except Exception as e: | |
| logger.error(f"Optimization failed: {e}") | |
| return self._rule_based_optimization() | |
| async def schedule_tasks(self) -> List[Dict[str, str]]: | |
| """ | |
| Schedule pending tasks to available nodes using AI optimization | |
| Returns: | |
| List of task assignments | |
| """ | |
| assignments = [] | |
| # Get optimization recommendations | |
| recommendations = await self.optimize_task_distribution() | |
| # Process pending tasks | |
| for task_id in self.task_queue[:]: | |
| task = self.tasks.get(task_id) | |
| if not task or task.status != "pending": | |
| continue | |
| # Find optimal node for this task | |
| node = self._select_optimal_node(task, recommendations) | |
| if node: | |
| # Assign task to node | |
| task.assigned_node = node.node_id | |
| task.status = "assigned" | |
| node.current_load += 0.1 # Increment load | |
| assignments.append({ | |
| "task_id": task_id, | |
| "node_id": node.node_id, | |
| "priority": task.priority | |
| }) | |
| self.task_queue.remove(task_id) | |
| logger.info(f"Task {task_id} assigned to node {node.node_id}") | |
| return assignments | |
| def _select_optimal_node(self, task: Task, recommendations: Dict) -> Optional[ComputeNode]: | |
| """ | |
| Select the optimal node for a task based on AI recommendations | |
| Args: | |
| task: Task to assign | |
| recommendations: AI recommendations | |
| Returns: | |
| Selected ComputeNode or None | |
| """ | |
| # Filter available nodes | |
| available_nodes = [ | |
| node for node in self.nodes.values() | |
| if node.is_active and node.current_load < 0.9 | |
| ] | |
| if not available_nodes: | |
| return None | |
| # Prefer GPU nodes for GPU tasks | |
| if task.use_gpu: | |
| gpu_nodes = [n for n in available_nodes if n.gpu_available] | |
| if gpu_nodes: | |
| available_nodes = gpu_nodes | |
| # Sort by load and performance | |
| available_nodes.sort(key=lambda n: ( | |
| n.current_load, | |
| -n.tasks_completed, | |
| n.average_task_time | |
| )) | |
| # Apply priority boost for high-priority tasks | |
| if task.priority == "critical": | |
| # Select fastest node regardless of load | |
| available_nodes.sort(key=lambda n: n.average_task_time) | |
| return available_nodes[0] if available_nodes else None | |
| async def _query_cloud_agents(self, prompt: str) -> str: | |
| """ | |
| Query Cloud Agents model for intelligent decision making | |
| Args: | |
| prompt: Input prompt | |
| Returns: | |
| AI response | |
| """ | |
| try: | |
| # Use HuggingFace Inference API | |
| response = self.client.text_generation( | |
| prompt, | |
| max_new_tokens=500, | |
| temperature=0.7, | |
| top_p=0.9 | |
| ) | |
| return response | |
| except Exception as e: | |
| logger.error(f"Cloud Agents query failed: {e}") | |
| return "" | |
| def _create_optimization_prompt(self, context: Dict) -> str: | |
| """ | |
| Create optimization prompt for Cloud Agents | |
| Args: | |
| context: System context | |
| Returns: | |
| Formatted prompt | |
| """ | |
| prompt = f""" | |
| You are an AI orchestrator for a distributed molecular docking system. | |
| Current System Status: | |
| - Total Tasks: {context['total_tasks']} | |
| - Pending Tasks: {context['pending_tasks']} | |
| - Active Nodes: {context['active_nodes']} | |
| - GPU-enabled Nodes: {context['gpu_nodes']} | |
| - Average Node Load: {context['avg_node_load']:.2f} | |
| Task: Optimize task distribution to: | |
| 1. Maximize throughput | |
| 2. Minimize waiting time for high-priority tasks | |
| 3. Balance load across nodes | |
| 4. Utilize GPU resources efficiently | |
| Provide recommendations for: | |
| - Load balancing strategy | |
| - Priority handling | |
| - GPU allocation | |
| - Estimated completion time | |
| Response format (JSON): | |
| """ | |
| return prompt | |
| def _parse_ai_response(self, response: str) -> Dict[str, Any]: | |
| """ | |
| Parse AI response into actionable recommendations | |
| Args: | |
| response: Raw AI response | |
| Returns: | |
| Parsed recommendations | |
| """ | |
| try: | |
| # Attempt to parse JSON response | |
| recommendations = json.loads(response) | |
| return recommendations | |
| except: | |
| # Fallback to default recommendations | |
| return self._rule_based_optimization() | |
| def _rule_based_optimization(self) -> Dict[str, Any]: | |
| """ | |
| Fallback rule-based optimization | |
| Returns: | |
| Optimization recommendations | |
| """ | |
| return { | |
| "strategy": "load_balanced", | |
| "gpu_priority": True, | |
| "max_tasks_per_node": 10, | |
| "rebalance_threshold": 0.8 | |
| } | |
| def get_task_status(self, task_id: str) -> Optional[Dict[str, Any]]: | |
| """ | |
| Get status of a specific task | |
| Args: | |
| task_id: Task ID | |
| Returns: | |
| Task status dictionary | |
| """ | |
| task = self.tasks.get(task_id) | |
| if not task: | |
| return None | |
| return asdict(task) | |
| def get_system_statistics(self) -> Dict[str, Any]: | |
| """ | |
| Get overall system statistics | |
| Returns: | |
| Statistics dictionary | |
| """ | |
| total_tasks = len(self.tasks) | |
| completed_tasks = len([t for t in self.tasks.values() if t.status == "completed"]) | |
| pending_tasks = len(self.task_queue) | |
| active_nodes = [n for n in self.nodes.values() if n.is_active] | |
| total_compute_power = sum(n.cpu_cores for n in active_nodes) | |
| return { | |
| "total_tasks": total_tasks, | |
| "completed_tasks": completed_tasks, | |
| "pending_tasks": pending_tasks, | |
| "active_nodes": len(active_nodes), | |
| "total_compute_power": total_compute_power, | |
| "gpu_nodes": len([n for n in active_nodes if n.gpu_available]), | |
| "average_node_load": sum(n.current_load for n in active_nodes) / max(len(active_nodes), 1), | |
| "throughput": completed_tasks / max((datetime.now() - list(self.tasks.values())[0].created_at).total_seconds() / 3600, 1) if self.tasks else 0 | |
| } | |
| async def auto_scale(self) -> Dict[str, Any]: | |
| """ | |
| Automatically scale resources based on workload | |
| Returns: | |
| Scaling recommendations | |
| """ | |
| stats = self.get_system_statistics() | |
| recommendations = { | |
| "action": "none", | |
| "reason": "", | |
| "suggested_nodes": 0 | |
| } | |
| # Check if we need more resources | |
| if stats["pending_tasks"] > stats["active_nodes"] * 5: | |
| recommendations["action"] = "scale_up" | |
| recommendations["suggested_nodes"] = stats["pending_tasks"] // 5 | |
| recommendations["reason"] = "High pending task count" | |
| # Check if we have excess capacity | |
| elif stats["average_node_load"] < 0.3 and stats["pending_tasks"] == 0: | |
| recommendations["action"] = "scale_down" | |
| recommendations["suggested_nodes"] = -1 | |
| recommendations["reason"] = "Low resource utilization" | |
| logger.info(f"Auto-scale recommendation: {recommendations}") | |
| return recommendations | |
| async def main(): | |
| """Example usage of Cloud Agents orchestrator""" | |
| # Initialize orchestrator | |
| orchestrator = CloudAgentsOrchestrator() | |
| await orchestrator.initialize() | |
| # Register some compute nodes | |
| node1 = ComputeNode( | |
| node_id="node_1", | |
| cpu_cores=16, | |
| gpu_available=True, | |
| gpu_type="RTX 3090", | |
| memory_gb=64 | |
| ) | |
| node2 = ComputeNode( | |
| node_id="node_2", | |
| cpu_cores=8, | |
| gpu_available=False, | |
| memory_gb=32 | |
| ) | |
| orchestrator.register_node(node1) | |
| orchestrator.register_node(node2) | |
| # Submit tasks | |
| for i in range(5): | |
| task = Task( | |
| task_id=f"task_{i}", | |
| ligand_file=f"ligand_{i}.pdbqt", | |
| receptor_file="receptor.pdbqt", | |
| priority="normal" if i < 3 else "high" | |
| ) | |
| orchestrator.submit_task(task) | |
| # Schedule tasks | |
| assignments = await orchestrator.schedule_tasks() | |
| print(f"Scheduled {len(assignments)} tasks") | |
| # Get statistics | |
| stats = orchestrator.get_system_statistics() | |
| print(f"System stats: {json.dumps(stats, indent=2)}") | |
| if __name__ == "__main__": | |
| asyncio.run(main()) | |